diff --git a/workflows/sra/tests/main.nf.test b/workflows/sra/tests/main.nf.test
index 6704652c..b0c19a25 100644
--- a/workflows/sra/tests/main.nf.test
+++ b/workflows/sra/tests/main.nf.test
@@ -28,7 +28,13 @@ nextflow_workflow {
         then {
             assertAll(
                 { assert workflow.success},
-                { assert snapshot(workflow.out).match() }
+                { assert snapshot(
+                    file(workflow.out.samplesheet[0]).name,
+                    workflow.out.mappings,
+                    workflow.out.sample_mappings,
+                    workflow.out.sra_metadata,
+                    workflow.out.versions
+                ).match() }
             )
         }
     }
diff --git a/workflows/sra/tests/main.nf.test.snap b/workflows/sra/tests/main.nf.test.snap
index 17beee5d..aca9cfd8 100644
--- a/workflows/sra/tests/main.nf.test.snap
+++ b/workflows/sra/tests/main.nf.test.snap
@@ -1,281 +1,143 @@
 {
     "Parameters: default": {
         "content": [
-            {
-                "0": [
-                    "samplesheet.csv:md5,636ddfb5fcd882e17303628f80df98d8"
-                ],
-                "1": [
-                    "id_mappings.csv:md5,3e41ce6ab19feb76f2b20fa77a910ad3"
-                ],
-                "2": [
-                    "multiqc_config.yml:md5,1ac06bb95b503703430e74660bbdd768"
-                ],
-                "3": [
-                    {
-                        "base_count": "194930",
-                        "experiment_accession": "DRX026011",
-                        "experiment_alias": "DRX026011",
-                        "experiment_title": "Illumina HiSeq 2500 paired end sequencing: Illumina HiSeq 2500 paired end sequencing of SAMD00024405",
-                        "fastq_1": "DRX026011_DRR028935_1.fastq.gz:md5,f9b4a5d25aa7d6ab4050dbe0764eb04d",
-                        "fastq_2": "DRX026011_DRR028935_2.fastq.gz:md5,dc0d2e1fc46f4d4581a477f87ec3ff15",
-                        "fastq_aspera": "fasp.sra.ebi.ac.uk:/vol1/fastq/DRR028/DRR028935/DRR028935_1.fastq.gz;fasp.sra.ebi.ac.uk:/vol1/fastq/DRR028/DRR028935/DRR028935_2.fastq.gz",
-                        "fastq_bytes": "60275;61610",
-                        "fastq_ftp": "ftp.sra.ebi.ac.uk/vol1/fastq/DRR028/DRR028935/DRR028935_1.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/DRR028/DRR028935/DRR028935_2.fastq.gz",
-                        "fastq_galaxy": "ftp.sra.ebi.ac.uk/vol1/fastq/DRR028/DRR028935/DRR028935_1.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/DRR028/DRR028935/DRR028935_2.fastq.gz",
-                        "fastq_md5": "cc01df82a9354bb6b3be93483b20c35a;941c9998d746416dad53c94c480ddf30",
-                        "id": "DRX026011_DRR028935",
-                        "instrument_model": "Illumina HiSeq 2500",
-                        "instrument_platform": "ILLUMINA",
-                        "library_layout": "PAIRED",
-                        "library_name": "day0_BbSQE-I",
-                        "library_selection": "cDNA",
-                        "library_source": "TRANSCRIPTOMIC",
-                        "library_strategy": "RNA-Seq",
-                        "md5_1": "cc01df82a9354bb6b3be93483b20c35a",
-                        "md5_2": "941c9998d746416dad53c94c480ddf30",
-                        "read_count": "965",
-                        "run_accession": "DRR028935",
-                        "run_alias": "DRR028935",
-                        "sample_accession": "SAMD00024405",
-                        "sample_alias": "SAMD00024405",
-                        "sample_description": "Liquid culture",
-                        "sample_title": "Botryococcus braunii Showa at day 0 after inoculation into fresh culture medium",
-                        "scientific_name": "Botryococcus braunii Showa",
-                        "secondary_sample_accession": "DRS019431",
-                        "secondary_study_accession": "DRP002616",
-                        "single_end": false,
-                        "study_accession": "PRJDB3420",
-                        "study_alias": "DRP002616",
-                        "study_title": "Liquid culture of Botryococcus braunii, race B, Showa",
-                        "submission_accession": "DRA002949",
-                        "tax_id": "1202541"
-                    },
-                    {
-                        "base_count": "1996273",
-                        "experiment_accession": "SRX6725035",
-                        "experiment_alias": "Emb289P1_bin131",
-                        "experiment_title": "Illumina HiSeq 2500 sequencing: Binning of metagenomic reads from the P1 gut compartment of Embiratermes neotenicus",
-                        "fastq_1": "SRX6725035_SRR9984183.fastq.gz:md5,c9b4c2c4abf19da7082caf442fdefea7",
-                        "fastq_2": "",
-                        "fastq_aspera": "fasp.sra.ebi.ac.uk:/vol1/fastq/SRR998/003/SRR9984183/SRR9984183.fastq.gz",
-                        "fastq_bytes": "605358",
-                        "fastq_ftp": "ftp.sra.ebi.ac.uk/vol1/fastq/SRR998/003/SRR9984183/SRR9984183.fastq.gz",
-                        "fastq_galaxy": "ftp.sra.ebi.ac.uk/vol1/fastq/SRR998/003/SRR9984183/SRR9984183.fastq.gz",
-                        "fastq_md5": "0b512d2dc31685983456bd56fd836544",
-                        "id": "SRX6725035_SRR9984183",
-                        "instrument_model": "Illumina HiSeq 2500",
-                        "instrument_platform": "ILLUMINA",
-                        "library_layout": "SINGLE",
-                        "library_name": "Emb289P1_bin131",
-                        "library_selection": "RANDOM",
-                        "library_source": "METAGENOMIC",
-                        "library_strategy": "WGS",
-                        "md5_1": "0b512d2dc31685983456bd56fd836544",
-                        "md5_2": "",
-                        "read_count": "58",
-                        "run_accession": "SRR9984183",
-                        "run_alias": "Emb289P1_bin131.fastq",
-                        "sample_accession": "SAMN12581720",
-                        "sample_alias": "Emb289P1_bin131",
-                        "sample_description": "Keywords: GSC:MIxS MIMAG:5.0",
-                        "sample_title": "MIMAG Metagenome-assembled Genome sample from Defluviitaleaceae bacterium",
-                        "scientific_name": "Defluviitaleaceae bacterium",
-                        "secondary_sample_accession": "SRS5277011",
-                        "secondary_study_accession": "SRP218535",
-                        "single_end": true,
-                        "study_accession": "PRJNA560329",
-                        "study_alias": "PRJNA560329",
-                        "study_title": "Phylogenomic analysis of 589 metagenome-assembled genomes encompassing all major prokaryotic lineages from the gut of higher termites",
-                        "submission_accession": "SRA942061",
-                        "tax_id": "2660712"
-                    },
-                    {
-                        "base_count": "35658",
-                        "experiment_accession": "ERX1234253",
-                        "experiment_alias": "qiita_ptid_1263:10317.BLANK.93.3E.r22",
-                        "experiment_title": "Illumina HiSeq 2500 sequencing: qiita_ptid_1263:10317.BLANK.93.3E.r22",
-                        "fastq_1": "ERX1234253_ERR1160846.fastq.gz:md5,b1de59f829fbd2d60a1ed4bc3da55709",
-                        "fastq_2": "",
-                        "fastq_aspera": "fasp.sra.ebi.ac.uk:/vol1/fastq/ERR116/006/ERR1160846/ERR1160846.fastq.gz",
-                        "fastq_bytes": "18077",
-                        "fastq_ftp": "ftp.sra.ebi.ac.uk/vol1/fastq/ERR116/006/ERR1160846/ERR1160846.fastq.gz",
-                        "fastq_galaxy": "ftp.sra.ebi.ac.uk/vol1/fastq/ERR116/006/ERR1160846/ERR1160846.fastq.gz",
-                        "fastq_md5": "5924f20ef547ebdfed7cad795bbab6e6",
-                        "id": "ERX1234253_ERR1160846",
-                        "instrument_model": "Illumina HiSeq 2500",
-                        "instrument_platform": "ILLUMINA",
-                        "library_layout": "SINGLE",
-                        "library_name": "10317.BLANK.93.3E.r22",
-                        "library_selection": "PCR",
-                        "library_source": "METAGENOMIC",
-                        "library_strategy": "AMPLICON",
-                        "md5_1": "5924f20ef547ebdfed7cad795bbab6e6",
-                        "md5_2": "",
-                        "read_count": "283",
-                        "run_accession": "ERR1160846",
-                        "run_alias": "qiita_ppdid_706:10317.BLANK.93.3E.r22",
-                        "sample_accession": "SAMEA3687214",
-                        "sample_alias": "qiita_sid_10317:10317.BLANK.93.3E.r22",
-                        "sample_description": "American Gut control",
-                        "sample_title": "10317.BLANK.93.3E.r22",
-                        "scientific_name": "metagenome",
-                        "secondary_sample_accession": "ERS994363",
-                        "secondary_study_accession": "ERP012803",
-                        "single_end": true,
-                        "study_accession": "PRJEB11419",
-                        "study_alias": "qiita_sid_10317",
-                        "study_title": "American Gut Project",
-                        "submission_accession": "ERA541392",
-                        "tax_id": "256318"
-                    }
-                ],
-                "4": [
-                    "versions.yml:md5,1496d1cbc9041e07ab8a0c25f0b054d9",
-                    "versions.yml:md5,9b17045ca8bdc272cb3f9d349a81d206",
-                    "versions.yml:md5,b52279f7d6b891a6523d9321f3f85b47",
-                    "versions.yml:md5,c19fc0f920e57875881761cc944a46d7"
-                ],
-                "mappings": [
-                    "id_mappings.csv:md5,3e41ce6ab19feb76f2b20fa77a910ad3"
-                ],
-                "sample_mappings": [
-                    "multiqc_config.yml:md5,1ac06bb95b503703430e74660bbdd768"
-                ],
-                "samplesheet": [
-                    "samplesheet.csv:md5,636ddfb5fcd882e17303628f80df98d8"
-                ],
-                "sra_metadata": [
-                    {
-                        "base_count": "194930",
-                        "experiment_accession": "DRX026011",
-                        "experiment_alias": "DRX026011",
-                        "experiment_title": "Illumina HiSeq 2500 paired end sequencing: Illumina HiSeq 2500 paired end sequencing of SAMD00024405",
-                        "fastq_1": "DRX026011_DRR028935_1.fastq.gz:md5,f9b4a5d25aa7d6ab4050dbe0764eb04d",
-                        "fastq_2": "DRX026011_DRR028935_2.fastq.gz:md5,dc0d2e1fc46f4d4581a477f87ec3ff15",
-                        "fastq_aspera": "fasp.sra.ebi.ac.uk:/vol1/fastq/DRR028/DRR028935/DRR028935_1.fastq.gz;fasp.sra.ebi.ac.uk:/vol1/fastq/DRR028/DRR028935/DRR028935_2.fastq.gz",
-                        "fastq_bytes": "60275;61610",
-                        "fastq_ftp": "ftp.sra.ebi.ac.uk/vol1/fastq/DRR028/DRR028935/DRR028935_1.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/DRR028/DRR028935/DRR028935_2.fastq.gz",
-                        "fastq_galaxy": "ftp.sra.ebi.ac.uk/vol1/fastq/DRR028/DRR028935/DRR028935_1.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/DRR028/DRR028935/DRR028935_2.fastq.gz",
-                        "fastq_md5": "cc01df82a9354bb6b3be93483b20c35a;941c9998d746416dad53c94c480ddf30",
-                        "id": "DRX026011_DRR028935",
-                        "instrument_model": "Illumina HiSeq 2500",
-                        "instrument_platform": "ILLUMINA",
-                        "library_layout": "PAIRED",
-                        "library_name": "day0_BbSQE-I",
-                        "library_selection": "cDNA",
-                        "library_source": "TRANSCRIPTOMIC",
-                        "library_strategy": "RNA-Seq",
-                        "md5_1": "cc01df82a9354bb6b3be93483b20c35a",
-                        "md5_2": "941c9998d746416dad53c94c480ddf30",
-                        "read_count": "965",
-                        "run_accession": "DRR028935",
-                        "run_alias": "DRR028935",
-                        "sample_accession": "SAMD00024405",
-                        "sample_alias": "SAMD00024405",
-                        "sample_description": "Liquid culture",
-                        "sample_title": "Botryococcus braunii Showa at day 0 after inoculation into fresh culture medium",
-                        "scientific_name": "Botryococcus braunii Showa",
-                        "secondary_sample_accession": "DRS019431",
-                        "secondary_study_accession": "DRP002616",
-                        "single_end": false,
-                        "study_accession": "PRJDB3420",
-                        "study_alias": "DRP002616",
-                        "study_title": "Liquid culture of Botryococcus braunii, race B, Showa",
-                        "submission_accession": "DRA002949",
-                        "tax_id": "1202541"
-                    },
-                    {
-                        "base_count": "1996273",
-                        "experiment_accession": "SRX6725035",
-                        "experiment_alias": "Emb289P1_bin131",
-                        "experiment_title": "Illumina HiSeq 2500 sequencing: Binning of metagenomic reads from the P1 gut compartment of Embiratermes neotenicus",
-                        "fastq_1": "SRX6725035_SRR9984183.fastq.gz:md5,c9b4c2c4abf19da7082caf442fdefea7",
-                        "fastq_2": "",
-                        "fastq_aspera": "fasp.sra.ebi.ac.uk:/vol1/fastq/SRR998/003/SRR9984183/SRR9984183.fastq.gz",
-                        "fastq_bytes": "605358",
-                        "fastq_ftp": "ftp.sra.ebi.ac.uk/vol1/fastq/SRR998/003/SRR9984183/SRR9984183.fastq.gz",
-                        "fastq_galaxy": "ftp.sra.ebi.ac.uk/vol1/fastq/SRR998/003/SRR9984183/SRR9984183.fastq.gz",
-                        "fastq_md5": "0b512d2dc31685983456bd56fd836544",
-                        "id": "SRX6725035_SRR9984183",
-                        "instrument_model": "Illumina HiSeq 2500",
-                        "instrument_platform": "ILLUMINA",
-                        "library_layout": "SINGLE",
-                        "library_name": "Emb289P1_bin131",
-                        "library_selection": "RANDOM",
-                        "library_source": "METAGENOMIC",
-                        "library_strategy": "WGS",
-                        "md5_1": "0b512d2dc31685983456bd56fd836544",
-                        "md5_2": "",
-                        "read_count": "58",
-                        "run_accession": "SRR9984183",
-                        "run_alias": "Emb289P1_bin131.fastq",
-                        "sample_accession": "SAMN12581720",
-                        "sample_alias": "Emb289P1_bin131",
-                        "sample_description": "Keywords: GSC:MIxS MIMAG:5.0",
-                        "sample_title": "MIMAG Metagenome-assembled Genome sample from Defluviitaleaceae bacterium",
-                        "scientific_name": "Defluviitaleaceae bacterium",
-                        "secondary_sample_accession": "SRS5277011",
-                        "secondary_study_accession": "SRP218535",
-                        "single_end": true,
-                        "study_accession": "PRJNA560329",
-                        "study_alias": "PRJNA560329",
-                        "study_title": "Phylogenomic analysis of 589 metagenome-assembled genomes encompassing all major prokaryotic lineages from the gut of higher termites",
-                        "submission_accession": "SRA942061",
-                        "tax_id": "2660712"
-                    },
-                    {
-                        "base_count": "35658",
-                        "experiment_accession": "ERX1234253",
-                        "experiment_alias": "qiita_ptid_1263:10317.BLANK.93.3E.r22",
-                        "experiment_title": "Illumina HiSeq 2500 sequencing: qiita_ptid_1263:10317.BLANK.93.3E.r22",
-                        "fastq_1": "ERX1234253_ERR1160846.fastq.gz:md5,b1de59f829fbd2d60a1ed4bc3da55709",
-                        "fastq_2": "",
-                        "fastq_aspera": "fasp.sra.ebi.ac.uk:/vol1/fastq/ERR116/006/ERR1160846/ERR1160846.fastq.gz",
-                        "fastq_bytes": "18077",
-                        "fastq_ftp": "ftp.sra.ebi.ac.uk/vol1/fastq/ERR116/006/ERR1160846/ERR1160846.fastq.gz",
-                        "fastq_galaxy": "ftp.sra.ebi.ac.uk/vol1/fastq/ERR116/006/ERR1160846/ERR1160846.fastq.gz",
-                        "fastq_md5": "5924f20ef547ebdfed7cad795bbab6e6",
-                        "id": "ERX1234253_ERR1160846",
-                        "instrument_model": "Illumina HiSeq 2500",
-                        "instrument_platform": "ILLUMINA",
-                        "library_layout": "SINGLE",
-                        "library_name": "10317.BLANK.93.3E.r22",
-                        "library_selection": "PCR",
-                        "library_source": "METAGENOMIC",
-                        "library_strategy": "AMPLICON",
-                        "md5_1": "5924f20ef547ebdfed7cad795bbab6e6",
-                        "md5_2": "",
-                        "read_count": "283",
-                        "run_accession": "ERR1160846",
-                        "run_alias": "qiita_ppdid_706:10317.BLANK.93.3E.r22",
-                        "sample_accession": "SAMEA3687214",
-                        "sample_alias": "qiita_sid_10317:10317.BLANK.93.3E.r22",
-                        "sample_description": "American Gut control",
-                        "sample_title": "10317.BLANK.93.3E.r22",
-                        "scientific_name": "metagenome",
-                        "secondary_sample_accession": "ERS994363",
-                        "secondary_study_accession": "ERP012803",
-                        "single_end": true,
-                        "study_accession": "PRJEB11419",
-                        "study_alias": "qiita_sid_10317",
-                        "study_title": "American Gut Project",
-                        "submission_accession": "ERA541392",
-                        "tax_id": "256318"
-                    }
-                ],
-                "versions": [
-                    "versions.yml:md5,1496d1cbc9041e07ab8a0c25f0b054d9",
-                    "versions.yml:md5,9b17045ca8bdc272cb3f9d349a81d206",
-                    "versions.yml:md5,b52279f7d6b891a6523d9321f3f85b47",
-                    "versions.yml:md5,c19fc0f920e57875881761cc944a46d7"
-                ]
-            }
+            "samplesheet.csv",
+            [
+                "id_mappings.csv:md5,3e41ce6ab19feb76f2b20fa77a910ad3"
+            ],
+            [
+                "multiqc_config.yml:md5,1ac06bb95b503703430e74660bbdd768"
+            ],
+            [
+                {
+                    "base_count": "194930",
+                    "experiment_accession": "DRX026011",
+                    "experiment_alias": "DRX026011",
+                    "experiment_title": "Illumina HiSeq 2500 paired end sequencing: Illumina HiSeq 2500 paired end sequencing of SAMD00024405",
+                    "fastq_1": "DRX026011_DRR028935_1.fastq.gz:md5,f9b4a5d25aa7d6ab4050dbe0764eb04d",
+                    "fastq_2": "DRX026011_DRR028935_2.fastq.gz:md5,dc0d2e1fc46f4d4581a477f87ec3ff15",
+                    "fastq_aspera": "fasp.sra.ebi.ac.uk:/vol1/fastq/DRR028/DRR028935/DRR028935_1.fastq.gz;fasp.sra.ebi.ac.uk:/vol1/fastq/DRR028/DRR028935/DRR028935_2.fastq.gz",
+                    "fastq_bytes": "60275;61610",
+                    "fastq_ftp": "ftp.sra.ebi.ac.uk/vol1/fastq/DRR028/DRR028935/DRR028935_1.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/DRR028/DRR028935/DRR028935_2.fastq.gz",
+                    "fastq_galaxy": "ftp.sra.ebi.ac.uk/vol1/fastq/DRR028/DRR028935/DRR028935_1.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/DRR028/DRR028935/DRR028935_2.fastq.gz",
+                    "fastq_md5": "cc01df82a9354bb6b3be93483b20c35a;941c9998d746416dad53c94c480ddf30",
+                    "id": "DRX026011_DRR028935",
+                    "instrument_model": "Illumina HiSeq 2500",
+                    "instrument_platform": "ILLUMINA",
+                    "library_layout": "PAIRED",
+                    "library_name": "day0_BbSQE-I",
+                    "library_selection": "cDNA",
+                    "library_source": "TRANSCRIPTOMIC",
+                    "library_strategy": "RNA-Seq",
+                    "md5_1": "cc01df82a9354bb6b3be93483b20c35a",
+                    "md5_2": "941c9998d746416dad53c94c480ddf30",
+                    "read_count": "965",
+                    "run_accession": "DRR028935",
+                    "run_alias": "DRR028935",
+                    "sample_accession": "SAMD00024405",
+                    "sample_alias": "SAMD00024405",
+                    "sample_description": "Liquid culture",
+                    "sample_title": "Botryococcus braunii Showa at day 0 after inoculation into fresh culture medium",
+                    "scientific_name": "Botryococcus braunii Showa",
+                    "secondary_sample_accession": "DRS019431",
+                    "secondary_study_accession": "DRP002616",
+                    "single_end": false,
+                    "study_accession": "PRJDB3420",
+                    "study_alias": "DRP002616",
+                    "study_title": "Liquid culture of Botryococcus braunii, race B, Showa",
+                    "submission_accession": "DRA002949",
+                    "tax_id": "1202541"
+                },
+                {
+                    "base_count": "1996273",
+                    "experiment_accession": "SRX6725035",
+                    "experiment_alias": "Emb289P1_bin131",
+                    "experiment_title": "Illumina HiSeq 2500 sequencing: Binning of metagenomic reads from the P1 gut compartment of Embiratermes neotenicus",
+                    "fastq_1": "SRX6725035_SRR9984183.fastq.gz:md5,c9b4c2c4abf19da7082caf442fdefea7",
+                    "fastq_2": "",
+                    "fastq_aspera": "fasp.sra.ebi.ac.uk:/vol1/fastq/SRR998/003/SRR9984183/SRR9984183.fastq.gz",
+                    "fastq_bytes": "605358",
+                    "fastq_ftp": "ftp.sra.ebi.ac.uk/vol1/fastq/SRR998/003/SRR9984183/SRR9984183.fastq.gz",
+                    "fastq_galaxy": "ftp.sra.ebi.ac.uk/vol1/fastq/SRR998/003/SRR9984183/SRR9984183.fastq.gz",
+                    "fastq_md5": "0b512d2dc31685983456bd56fd836544",
+                    "id": "SRX6725035_SRR9984183",
+                    "instrument_model": "Illumina HiSeq 2500",
+                    "instrument_platform": "ILLUMINA",
+                    "library_layout": "SINGLE",
+                    "library_name": "Emb289P1_bin131",
+                    "library_selection": "RANDOM",
+                    "library_source": "METAGENOMIC",
+                    "library_strategy": "WGS",
+                    "md5_1": "0b512d2dc31685983456bd56fd836544",
+                    "md5_2": "",
+                    "read_count": "58",
+                    "run_accession": "SRR9984183",
+                    "run_alias": "Emb289P1_bin131.fastq",
+                    "sample_accession": "SAMN12581720",
+                    "sample_alias": "Emb289P1_bin131",
+                    "sample_description": "Keywords: GSC:MIxS MIMAG:5.0",
+                    "sample_title": "MIMAG Metagenome-assembled Genome sample from Defluviitaleaceae bacterium",
+                    "scientific_name": "Defluviitaleaceae bacterium",
+                    "secondary_sample_accession": "SRS5277011",
+                    "secondary_study_accession": "SRP218535",
+                    "single_end": true,
+                    "study_accession": "PRJNA560329",
+                    "study_alias": "PRJNA560329",
+                    "study_title": "Phylogenomic analysis of 589 metagenome-assembled genomes encompassing all major prokaryotic lineages from the gut of higher termites",
+                    "submission_accession": "SRA942061",
+                    "tax_id": "2660712"
+                },
+                {
+                    "base_count": "35658",
+                    "experiment_accession": "ERX1234253",
+                    "experiment_alias": "qiita_ptid_1263:10317.BLANK.93.3E.r22",
+                    "experiment_title": "Illumina HiSeq 2500 sequencing: qiita_ptid_1263:10317.BLANK.93.3E.r22",
+                    "fastq_1": "ERX1234253_ERR1160846.fastq.gz:md5,b1de59f829fbd2d60a1ed4bc3da55709",
+                    "fastq_2": "",
+                    "fastq_aspera": "fasp.sra.ebi.ac.uk:/vol1/fastq/ERR116/006/ERR1160846/ERR1160846.fastq.gz",
+                    "fastq_bytes": "18077",
+                    "fastq_ftp": "ftp.sra.ebi.ac.uk/vol1/fastq/ERR116/006/ERR1160846/ERR1160846.fastq.gz",
+                    "fastq_galaxy": "ftp.sra.ebi.ac.uk/vol1/fastq/ERR116/006/ERR1160846/ERR1160846.fastq.gz",
+                    "fastq_md5": "5924f20ef547ebdfed7cad795bbab6e6",
+                    "id": "ERX1234253_ERR1160846",
+                    "instrument_model": "Illumina HiSeq 2500",
+                    "instrument_platform": "ILLUMINA",
+                    "library_layout": "SINGLE",
+                    "library_name": "10317.BLANK.93.3E.r22",
+                    "library_selection": "PCR",
+                    "library_source": "METAGENOMIC",
+                    "library_strategy": "AMPLICON",
+                    "md5_1": "5924f20ef547ebdfed7cad795bbab6e6",
+                    "md5_2": "",
+                    "read_count": "283",
+                    "run_accession": "ERR1160846",
+                    "run_alias": "qiita_ppdid_706:10317.BLANK.93.3E.r22",
+                    "sample_accession": "SAMEA3687214",
+                    "sample_alias": "qiita_sid_10317:10317.BLANK.93.3E.r22",
+                    "sample_description": "American Gut control",
+                    "sample_title": "10317.BLANK.93.3E.r22",
+                    "scientific_name": "metagenome",
+                    "secondary_sample_accession": "ERS994363",
+                    "secondary_study_accession": "ERP012803",
+                    "single_end": true,
+                    "study_accession": "PRJEB11419",
+                    "study_alias": "qiita_sid_10317",
+                    "study_title": "American Gut Project",
+                    "submission_accession": "ERA541392",
+                    "tax_id": "256318"
+                }
+            ],
+            [
+                "versions.yml:md5,1496d1cbc9041e07ab8a0c25f0b054d9",
+                "versions.yml:md5,9b17045ca8bdc272cb3f9d349a81d206",
+                "versions.yml:md5,b52279f7d6b891a6523d9321f3f85b47",
+                "versions.yml:md5,c19fc0f920e57875881761cc944a46d7"
+            ]
         ],
         "meta": {
             "nf-test": "0.9.0",
             "nextflow": "24.09.2"
         },
-        "timestamp": "2024-10-15T12:58:48.512328"
+        "timestamp": "2024-10-15T13:35:40.78967"
     }
 }
\ No newline at end of file
diff --git a/workflows/sra/tests/sra_custom_ena_metadata_fields.nf.test b/workflows/sra/tests/sra_custom_ena_metadata_fields.nf.test
index 1aa68be2..a4879a19 100644
--- a/workflows/sra/tests/sra_custom_ena_metadata_fields.nf.test
+++ b/workflows/sra/tests/sra_custom_ena_metadata_fields.nf.test
@@ -31,7 +31,13 @@ nextflow_workflow {
         then {
             assertAll(
                 { assert workflow.success},
-                { assert snapshot(workflow.out).match() }
+                { assert snapshot(
+                    file(workflow.out.samplesheet[0]).name,
+                    workflow.out.mappings,
+                    workflow.out.sample_mappings,
+                    workflow.out.sra_metadata,
+                    workflow.out.versions
+                ).match() }
             )
         }
     }
diff --git a/workflows/sra/tests/sra_custom_ena_metadata_fields.nf.test.snap b/workflows/sra/tests/sra_custom_ena_metadata_fields.nf.test.snap
index b85b2dd4..7055b4c4 100644
--- a/workflows/sra/tests/sra_custom_ena_metadata_fields.nf.test.snap
+++ b/workflows/sra/tests/sra_custom_ena_metadata_fields.nf.test.snap
@@ -1,125 +1,65 @@
 {
     "Parameters: --nf_core_pipeline rnaseq --ena_metadata_fields ... --sample_mapping_fields ...": {
         "content": [
-            {
-                "0": [
-                    "samplesheet.csv:md5,5f79ecf678ce5af375cf8749b56da139"
-                ],
-                "1": [
-                    "id_mappings.csv:md5,7345715e7db0a160efb8dd3be9ce58ac"
-                ],
-                "2": [
-                    "multiqc_config.yml:md5,3b70bc9658eab4ba2f4ec98cb749ac9d"
-                ],
-                "3": [
-                    {
-                        "experiment_accession": "DRX026011",
-                        "fastq_1": "DRX026011_DRR028935_1.fastq.gz:md5,f9b4a5d25aa7d6ab4050dbe0764eb04d",
-                        "fastq_2": "DRX026011_DRR028935_2.fastq.gz:md5,dc0d2e1fc46f4d4581a477f87ec3ff15",
-                        "fastq_ftp": "ftp.sra.ebi.ac.uk/vol1/fastq/DRR028/DRR028935/DRR028935_1.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/DRR028/DRR028935/DRR028935_2.fastq.gz",
-                        "fastq_md5": "cc01df82a9354bb6b3be93483b20c35a;941c9998d746416dad53c94c480ddf30",
-                        "id": "DRX026011_DRR028935",
-                        "library_layout": "PAIRED",
-                        "md5_1": "cc01df82a9354bb6b3be93483b20c35a",
-                        "md5_2": "941c9998d746416dad53c94c480ddf30",
-                        "run_accession": "DRR028935",
-                        "single_end": false
-                    },
-                    {
-                        "experiment_accession": "ERX1234253",
-                        "fastq_1": "ERX1234253_ERR1160846.fastq.gz:md5,b1de59f829fbd2d60a1ed4bc3da55709",
-                        "fastq_2": "",
-                        "fastq_ftp": "ftp.sra.ebi.ac.uk/vol1/fastq/ERR116/006/ERR1160846/ERR1160846.fastq.gz",
-                        "fastq_md5": "5924f20ef547ebdfed7cad795bbab6e6",
-                        "id": "ERX1234253_ERR1160846",
-                        "library_layout": "SINGLE",
-                        "md5_1": "5924f20ef547ebdfed7cad795bbab6e6",
-                        "md5_2": "",
-                        "run_accession": "ERR1160846",
-                        "single_end": true
-                    },
-                    {
-                        "experiment_accession": "SRX6725035",
-                        "fastq_1": "SRX6725035_SRR9984183.fastq.gz:md5,c9b4c2c4abf19da7082caf442fdefea7",
-                        "fastq_2": "",
-                        "fastq_ftp": "ftp.sra.ebi.ac.uk/vol1/fastq/SRR998/003/SRR9984183/SRR9984183.fastq.gz",
-                        "fastq_md5": "0b512d2dc31685983456bd56fd836544",
-                        "id": "SRX6725035_SRR9984183",
-                        "library_layout": "SINGLE",
-                        "md5_1": "0b512d2dc31685983456bd56fd836544",
-                        "md5_2": "",
-                        "run_accession": "SRR9984183",
-                        "single_end": true
-                    }
-                ],
-                "4": [
-                    "versions.yml:md5,1496d1cbc9041e07ab8a0c25f0b054d9",
-                    "versions.yml:md5,9b17045ca8bdc272cb3f9d349a81d206",
-                    "versions.yml:md5,b52279f7d6b891a6523d9321f3f85b47",
-                    "versions.yml:md5,c19fc0f920e57875881761cc944a46d7"
-                ],
-                "mappings": [
-                    "id_mappings.csv:md5,7345715e7db0a160efb8dd3be9ce58ac"
-                ],
-                "sample_mappings": [
-                    "multiqc_config.yml:md5,3b70bc9658eab4ba2f4ec98cb749ac9d"
-                ],
-                "samplesheet": [
-                    "samplesheet.csv:md5,5f79ecf678ce5af375cf8749b56da139"
-                ],
-                "sra_metadata": [
-                    {
-                        "experiment_accession": "DRX026011",
-                        "fastq_1": "DRX026011_DRR028935_1.fastq.gz:md5,f9b4a5d25aa7d6ab4050dbe0764eb04d",
-                        "fastq_2": "DRX026011_DRR028935_2.fastq.gz:md5,dc0d2e1fc46f4d4581a477f87ec3ff15",
-                        "fastq_ftp": "ftp.sra.ebi.ac.uk/vol1/fastq/DRR028/DRR028935/DRR028935_1.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/DRR028/DRR028935/DRR028935_2.fastq.gz",
-                        "fastq_md5": "cc01df82a9354bb6b3be93483b20c35a;941c9998d746416dad53c94c480ddf30",
-                        "id": "DRX026011_DRR028935",
-                        "library_layout": "PAIRED",
-                        "md5_1": "cc01df82a9354bb6b3be93483b20c35a",
-                        "md5_2": "941c9998d746416dad53c94c480ddf30",
-                        "run_accession": "DRR028935",
-                        "single_end": false
-                    },
-                    {
-                        "experiment_accession": "ERX1234253",
-                        "fastq_1": "ERX1234253_ERR1160846.fastq.gz:md5,b1de59f829fbd2d60a1ed4bc3da55709",
-                        "fastq_2": "",
-                        "fastq_ftp": "ftp.sra.ebi.ac.uk/vol1/fastq/ERR116/006/ERR1160846/ERR1160846.fastq.gz",
-                        "fastq_md5": "5924f20ef547ebdfed7cad795bbab6e6",
-                        "id": "ERX1234253_ERR1160846",
-                        "library_layout": "SINGLE",
-                        "md5_1": "5924f20ef547ebdfed7cad795bbab6e6",
-                        "md5_2": "",
-                        "run_accession": "ERR1160846",
-                        "single_end": true
-                    },
-                    {
-                        "experiment_accession": "SRX6725035",
-                        "fastq_1": "SRX6725035_SRR9984183.fastq.gz:md5,c9b4c2c4abf19da7082caf442fdefea7",
-                        "fastq_2": "",
-                        "fastq_ftp": "ftp.sra.ebi.ac.uk/vol1/fastq/SRR998/003/SRR9984183/SRR9984183.fastq.gz",
-                        "fastq_md5": "0b512d2dc31685983456bd56fd836544",
-                        "id": "SRX6725035_SRR9984183",
-                        "library_layout": "SINGLE",
-                        "md5_1": "0b512d2dc31685983456bd56fd836544",
-                        "md5_2": "",
-                        "run_accession": "SRR9984183",
-                        "single_end": true
-                    }
-                ],
-                "versions": [
-                    "versions.yml:md5,1496d1cbc9041e07ab8a0c25f0b054d9",
-                    "versions.yml:md5,9b17045ca8bdc272cb3f9d349a81d206",
-                    "versions.yml:md5,b52279f7d6b891a6523d9321f3f85b47",
-                    "versions.yml:md5,c19fc0f920e57875881761cc944a46d7"
-                ]
-            }
+            "samplesheet.csv",
+            [
+                "id_mappings.csv:md5,7345715e7db0a160efb8dd3be9ce58ac"
+            ],
+            [
+                "multiqc_config.yml:md5,3b70bc9658eab4ba2f4ec98cb749ac9d"
+            ],
+            [
+                {
+                    "experiment_accession": "DRX026011",
+                    "fastq_1": "DRX026011_DRR028935_1.fastq.gz:md5,f9b4a5d25aa7d6ab4050dbe0764eb04d",
+                    "fastq_2": "DRX026011_DRR028935_2.fastq.gz:md5,dc0d2e1fc46f4d4581a477f87ec3ff15",
+                    "fastq_ftp": "ftp.sra.ebi.ac.uk/vol1/fastq/DRR028/DRR028935/DRR028935_1.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/DRR028/DRR028935/DRR028935_2.fastq.gz",
+                    "fastq_md5": "cc01df82a9354bb6b3be93483b20c35a;941c9998d746416dad53c94c480ddf30",
+                    "id": "DRX026011_DRR028935",
+                    "library_layout": "PAIRED",
+                    "md5_1": "cc01df82a9354bb6b3be93483b20c35a",
+                    "md5_2": "941c9998d746416dad53c94c480ddf30",
+                    "run_accession": "DRR028935",
+                    "single_end": false
+                },
+                {
+                    "experiment_accession": "ERX1234253",
+                    "fastq_1": "ERX1234253_ERR1160846.fastq.gz:md5,b1de59f829fbd2d60a1ed4bc3da55709",
+                    "fastq_2": "",
+                    "fastq_ftp": "ftp.sra.ebi.ac.uk/vol1/fastq/ERR116/006/ERR1160846/ERR1160846.fastq.gz",
+                    "fastq_md5": "5924f20ef547ebdfed7cad795bbab6e6",
+                    "id": "ERX1234253_ERR1160846",
+                    "library_layout": "SINGLE",
+                    "md5_1": "5924f20ef547ebdfed7cad795bbab6e6",
+                    "md5_2": "",
+                    "run_accession": "ERR1160846",
+                    "single_end": true
+                },
+                {
+                    "experiment_accession": "SRX6725035",
+                    "fastq_1": "SRX6725035_SRR9984183.fastq.gz:md5,c9b4c2c4abf19da7082caf442fdefea7",
+                    "fastq_2": "",
+                    "fastq_ftp": "ftp.sra.ebi.ac.uk/vol1/fastq/SRR998/003/SRR9984183/SRR9984183.fastq.gz",
+                    "fastq_md5": "0b512d2dc31685983456bd56fd836544",
+                    "id": "SRX6725035_SRR9984183",
+                    "library_layout": "SINGLE",
+                    "md5_1": "0b512d2dc31685983456bd56fd836544",
+                    "md5_2": "",
+                    "run_accession": "SRR9984183",
+                    "single_end": true
+                }
+            ],
+            [
+                "versions.yml:md5,1496d1cbc9041e07ab8a0c25f0b054d9",
+                "versions.yml:md5,9b17045ca8bdc272cb3f9d349a81d206",
+                "versions.yml:md5,b52279f7d6b891a6523d9321f3f85b47",
+                "versions.yml:md5,c19fc0f920e57875881761cc944a46d7"
+            ]
         ],
         "meta": {
             "nf-test": "0.9.0",
             "nextflow": "24.09.2"
         },
-        "timestamp": "2024-10-15T13:03:36.272997"
+        "timestamp": "2024-10-15T13:35:58.788293"
     }
 }
\ No newline at end of file
diff --git a/workflows/sra/tests/sra_download_method_aspera.nf.test b/workflows/sra/tests/sra_download_method_aspera.nf.test
index b6bc42af..62a423e0 100644
--- a/workflows/sra/tests/sra_download_method_aspera.nf.test
+++ b/workflows/sra/tests/sra_download_method_aspera.nf.test
@@ -29,7 +29,13 @@ nextflow_workflow {
         then {
             assertAll(
                 { assert workflow.success},
-                { assert snapshot(workflow.out).match() }
+                { assert snapshot(
+                    file(workflow.out.samplesheet[0]).name,
+                    workflow.out.mappings,
+                    workflow.out.sample_mappings,
+                    workflow.out.sra_metadata,
+                    workflow.out.versions
+                ).match() }
             )
         }
     }
diff --git a/workflows/sra/tests/sra_download_method_aspera.nf.test.snap b/workflows/sra/tests/sra_download_method_aspera.nf.test.snap
index 04a630a8..62b8319c 100644
--- a/workflows/sra/tests/sra_download_method_aspera.nf.test.snap
+++ b/workflows/sra/tests/sra_download_method_aspera.nf.test.snap
@@ -1,281 +1,143 @@
 {
     "Parameters: --download_method aspera": {
         "content": [
-            {
-                "0": [
-                    "samplesheet.csv:md5,d0f905867fa38eb136c88285669900c5"
-                ],
-                "1": [
-                    "id_mappings.csv:md5,3e41ce6ab19feb76f2b20fa77a910ad3"
-                ],
-                "2": [
-                    "multiqc_config.yml:md5,1ac06bb95b503703430e74660bbdd768"
-                ],
-                "3": [
-                    {
-                        "base_count": "194930",
-                        "experiment_accession": "DRX026011",
-                        "experiment_alias": "DRX026011",
-                        "experiment_title": "Illumina HiSeq 2500 paired end sequencing: Illumina HiSeq 2500 paired end sequencing of SAMD00024405",
-                        "fastq_1": "DRX026011_DRR028935_1.fastq.gz:md5,f9b4a5d25aa7d6ab4050dbe0764eb04d",
-                        "fastq_2": "DRX026011_DRR028935_2.fastq.gz:md5,dc0d2e1fc46f4d4581a477f87ec3ff15",
-                        "fastq_aspera": "fasp.sra.ebi.ac.uk:/vol1/fastq/DRR028/DRR028935/DRR028935_1.fastq.gz;fasp.sra.ebi.ac.uk:/vol1/fastq/DRR028/DRR028935/DRR028935_2.fastq.gz",
-                        "fastq_bytes": "60275;61610",
-                        "fastq_ftp": "ftp.sra.ebi.ac.uk/vol1/fastq/DRR028/DRR028935/DRR028935_1.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/DRR028/DRR028935/DRR028935_2.fastq.gz",
-                        "fastq_galaxy": "ftp.sra.ebi.ac.uk/vol1/fastq/DRR028/DRR028935/DRR028935_1.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/DRR028/DRR028935/DRR028935_2.fastq.gz",
-                        "fastq_md5": "cc01df82a9354bb6b3be93483b20c35a;941c9998d746416dad53c94c480ddf30",
-                        "id": "DRX026011_DRR028935",
-                        "instrument_model": "Illumina HiSeq 2500",
-                        "instrument_platform": "ILLUMINA",
-                        "library_layout": "PAIRED",
-                        "library_name": "day0_BbSQE-I",
-                        "library_selection": "cDNA",
-                        "library_source": "TRANSCRIPTOMIC",
-                        "library_strategy": "RNA-Seq",
-                        "md5_1": "cc01df82a9354bb6b3be93483b20c35a",
-                        "md5_2": "941c9998d746416dad53c94c480ddf30",
-                        "read_count": "965",
-                        "run_accession": "DRR028935",
-                        "run_alias": "DRR028935",
-                        "sample_accession": "SAMD00024405",
-                        "sample_alias": "SAMD00024405",
-                        "sample_description": "Liquid culture",
-                        "sample_title": "Botryococcus braunii Showa at day 0 after inoculation into fresh culture medium",
-                        "scientific_name": "Botryococcus braunii Showa",
-                        "secondary_sample_accession": "DRS019431",
-                        "secondary_study_accession": "DRP002616",
-                        "single_end": false,
-                        "study_accession": "PRJDB3420",
-                        "study_alias": "DRP002616",
-                        "study_title": "Liquid culture of Botryococcus braunii, race B, Showa",
-                        "submission_accession": "DRA002949",
-                        "tax_id": "1202541"
-                    },
-                    {
-                        "base_count": "1996273",
-                        "experiment_accession": "SRX6725035",
-                        "experiment_alias": "Emb289P1_bin131",
-                        "experiment_title": "Illumina HiSeq 2500 sequencing: Binning of metagenomic reads from the P1 gut compartment of Embiratermes neotenicus",
-                        "fastq_1": "SRX6725035_SRR9984183.fastq.gz:md5,c9b4c2c4abf19da7082caf442fdefea7",
-                        "fastq_2": "",
-                        "fastq_aspera": "fasp.sra.ebi.ac.uk:/vol1/fastq/SRR998/003/SRR9984183/SRR9984183.fastq.gz",
-                        "fastq_bytes": "605358",
-                        "fastq_ftp": "ftp.sra.ebi.ac.uk/vol1/fastq/SRR998/003/SRR9984183/SRR9984183.fastq.gz",
-                        "fastq_galaxy": "ftp.sra.ebi.ac.uk/vol1/fastq/SRR998/003/SRR9984183/SRR9984183.fastq.gz",
-                        "fastq_md5": "0b512d2dc31685983456bd56fd836544",
-                        "id": "SRX6725035_SRR9984183",
-                        "instrument_model": "Illumina HiSeq 2500",
-                        "instrument_platform": "ILLUMINA",
-                        "library_layout": "SINGLE",
-                        "library_name": "Emb289P1_bin131",
-                        "library_selection": "RANDOM",
-                        "library_source": "METAGENOMIC",
-                        "library_strategy": "WGS",
-                        "md5_1": "0b512d2dc31685983456bd56fd836544",
-                        "md5_2": "",
-                        "read_count": "58",
-                        "run_accession": "SRR9984183",
-                        "run_alias": "Emb289P1_bin131.fastq",
-                        "sample_accession": "SAMN12581720",
-                        "sample_alias": "Emb289P1_bin131",
-                        "sample_description": "Keywords: GSC:MIxS MIMAG:5.0",
-                        "sample_title": "MIMAG Metagenome-assembled Genome sample from Defluviitaleaceae bacterium",
-                        "scientific_name": "Defluviitaleaceae bacterium",
-                        "secondary_sample_accession": "SRS5277011",
-                        "secondary_study_accession": "SRP218535",
-                        "single_end": true,
-                        "study_accession": "PRJNA560329",
-                        "study_alias": "PRJNA560329",
-                        "study_title": "Phylogenomic analysis of 589 metagenome-assembled genomes encompassing all major prokaryotic lineages from the gut of higher termites",
-                        "submission_accession": "SRA942061",
-                        "tax_id": "2660712"
-                    },
-                    {
-                        "base_count": "35658",
-                        "experiment_accession": "ERX1234253",
-                        "experiment_alias": "qiita_ptid_1263:10317.BLANK.93.3E.r22",
-                        "experiment_title": "Illumina HiSeq 2500 sequencing: qiita_ptid_1263:10317.BLANK.93.3E.r22",
-                        "fastq_1": "ERX1234253_ERR1160846.fastq.gz:md5,b1de59f829fbd2d60a1ed4bc3da55709",
-                        "fastq_2": "",
-                        "fastq_aspera": "fasp.sra.ebi.ac.uk:/vol1/fastq/ERR116/006/ERR1160846/ERR1160846.fastq.gz",
-                        "fastq_bytes": "18077",
-                        "fastq_ftp": "ftp.sra.ebi.ac.uk/vol1/fastq/ERR116/006/ERR1160846/ERR1160846.fastq.gz",
-                        "fastq_galaxy": "ftp.sra.ebi.ac.uk/vol1/fastq/ERR116/006/ERR1160846/ERR1160846.fastq.gz",
-                        "fastq_md5": "5924f20ef547ebdfed7cad795bbab6e6",
-                        "id": "ERX1234253_ERR1160846",
-                        "instrument_model": "Illumina HiSeq 2500",
-                        "instrument_platform": "ILLUMINA",
-                        "library_layout": "SINGLE",
-                        "library_name": "10317.BLANK.93.3E.r22",
-                        "library_selection": "PCR",
-                        "library_source": "METAGENOMIC",
-                        "library_strategy": "AMPLICON",
-                        "md5_1": "5924f20ef547ebdfed7cad795bbab6e6",
-                        "md5_2": "",
-                        "read_count": "283",
-                        "run_accession": "ERR1160846",
-                        "run_alias": "qiita_ppdid_706:10317.BLANK.93.3E.r22",
-                        "sample_accession": "SAMEA3687214",
-                        "sample_alias": "qiita_sid_10317:10317.BLANK.93.3E.r22",
-                        "sample_description": "American Gut control",
-                        "sample_title": "10317.BLANK.93.3E.r22",
-                        "scientific_name": "metagenome",
-                        "secondary_sample_accession": "ERS994363",
-                        "secondary_study_accession": "ERP012803",
-                        "single_end": true,
-                        "study_accession": "PRJEB11419",
-                        "study_alias": "qiita_sid_10317",
-                        "study_title": "American Gut Project",
-                        "submission_accession": "ERA541392",
-                        "tax_id": "256318"
-                    }
-                ],
-                "4": [
-                    "versions.yml:md5,0aae1b802eabfe94891bf2d0fd0ddf60",
-                    "versions.yml:md5,1496d1cbc9041e07ab8a0c25f0b054d9",
-                    "versions.yml:md5,9b17045ca8bdc272cb3f9d349a81d206",
-                    "versions.yml:md5,b52279f7d6b891a6523d9321f3f85b47"
-                ],
-                "mappings": [
-                    "id_mappings.csv:md5,3e41ce6ab19feb76f2b20fa77a910ad3"
-                ],
-                "sample_mappings": [
-                    "multiqc_config.yml:md5,1ac06bb95b503703430e74660bbdd768"
-                ],
-                "samplesheet": [
-                    "samplesheet.csv:md5,d0f905867fa38eb136c88285669900c5"
-                ],
-                "sra_metadata": [
-                    {
-                        "base_count": "194930",
-                        "experiment_accession": "DRX026011",
-                        "experiment_alias": "DRX026011",
-                        "experiment_title": "Illumina HiSeq 2500 paired end sequencing: Illumina HiSeq 2500 paired end sequencing of SAMD00024405",
-                        "fastq_1": "DRX026011_DRR028935_1.fastq.gz:md5,f9b4a5d25aa7d6ab4050dbe0764eb04d",
-                        "fastq_2": "DRX026011_DRR028935_2.fastq.gz:md5,dc0d2e1fc46f4d4581a477f87ec3ff15",
-                        "fastq_aspera": "fasp.sra.ebi.ac.uk:/vol1/fastq/DRR028/DRR028935/DRR028935_1.fastq.gz;fasp.sra.ebi.ac.uk:/vol1/fastq/DRR028/DRR028935/DRR028935_2.fastq.gz",
-                        "fastq_bytes": "60275;61610",
-                        "fastq_ftp": "ftp.sra.ebi.ac.uk/vol1/fastq/DRR028/DRR028935/DRR028935_1.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/DRR028/DRR028935/DRR028935_2.fastq.gz",
-                        "fastq_galaxy": "ftp.sra.ebi.ac.uk/vol1/fastq/DRR028/DRR028935/DRR028935_1.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/DRR028/DRR028935/DRR028935_2.fastq.gz",
-                        "fastq_md5": "cc01df82a9354bb6b3be93483b20c35a;941c9998d746416dad53c94c480ddf30",
-                        "id": "DRX026011_DRR028935",
-                        "instrument_model": "Illumina HiSeq 2500",
-                        "instrument_platform": "ILLUMINA",
-                        "library_layout": "PAIRED",
-                        "library_name": "day0_BbSQE-I",
-                        "library_selection": "cDNA",
-                        "library_source": "TRANSCRIPTOMIC",
-                        "library_strategy": "RNA-Seq",
-                        "md5_1": "cc01df82a9354bb6b3be93483b20c35a",
-                        "md5_2": "941c9998d746416dad53c94c480ddf30",
-                        "read_count": "965",
-                        "run_accession": "DRR028935",
-                        "run_alias": "DRR028935",
-                        "sample_accession": "SAMD00024405",
-                        "sample_alias": "SAMD00024405",
-                        "sample_description": "Liquid culture",
-                        "sample_title": "Botryococcus braunii Showa at day 0 after inoculation into fresh culture medium",
-                        "scientific_name": "Botryococcus braunii Showa",
-                        "secondary_sample_accession": "DRS019431",
-                        "secondary_study_accession": "DRP002616",
-                        "single_end": false,
-                        "study_accession": "PRJDB3420",
-                        "study_alias": "DRP002616",
-                        "study_title": "Liquid culture of Botryococcus braunii, race B, Showa",
-                        "submission_accession": "DRA002949",
-                        "tax_id": "1202541"
-                    },
-                    {
-                        "base_count": "1996273",
-                        "experiment_accession": "SRX6725035",
-                        "experiment_alias": "Emb289P1_bin131",
-                        "experiment_title": "Illumina HiSeq 2500 sequencing: Binning of metagenomic reads from the P1 gut compartment of Embiratermes neotenicus",
-                        "fastq_1": "SRX6725035_SRR9984183.fastq.gz:md5,c9b4c2c4abf19da7082caf442fdefea7",
-                        "fastq_2": "",
-                        "fastq_aspera": "fasp.sra.ebi.ac.uk:/vol1/fastq/SRR998/003/SRR9984183/SRR9984183.fastq.gz",
-                        "fastq_bytes": "605358",
-                        "fastq_ftp": "ftp.sra.ebi.ac.uk/vol1/fastq/SRR998/003/SRR9984183/SRR9984183.fastq.gz",
-                        "fastq_galaxy": "ftp.sra.ebi.ac.uk/vol1/fastq/SRR998/003/SRR9984183/SRR9984183.fastq.gz",
-                        "fastq_md5": "0b512d2dc31685983456bd56fd836544",
-                        "id": "SRX6725035_SRR9984183",
-                        "instrument_model": "Illumina HiSeq 2500",
-                        "instrument_platform": "ILLUMINA",
-                        "library_layout": "SINGLE",
-                        "library_name": "Emb289P1_bin131",
-                        "library_selection": "RANDOM",
-                        "library_source": "METAGENOMIC",
-                        "library_strategy": "WGS",
-                        "md5_1": "0b512d2dc31685983456bd56fd836544",
-                        "md5_2": "",
-                        "read_count": "58",
-                        "run_accession": "SRR9984183",
-                        "run_alias": "Emb289P1_bin131.fastq",
-                        "sample_accession": "SAMN12581720",
-                        "sample_alias": "Emb289P1_bin131",
-                        "sample_description": "Keywords: GSC:MIxS MIMAG:5.0",
-                        "sample_title": "MIMAG Metagenome-assembled Genome sample from Defluviitaleaceae bacterium",
-                        "scientific_name": "Defluviitaleaceae bacterium",
-                        "secondary_sample_accession": "SRS5277011",
-                        "secondary_study_accession": "SRP218535",
-                        "single_end": true,
-                        "study_accession": "PRJNA560329",
-                        "study_alias": "PRJNA560329",
-                        "study_title": "Phylogenomic analysis of 589 metagenome-assembled genomes encompassing all major prokaryotic lineages from the gut of higher termites",
-                        "submission_accession": "SRA942061",
-                        "tax_id": "2660712"
-                    },
-                    {
-                        "base_count": "35658",
-                        "experiment_accession": "ERX1234253",
-                        "experiment_alias": "qiita_ptid_1263:10317.BLANK.93.3E.r22",
-                        "experiment_title": "Illumina HiSeq 2500 sequencing: qiita_ptid_1263:10317.BLANK.93.3E.r22",
-                        "fastq_1": "ERX1234253_ERR1160846.fastq.gz:md5,b1de59f829fbd2d60a1ed4bc3da55709",
-                        "fastq_2": "",
-                        "fastq_aspera": "fasp.sra.ebi.ac.uk:/vol1/fastq/ERR116/006/ERR1160846/ERR1160846.fastq.gz",
-                        "fastq_bytes": "18077",
-                        "fastq_ftp": "ftp.sra.ebi.ac.uk/vol1/fastq/ERR116/006/ERR1160846/ERR1160846.fastq.gz",
-                        "fastq_galaxy": "ftp.sra.ebi.ac.uk/vol1/fastq/ERR116/006/ERR1160846/ERR1160846.fastq.gz",
-                        "fastq_md5": "5924f20ef547ebdfed7cad795bbab6e6",
-                        "id": "ERX1234253_ERR1160846",
-                        "instrument_model": "Illumina HiSeq 2500",
-                        "instrument_platform": "ILLUMINA",
-                        "library_layout": "SINGLE",
-                        "library_name": "10317.BLANK.93.3E.r22",
-                        "library_selection": "PCR",
-                        "library_source": "METAGENOMIC",
-                        "library_strategy": "AMPLICON",
-                        "md5_1": "5924f20ef547ebdfed7cad795bbab6e6",
-                        "md5_2": "",
-                        "read_count": "283",
-                        "run_accession": "ERR1160846",
-                        "run_alias": "qiita_ppdid_706:10317.BLANK.93.3E.r22",
-                        "sample_accession": "SAMEA3687214",
-                        "sample_alias": "qiita_sid_10317:10317.BLANK.93.3E.r22",
-                        "sample_description": "American Gut control",
-                        "sample_title": "10317.BLANK.93.3E.r22",
-                        "scientific_name": "metagenome",
-                        "secondary_sample_accession": "ERS994363",
-                        "secondary_study_accession": "ERP012803",
-                        "single_end": true,
-                        "study_accession": "PRJEB11419",
-                        "study_alias": "qiita_sid_10317",
-                        "study_title": "American Gut Project",
-                        "submission_accession": "ERA541392",
-                        "tax_id": "256318"
-                    }
-                ],
-                "versions": [
-                    "versions.yml:md5,0aae1b802eabfe94891bf2d0fd0ddf60",
-                    "versions.yml:md5,1496d1cbc9041e07ab8a0c25f0b054d9",
-                    "versions.yml:md5,9b17045ca8bdc272cb3f9d349a81d206",
-                    "versions.yml:md5,b52279f7d6b891a6523d9321f3f85b47"
-                ]
-            }
+            "samplesheet.csv",
+            [
+                "id_mappings.csv:md5,3e41ce6ab19feb76f2b20fa77a910ad3"
+            ],
+            [
+                "multiqc_config.yml:md5,1ac06bb95b503703430e74660bbdd768"
+            ],
+            [
+                {
+                    "base_count": "194930",
+                    "experiment_accession": "DRX026011",
+                    "experiment_alias": "DRX026011",
+                    "experiment_title": "Illumina HiSeq 2500 paired end sequencing: Illumina HiSeq 2500 paired end sequencing of SAMD00024405",
+                    "fastq_1": "DRX026011_DRR028935_1.fastq.gz:md5,f9b4a5d25aa7d6ab4050dbe0764eb04d",
+                    "fastq_2": "DRX026011_DRR028935_2.fastq.gz:md5,dc0d2e1fc46f4d4581a477f87ec3ff15",
+                    "fastq_aspera": "fasp.sra.ebi.ac.uk:/vol1/fastq/DRR028/DRR028935/DRR028935_1.fastq.gz;fasp.sra.ebi.ac.uk:/vol1/fastq/DRR028/DRR028935/DRR028935_2.fastq.gz",
+                    "fastq_bytes": "60275;61610",
+                    "fastq_ftp": "ftp.sra.ebi.ac.uk/vol1/fastq/DRR028/DRR028935/DRR028935_1.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/DRR028/DRR028935/DRR028935_2.fastq.gz",
+                    "fastq_galaxy": "ftp.sra.ebi.ac.uk/vol1/fastq/DRR028/DRR028935/DRR028935_1.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/DRR028/DRR028935/DRR028935_2.fastq.gz",
+                    "fastq_md5": "cc01df82a9354bb6b3be93483b20c35a;941c9998d746416dad53c94c480ddf30",
+                    "id": "DRX026011_DRR028935",
+                    "instrument_model": "Illumina HiSeq 2500",
+                    "instrument_platform": "ILLUMINA",
+                    "library_layout": "PAIRED",
+                    "library_name": "day0_BbSQE-I",
+                    "library_selection": "cDNA",
+                    "library_source": "TRANSCRIPTOMIC",
+                    "library_strategy": "RNA-Seq",
+                    "md5_1": "cc01df82a9354bb6b3be93483b20c35a",
+                    "md5_2": "941c9998d746416dad53c94c480ddf30",
+                    "read_count": "965",
+                    "run_accession": "DRR028935",
+                    "run_alias": "DRR028935",
+                    "sample_accession": "SAMD00024405",
+                    "sample_alias": "SAMD00024405",
+                    "sample_description": "Liquid culture",
+                    "sample_title": "Botryococcus braunii Showa at day 0 after inoculation into fresh culture medium",
+                    "scientific_name": "Botryococcus braunii Showa",
+                    "secondary_sample_accession": "DRS019431",
+                    "secondary_study_accession": "DRP002616",
+                    "single_end": false,
+                    "study_accession": "PRJDB3420",
+                    "study_alias": "DRP002616",
+                    "study_title": "Liquid culture of Botryococcus braunii, race B, Showa",
+                    "submission_accession": "DRA002949",
+                    "tax_id": "1202541"
+                },
+                {
+                    "base_count": "1996273",
+                    "experiment_accession": "SRX6725035",
+                    "experiment_alias": "Emb289P1_bin131",
+                    "experiment_title": "Illumina HiSeq 2500 sequencing: Binning of metagenomic reads from the P1 gut compartment of Embiratermes neotenicus",
+                    "fastq_1": "SRX6725035_SRR9984183.fastq.gz:md5,c9b4c2c4abf19da7082caf442fdefea7",
+                    "fastq_2": "",
+                    "fastq_aspera": "fasp.sra.ebi.ac.uk:/vol1/fastq/SRR998/003/SRR9984183/SRR9984183.fastq.gz",
+                    "fastq_bytes": "605358",
+                    "fastq_ftp": "ftp.sra.ebi.ac.uk/vol1/fastq/SRR998/003/SRR9984183/SRR9984183.fastq.gz",
+                    "fastq_galaxy": "ftp.sra.ebi.ac.uk/vol1/fastq/SRR998/003/SRR9984183/SRR9984183.fastq.gz",
+                    "fastq_md5": "0b512d2dc31685983456bd56fd836544",
+                    "id": "SRX6725035_SRR9984183",
+                    "instrument_model": "Illumina HiSeq 2500",
+                    "instrument_platform": "ILLUMINA",
+                    "library_layout": "SINGLE",
+                    "library_name": "Emb289P1_bin131",
+                    "library_selection": "RANDOM",
+                    "library_source": "METAGENOMIC",
+                    "library_strategy": "WGS",
+                    "md5_1": "0b512d2dc31685983456bd56fd836544",
+                    "md5_2": "",
+                    "read_count": "58",
+                    "run_accession": "SRR9984183",
+                    "run_alias": "Emb289P1_bin131.fastq",
+                    "sample_accession": "SAMN12581720",
+                    "sample_alias": "Emb289P1_bin131",
+                    "sample_description": "Keywords: GSC:MIxS MIMAG:5.0",
+                    "sample_title": "MIMAG Metagenome-assembled Genome sample from Defluviitaleaceae bacterium",
+                    "scientific_name": "Defluviitaleaceae bacterium",
+                    "secondary_sample_accession": "SRS5277011",
+                    "secondary_study_accession": "SRP218535",
+                    "single_end": true,
+                    "study_accession": "PRJNA560329",
+                    "study_alias": "PRJNA560329",
+                    "study_title": "Phylogenomic analysis of 589 metagenome-assembled genomes encompassing all major prokaryotic lineages from the gut of higher termites",
+                    "submission_accession": "SRA942061",
+                    "tax_id": "2660712"
+                },
+                {
+                    "base_count": "35658",
+                    "experiment_accession": "ERX1234253",
+                    "experiment_alias": "qiita_ptid_1263:10317.BLANK.93.3E.r22",
+                    "experiment_title": "Illumina HiSeq 2500 sequencing: qiita_ptid_1263:10317.BLANK.93.3E.r22",
+                    "fastq_1": "ERX1234253_ERR1160846.fastq.gz:md5,b1de59f829fbd2d60a1ed4bc3da55709",
+                    "fastq_2": "",
+                    "fastq_aspera": "fasp.sra.ebi.ac.uk:/vol1/fastq/ERR116/006/ERR1160846/ERR1160846.fastq.gz",
+                    "fastq_bytes": "18077",
+                    "fastq_ftp": "ftp.sra.ebi.ac.uk/vol1/fastq/ERR116/006/ERR1160846/ERR1160846.fastq.gz",
+                    "fastq_galaxy": "ftp.sra.ebi.ac.uk/vol1/fastq/ERR116/006/ERR1160846/ERR1160846.fastq.gz",
+                    "fastq_md5": "5924f20ef547ebdfed7cad795bbab6e6",
+                    "id": "ERX1234253_ERR1160846",
+                    "instrument_model": "Illumina HiSeq 2500",
+                    "instrument_platform": "ILLUMINA",
+                    "library_layout": "SINGLE",
+                    "library_name": "10317.BLANK.93.3E.r22",
+                    "library_selection": "PCR",
+                    "library_source": "METAGENOMIC",
+                    "library_strategy": "AMPLICON",
+                    "md5_1": "5924f20ef547ebdfed7cad795bbab6e6",
+                    "md5_2": "",
+                    "read_count": "283",
+                    "run_accession": "ERR1160846",
+                    "run_alias": "qiita_ppdid_706:10317.BLANK.93.3E.r22",
+                    "sample_accession": "SAMEA3687214",
+                    "sample_alias": "qiita_sid_10317:10317.BLANK.93.3E.r22",
+                    "sample_description": "American Gut control",
+                    "sample_title": "10317.BLANK.93.3E.r22",
+                    "scientific_name": "metagenome",
+                    "secondary_sample_accession": "ERS994363",
+                    "secondary_study_accession": "ERP012803",
+                    "single_end": true,
+                    "study_accession": "PRJEB11419",
+                    "study_alias": "qiita_sid_10317",
+                    "study_title": "American Gut Project",
+                    "submission_accession": "ERA541392",
+                    "tax_id": "256318"
+                }
+            ],
+            [
+                "versions.yml:md5,0aae1b802eabfe94891bf2d0fd0ddf60",
+                "versions.yml:md5,1496d1cbc9041e07ab8a0c25f0b054d9",
+                "versions.yml:md5,9b17045ca8bdc272cb3f9d349a81d206",
+                "versions.yml:md5,b52279f7d6b891a6523d9321f3f85b47"
+            ]
         ],
         "meta": {
             "nf-test": "0.9.0",
             "nextflow": "24.09.2"
         },
-        "timestamp": "2024-10-15T13:04:11.866017"
+        "timestamp": "2024-10-15T13:36:29.262179"
     }
 }
\ No newline at end of file
diff --git a/workflows/sra/tests/sra_download_method_sratools.nf.test b/workflows/sra/tests/sra_download_method_sratools.nf.test
index 33e048a5..74de5060 100644
--- a/workflows/sra/tests/sra_download_method_sratools.nf.test
+++ b/workflows/sra/tests/sra_download_method_sratools.nf.test
@@ -29,7 +29,13 @@ nextflow_workflow {
         then {
             assertAll(
                 { assert workflow.success},
-                { assert snapshot(workflow.out).match() }
+                { assert snapshot(
+                    file(workflow.out.samplesheet[0]).name,
+                    workflow.out.mappings,
+                    workflow.out.sample_mappings,
+                    workflow.out.sra_metadata,
+                    workflow.out.versions
+                ).match() }
             )
         }
     }
diff --git a/workflows/sra/tests/sra_download_method_sratools.nf.test.snap b/workflows/sra/tests/sra_download_method_sratools.nf.test.snap
index 2203c2e0..416ff9a5 100644
--- a/workflows/sra/tests/sra_download_method_sratools.nf.test.snap
+++ b/workflows/sra/tests/sra_download_method_sratools.nf.test.snap
@@ -1,281 +1,143 @@
 {
     "Parameters: --download_method sratools": {
         "content": [
-            {
-                "0": [
-                    "samplesheet.csv:md5,1dc8ec98b2cc2d9f07ebd0f033c5e4eb"
-                ],
-                "1": [
-                    "id_mappings.csv:md5,3e41ce6ab19feb76f2b20fa77a910ad3"
-                ],
-                "2": [
-                    "multiqc_config.yml:md5,1ac06bb95b503703430e74660bbdd768"
-                ],
-                "3": [
-                    {
-                        "base_count": "194930",
-                        "experiment_accession": "DRX026011",
-                        "experiment_alias": "DRX026011",
-                        "experiment_title": "Illumina HiSeq 2500 paired end sequencing: Illumina HiSeq 2500 paired end sequencing of SAMD00024405",
-                        "fastq_1": "DRX026011_DRR028935_1.fastq.gz:md5,1c3a691ea99767f25de2492440a02cb7",
-                        "fastq_2": "DRX026011_DRR028935_2.fastq.gz:md5,6fa02d3e52613cfe3464cc7a29f227d4",
-                        "fastq_aspera": "fasp.sra.ebi.ac.uk:/vol1/fastq/DRR028/DRR028935/DRR028935_1.fastq.gz;fasp.sra.ebi.ac.uk:/vol1/fastq/DRR028/DRR028935/DRR028935_2.fastq.gz",
-                        "fastq_bytes": "60275;61610",
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+                    "sample_description": "American Gut control",
+                    "sample_title": "10317.BLANK.93.3E.r22",
+                    "scientific_name": "metagenome",
+                    "secondary_sample_accession": "ERS994363",
+                    "secondary_study_accession": "ERP012803",
+                    "single_end": true,
+                    "study_accession": "PRJEB11419",
+                    "study_alias": "qiita_sid_10317",
+                    "study_title": "American Gut Project",
+                    "submission_accession": "ERA541392",
+                    "tax_id": "256318"
+                }
+            ],
+            [
+                "versions.yml:md5,0bb049f166e93b3d9866ed7e4407c6c9",
+                "versions.yml:md5,1496d1cbc9041e07ab8a0c25f0b054d9",
+                "versions.yml:md5,9b17045ca8bdc272cb3f9d349a81d206",
+                "versions.yml:md5,b52279f7d6b891a6523d9321f3f85b47"
+            ]
         ],
         "meta": {
             "nf-test": "0.9.0",
             "nextflow": "24.09.2"
         },
-        "timestamp": "2024-10-15T13:04:40.461589"
+        "timestamp": "2024-10-15T13:36:57.95433"
     }
 }
\ No newline at end of file
diff --git a/workflows/sra/tests/sra_nf_core_pipeline_atacseq.nf.test b/workflows/sra/tests/sra_nf_core_pipeline_atacseq.nf.test
index 886aef19..656ee977 100644
--- a/workflows/sra/tests/sra_nf_core_pipeline_atacseq.nf.test
+++ b/workflows/sra/tests/sra_nf_core_pipeline_atacseq.nf.test
@@ -29,7 +29,13 @@ nextflow_workflow {
         then {
             assertAll(
                 { assert workflow.success},
-                { assert snapshot(workflow.out).match() }
+                { assert snapshot(
+                    file(workflow.out.samplesheet[0]).name,
+                    workflow.out.mappings,
+                    workflow.out.sample_mappings,
+                    workflow.out.sra_metadata,
+                    workflow.out.versions
+                ).match() }
             )
         }
     }
diff --git a/workflows/sra/tests/sra_nf_core_pipeline_atacseq.nf.test.snap b/workflows/sra/tests/sra_nf_core_pipeline_atacseq.nf.test.snap
index 12c26342..f1a21171 100644
--- a/workflows/sra/tests/sra_nf_core_pipeline_atacseq.nf.test.snap
+++ b/workflows/sra/tests/sra_nf_core_pipeline_atacseq.nf.test.snap
@@ -1,281 +1,143 @@
 {
     "Parameters: --nf_core_pipeline atacseq": {
         "content": [
-            {
-                "0": [
-                    "samplesheet.csv:md5,ec54a949c41851e8c5c20dc595992d25"
-                ],
-                "1": [
-                    "id_mappings.csv:md5,3e41ce6ab19feb76f2b20fa77a910ad3"
-                ],
-                "2": [
-                    "multiqc_config.yml:md5,1ac06bb95b503703430e74660bbdd768"
-                ],
-                "3": [
-                    {
-                        "base_count": "194930",
-                        "experiment_accession": "DRX026011",
-                        "experiment_alias": "DRX026011",
-                        "experiment_title": "Illumina HiSeq 2500 paired end sequencing: Illumina HiSeq 2500 paired end sequencing of SAMD00024405",
-                        "fastq_1": "DRX026011_DRR028935_1.fastq.gz:md5,f9b4a5d25aa7d6ab4050dbe0764eb04d",
-                        "fastq_2": "DRX026011_DRR028935_2.fastq.gz:md5,dc0d2e1fc46f4d4581a477f87ec3ff15",
-                        "fastq_aspera": "fasp.sra.ebi.ac.uk:/vol1/fastq/DRR028/DRR028935/DRR028935_1.fastq.gz;fasp.sra.ebi.ac.uk:/vol1/fastq/DRR028/DRR028935/DRR028935_2.fastq.gz",
-                        "fastq_bytes": "60275;61610",
-                        "fastq_ftp": "ftp.sra.ebi.ac.uk/vol1/fastq/DRR028/DRR028935/DRR028935_1.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/DRR028/DRR028935/DRR028935_2.fastq.gz",
-                        "fastq_galaxy": "ftp.sra.ebi.ac.uk/vol1/fastq/DRR028/DRR028935/DRR028935_1.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/DRR028/DRR028935/DRR028935_2.fastq.gz",
-                        "fastq_md5": "cc01df82a9354bb6b3be93483b20c35a;941c9998d746416dad53c94c480ddf30",
-                        "id": "DRX026011_DRR028935",
-                        "instrument_model": "Illumina HiSeq 2500",
-                        "instrument_platform": "ILLUMINA",
-                        "library_layout": "PAIRED",
-                        "library_name": "day0_BbSQE-I",
-                        "library_selection": "cDNA",
-                        "library_source": "TRANSCRIPTOMIC",
-                        "library_strategy": "RNA-Seq",
-                        "md5_1": "cc01df82a9354bb6b3be93483b20c35a",
-                        "md5_2": "941c9998d746416dad53c94c480ddf30",
-                        "read_count": "965",
-                        "run_accession": "DRR028935",
-                        "run_alias": "DRR028935",
-                        "sample_accession": "SAMD00024405",
-                        "sample_alias": "SAMD00024405",
-                        "sample_description": "Liquid culture",
-                        "sample_title": "Botryococcus braunii Showa at day 0 after inoculation into fresh culture medium",
-                        "scientific_name": "Botryococcus braunii Showa",
-                        "secondary_sample_accession": "DRS019431",
-                        "secondary_study_accession": "DRP002616",
-                        "single_end": false,
-                        "study_accession": "PRJDB3420",
-                        "study_alias": "DRP002616",
-                        "study_title": "Liquid culture of Botryococcus braunii, race B, Showa",
-                        "submission_accession": "DRA002949",
-                        "tax_id": "1202541"
-                    },
-                    {
-                        "base_count": "1996273",
-                        "experiment_accession": "SRX6725035",
-                        "experiment_alias": "Emb289P1_bin131",
-                        "experiment_title": "Illumina HiSeq 2500 sequencing: Binning of metagenomic reads from the P1 gut compartment of Embiratermes neotenicus",
-                        "fastq_1": "SRX6725035_SRR9984183.fastq.gz:md5,c9b4c2c4abf19da7082caf442fdefea7",
-                        "fastq_2": "",
-                        "fastq_aspera": "fasp.sra.ebi.ac.uk:/vol1/fastq/SRR998/003/SRR9984183/SRR9984183.fastq.gz",
-                        "fastq_bytes": "605358",
-                        "fastq_ftp": "ftp.sra.ebi.ac.uk/vol1/fastq/SRR998/003/SRR9984183/SRR9984183.fastq.gz",
-                        "fastq_galaxy": "ftp.sra.ebi.ac.uk/vol1/fastq/SRR998/003/SRR9984183/SRR9984183.fastq.gz",
-                        "fastq_md5": "0b512d2dc31685983456bd56fd836544",
-                        "id": "SRX6725035_SRR9984183",
-                        "instrument_model": "Illumina HiSeq 2500",
-                        "instrument_platform": "ILLUMINA",
-                        "library_layout": "SINGLE",
-                        "library_name": "Emb289P1_bin131",
-                        "library_selection": "RANDOM",
-                        "library_source": "METAGENOMIC",
-                        "library_strategy": "WGS",
-                        "md5_1": "0b512d2dc31685983456bd56fd836544",
-                        "md5_2": "",
-                        "read_count": "58",
-                        "run_accession": "SRR9984183",
-                        "run_alias": "Emb289P1_bin131.fastq",
-                        "sample_accession": "SAMN12581720",
-                        "sample_alias": "Emb289P1_bin131",
-                        "sample_description": "Keywords: GSC:MIxS MIMAG:5.0",
-                        "sample_title": "MIMAG Metagenome-assembled Genome sample from Defluviitaleaceae bacterium",
-                        "scientific_name": "Defluviitaleaceae bacterium",
-                        "secondary_sample_accession": "SRS5277011",
-                        "secondary_study_accession": "SRP218535",
-                        "single_end": true,
-                        "study_accession": "PRJNA560329",
-                        "study_alias": "PRJNA560329",
-                        "study_title": "Phylogenomic analysis of 589 metagenome-assembled genomes encompassing all major prokaryotic lineages from the gut of higher termites",
-                        "submission_accession": "SRA942061",
-                        "tax_id": "2660712"
-                    },
-                    {
-                        "base_count": "35658",
-                        "experiment_accession": "ERX1234253",
-                        "experiment_alias": "qiita_ptid_1263:10317.BLANK.93.3E.r22",
-                        "experiment_title": "Illumina HiSeq 2500 sequencing: qiita_ptid_1263:10317.BLANK.93.3E.r22",
-                        "fastq_1": "ERX1234253_ERR1160846.fastq.gz:md5,b1de59f829fbd2d60a1ed4bc3da55709",
-                        "fastq_2": "",
-                        "fastq_aspera": "fasp.sra.ebi.ac.uk:/vol1/fastq/ERR116/006/ERR1160846/ERR1160846.fastq.gz",
-                        "fastq_bytes": "18077",
-                        "fastq_ftp": "ftp.sra.ebi.ac.uk/vol1/fastq/ERR116/006/ERR1160846/ERR1160846.fastq.gz",
-                        "fastq_galaxy": "ftp.sra.ebi.ac.uk/vol1/fastq/ERR116/006/ERR1160846/ERR1160846.fastq.gz",
-                        "fastq_md5": "5924f20ef547ebdfed7cad795bbab6e6",
-                        "id": "ERX1234253_ERR1160846",
-                        "instrument_model": "Illumina HiSeq 2500",
-                        "instrument_platform": "ILLUMINA",
-                        "library_layout": "SINGLE",
-                        "library_name": "10317.BLANK.93.3E.r22",
-                        "library_selection": "PCR",
-                        "library_source": "METAGENOMIC",
-                        "library_strategy": "AMPLICON",
-                        "md5_1": "5924f20ef547ebdfed7cad795bbab6e6",
-                        "md5_2": "",
-                        "read_count": "283",
-                        "run_accession": "ERR1160846",
-                        "run_alias": "qiita_ppdid_706:10317.BLANK.93.3E.r22",
-                        "sample_accession": "SAMEA3687214",
-                        "sample_alias": "qiita_sid_10317:10317.BLANK.93.3E.r22",
-                        "sample_description": "American Gut control",
-                        "sample_title": "10317.BLANK.93.3E.r22",
-                        "scientific_name": "metagenome",
-                        "secondary_sample_accession": "ERS994363",
-                        "secondary_study_accession": "ERP012803",
-                        "single_end": true,
-                        "study_accession": "PRJEB11419",
-                        "study_alias": "qiita_sid_10317",
-                        "study_title": "American Gut Project",
-                        "submission_accession": "ERA541392",
-                        "tax_id": "256318"
-                    }
-                ],
-                "4": [
-                    "versions.yml:md5,1496d1cbc9041e07ab8a0c25f0b054d9",
-                    "versions.yml:md5,9b17045ca8bdc272cb3f9d349a81d206",
-                    "versions.yml:md5,b52279f7d6b891a6523d9321f3f85b47",
-                    "versions.yml:md5,c19fc0f920e57875881761cc944a46d7"
-                ],
-                "mappings": [
-                    "id_mappings.csv:md5,3e41ce6ab19feb76f2b20fa77a910ad3"
-                ],
-                "sample_mappings": [
-                    "multiqc_config.yml:md5,1ac06bb95b503703430e74660bbdd768"
-                ],
-                "samplesheet": [
-                    "samplesheet.csv:md5,ec54a949c41851e8c5c20dc595992d25"
-                ],
-                "sra_metadata": [
-                    {
-                        "base_count": "194930",
-                        "experiment_accession": "DRX026011",
-                        "experiment_alias": "DRX026011",
-                        "experiment_title": "Illumina HiSeq 2500 paired end sequencing: Illumina HiSeq 2500 paired end sequencing of SAMD00024405",
-                        "fastq_1": "DRX026011_DRR028935_1.fastq.gz:md5,f9b4a5d25aa7d6ab4050dbe0764eb04d",
-                        "fastq_2": "DRX026011_DRR028935_2.fastq.gz:md5,dc0d2e1fc46f4d4581a477f87ec3ff15",
-                        "fastq_aspera": "fasp.sra.ebi.ac.uk:/vol1/fastq/DRR028/DRR028935/DRR028935_1.fastq.gz;fasp.sra.ebi.ac.uk:/vol1/fastq/DRR028/DRR028935/DRR028935_2.fastq.gz",
-                        "fastq_bytes": "60275;61610",
-                        "fastq_ftp": "ftp.sra.ebi.ac.uk/vol1/fastq/DRR028/DRR028935/DRR028935_1.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/DRR028/DRR028935/DRR028935_2.fastq.gz",
-                        "fastq_galaxy": "ftp.sra.ebi.ac.uk/vol1/fastq/DRR028/DRR028935/DRR028935_1.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/DRR028/DRR028935/DRR028935_2.fastq.gz",
-                        "fastq_md5": "cc01df82a9354bb6b3be93483b20c35a;941c9998d746416dad53c94c480ddf30",
-                        "id": "DRX026011_DRR028935",
-                        "instrument_model": "Illumina HiSeq 2500",
-                        "instrument_platform": "ILLUMINA",
-                        "library_layout": "PAIRED",
-                        "library_name": "day0_BbSQE-I",
-                        "library_selection": "cDNA",
-                        "library_source": "TRANSCRIPTOMIC",
-                        "library_strategy": "RNA-Seq",
-                        "md5_1": "cc01df82a9354bb6b3be93483b20c35a",
-                        "md5_2": "941c9998d746416dad53c94c480ddf30",
-                        "read_count": "965",
-                        "run_accession": "DRR028935",
-                        "run_alias": "DRR028935",
-                        "sample_accession": "SAMD00024405",
-                        "sample_alias": "SAMD00024405",
-                        "sample_description": "Liquid culture",
-                        "sample_title": "Botryococcus braunii Showa at day 0 after inoculation into fresh culture medium",
-                        "scientific_name": "Botryococcus braunii Showa",
-                        "secondary_sample_accession": "DRS019431",
-                        "secondary_study_accession": "DRP002616",
-                        "single_end": false,
-                        "study_accession": "PRJDB3420",
-                        "study_alias": "DRP002616",
-                        "study_title": "Liquid culture of Botryococcus braunii, race B, Showa",
-                        "submission_accession": "DRA002949",
-                        "tax_id": "1202541"
-                    },
-                    {
-                        "base_count": "1996273",
-                        "experiment_accession": "SRX6725035",
-                        "experiment_alias": "Emb289P1_bin131",
-                        "experiment_title": "Illumina HiSeq 2500 sequencing: Binning of metagenomic reads from the P1 gut compartment of Embiratermes neotenicus",
-                        "fastq_1": "SRX6725035_SRR9984183.fastq.gz:md5,c9b4c2c4abf19da7082caf442fdefea7",
-                        "fastq_2": "",
-                        "fastq_aspera": "fasp.sra.ebi.ac.uk:/vol1/fastq/SRR998/003/SRR9984183/SRR9984183.fastq.gz",
-                        "fastq_bytes": "605358",
-                        "fastq_ftp": "ftp.sra.ebi.ac.uk/vol1/fastq/SRR998/003/SRR9984183/SRR9984183.fastq.gz",
-                        "fastq_galaxy": "ftp.sra.ebi.ac.uk/vol1/fastq/SRR998/003/SRR9984183/SRR9984183.fastq.gz",
-                        "fastq_md5": "0b512d2dc31685983456bd56fd836544",
-                        "id": "SRX6725035_SRR9984183",
-                        "instrument_model": "Illumina HiSeq 2500",
-                        "instrument_platform": "ILLUMINA",
-                        "library_layout": "SINGLE",
-                        "library_name": "Emb289P1_bin131",
-                        "library_selection": "RANDOM",
-                        "library_source": "METAGENOMIC",
-                        "library_strategy": "WGS",
-                        "md5_1": "0b512d2dc31685983456bd56fd836544",
-                        "md5_2": "",
-                        "read_count": "58",
-                        "run_accession": "SRR9984183",
-                        "run_alias": "Emb289P1_bin131.fastq",
-                        "sample_accession": "SAMN12581720",
-                        "sample_alias": "Emb289P1_bin131",
-                        "sample_description": "Keywords: GSC:MIxS MIMAG:5.0",
-                        "sample_title": "MIMAG Metagenome-assembled Genome sample from Defluviitaleaceae bacterium",
-                        "scientific_name": "Defluviitaleaceae bacterium",
-                        "secondary_sample_accession": "SRS5277011",
-                        "secondary_study_accession": "SRP218535",
-                        "single_end": true,
-                        "study_accession": "PRJNA560329",
-                        "study_alias": "PRJNA560329",
-                        "study_title": "Phylogenomic analysis of 589 metagenome-assembled genomes encompassing all major prokaryotic lineages from the gut of higher termites",
-                        "submission_accession": "SRA942061",
-                        "tax_id": "2660712"
-                    },
-                    {
-                        "base_count": "35658",
-                        "experiment_accession": "ERX1234253",
-                        "experiment_alias": "qiita_ptid_1263:10317.BLANK.93.3E.r22",
-                        "experiment_title": "Illumina HiSeq 2500 sequencing: qiita_ptid_1263:10317.BLANK.93.3E.r22",
-                        "fastq_1": "ERX1234253_ERR1160846.fastq.gz:md5,b1de59f829fbd2d60a1ed4bc3da55709",
-                        "fastq_2": "",
-                        "fastq_aspera": "fasp.sra.ebi.ac.uk:/vol1/fastq/ERR116/006/ERR1160846/ERR1160846.fastq.gz",
-                        "fastq_bytes": "18077",
-                        "fastq_ftp": "ftp.sra.ebi.ac.uk/vol1/fastq/ERR116/006/ERR1160846/ERR1160846.fastq.gz",
-                        "fastq_galaxy": "ftp.sra.ebi.ac.uk/vol1/fastq/ERR116/006/ERR1160846/ERR1160846.fastq.gz",
-                        "fastq_md5": "5924f20ef547ebdfed7cad795bbab6e6",
-                        "id": "ERX1234253_ERR1160846",
-                        "instrument_model": "Illumina HiSeq 2500",
-                        "instrument_platform": "ILLUMINA",
-                        "library_layout": "SINGLE",
-                        "library_name": "10317.BLANK.93.3E.r22",
-                        "library_selection": "PCR",
-                        "library_source": "METAGENOMIC",
-                        "library_strategy": "AMPLICON",
-                        "md5_1": "5924f20ef547ebdfed7cad795bbab6e6",
-                        "md5_2": "",
-                        "read_count": "283",
-                        "run_accession": "ERR1160846",
-                        "run_alias": "qiita_ppdid_706:10317.BLANK.93.3E.r22",
-                        "sample_accession": "SAMEA3687214",
-                        "sample_alias": "qiita_sid_10317:10317.BLANK.93.3E.r22",
-                        "sample_description": "American Gut control",
-                        "sample_title": "10317.BLANK.93.3E.r22",
-                        "scientific_name": "metagenome",
-                        "secondary_sample_accession": "ERS994363",
-                        "secondary_study_accession": "ERP012803",
-                        "single_end": true,
-                        "study_accession": "PRJEB11419",
-                        "study_alias": "qiita_sid_10317",
-                        "study_title": "American Gut Project",
-                        "submission_accession": "ERA541392",
-                        "tax_id": "256318"
-                    }
-                ],
-                "versions": [
-                    "versions.yml:md5,1496d1cbc9041e07ab8a0c25f0b054d9",
-                    "versions.yml:md5,9b17045ca8bdc272cb3f9d349a81d206",
-                    "versions.yml:md5,b52279f7d6b891a6523d9321f3f85b47",
-                    "versions.yml:md5,c19fc0f920e57875881761cc944a46d7"
-                ]
-            }
+            "samplesheet.csv",
+            [
+                "id_mappings.csv:md5,3e41ce6ab19feb76f2b20fa77a910ad3"
+            ],
+            [
+                "multiqc_config.yml:md5,1ac06bb95b503703430e74660bbdd768"
+            ],
+            [
+                {
+                    "base_count": "194930",
+                    "experiment_accession": "DRX026011",
+                    "experiment_alias": "DRX026011",
+                    "experiment_title": "Illumina HiSeq 2500 paired end sequencing: Illumina HiSeq 2500 paired end sequencing of SAMD00024405",
+                    "fastq_1": "DRX026011_DRR028935_1.fastq.gz:md5,f9b4a5d25aa7d6ab4050dbe0764eb04d",
+                    "fastq_2": "DRX026011_DRR028935_2.fastq.gz:md5,dc0d2e1fc46f4d4581a477f87ec3ff15",
+                    "fastq_aspera": "fasp.sra.ebi.ac.uk:/vol1/fastq/DRR028/DRR028935/DRR028935_1.fastq.gz;fasp.sra.ebi.ac.uk:/vol1/fastq/DRR028/DRR028935/DRR028935_2.fastq.gz",
+                    "fastq_bytes": "60275;61610",
+                    "fastq_ftp": "ftp.sra.ebi.ac.uk/vol1/fastq/DRR028/DRR028935/DRR028935_1.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/DRR028/DRR028935/DRR028935_2.fastq.gz",
+                    "fastq_galaxy": "ftp.sra.ebi.ac.uk/vol1/fastq/DRR028/DRR028935/DRR028935_1.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/DRR028/DRR028935/DRR028935_2.fastq.gz",
+                    "fastq_md5": "cc01df82a9354bb6b3be93483b20c35a;941c9998d746416dad53c94c480ddf30",
+                    "id": "DRX026011_DRR028935",
+                    "instrument_model": "Illumina HiSeq 2500",
+                    "instrument_platform": "ILLUMINA",
+                    "library_layout": "PAIRED",
+                    "library_name": "day0_BbSQE-I",
+                    "library_selection": "cDNA",
+                    "library_source": "TRANSCRIPTOMIC",
+                    "library_strategy": "RNA-Seq",
+                    "md5_1": "cc01df82a9354bb6b3be93483b20c35a",
+                    "md5_2": "941c9998d746416dad53c94c480ddf30",
+                    "read_count": "965",
+                    "run_accession": "DRR028935",
+                    "run_alias": "DRR028935",
+                    "sample_accession": "SAMD00024405",
+                    "sample_alias": "SAMD00024405",
+                    "sample_description": "Liquid culture",
+                    "sample_title": "Botryococcus braunii Showa at day 0 after inoculation into fresh culture medium",
+                    "scientific_name": "Botryococcus braunii Showa",
+                    "secondary_sample_accession": "DRS019431",
+                    "secondary_study_accession": "DRP002616",
+                    "single_end": false,
+                    "study_accession": "PRJDB3420",
+                    "study_alias": "DRP002616",
+                    "study_title": "Liquid culture of Botryococcus braunii, race B, Showa",
+                    "submission_accession": "DRA002949",
+                    "tax_id": "1202541"
+                },
+                {
+                    "base_count": "1996273",
+                    "experiment_accession": "SRX6725035",
+                    "experiment_alias": "Emb289P1_bin131",
+                    "experiment_title": "Illumina HiSeq 2500 sequencing: Binning of metagenomic reads from the P1 gut compartment of Embiratermes neotenicus",
+                    "fastq_1": "SRX6725035_SRR9984183.fastq.gz:md5,c9b4c2c4abf19da7082caf442fdefea7",
+                    "fastq_2": "",
+                    "fastq_aspera": "fasp.sra.ebi.ac.uk:/vol1/fastq/SRR998/003/SRR9984183/SRR9984183.fastq.gz",
+                    "fastq_bytes": "605358",
+                    "fastq_ftp": "ftp.sra.ebi.ac.uk/vol1/fastq/SRR998/003/SRR9984183/SRR9984183.fastq.gz",
+                    "fastq_galaxy": "ftp.sra.ebi.ac.uk/vol1/fastq/SRR998/003/SRR9984183/SRR9984183.fastq.gz",
+                    "fastq_md5": "0b512d2dc31685983456bd56fd836544",
+                    "id": "SRX6725035_SRR9984183",
+                    "instrument_model": "Illumina HiSeq 2500",
+                    "instrument_platform": "ILLUMINA",
+                    "library_layout": "SINGLE",
+                    "library_name": "Emb289P1_bin131",
+                    "library_selection": "RANDOM",
+                    "library_source": "METAGENOMIC",
+                    "library_strategy": "WGS",
+                    "md5_1": "0b512d2dc31685983456bd56fd836544",
+                    "md5_2": "",
+                    "read_count": "58",
+                    "run_accession": "SRR9984183",
+                    "run_alias": "Emb289P1_bin131.fastq",
+                    "sample_accession": "SAMN12581720",
+                    "sample_alias": "Emb289P1_bin131",
+                    "sample_description": "Keywords: GSC:MIxS MIMAG:5.0",
+                    "sample_title": "MIMAG Metagenome-assembled Genome sample from Defluviitaleaceae bacterium",
+                    "scientific_name": "Defluviitaleaceae bacterium",
+                    "secondary_sample_accession": "SRS5277011",
+                    "secondary_study_accession": "SRP218535",
+                    "single_end": true,
+                    "study_accession": "PRJNA560329",
+                    "study_alias": "PRJNA560329",
+                    "study_title": "Phylogenomic analysis of 589 metagenome-assembled genomes encompassing all major prokaryotic lineages from the gut of higher termites",
+                    "submission_accession": "SRA942061",
+                    "tax_id": "2660712"
+                },
+                {
+                    "base_count": "35658",
+                    "experiment_accession": "ERX1234253",
+                    "experiment_alias": "qiita_ptid_1263:10317.BLANK.93.3E.r22",
+                    "experiment_title": "Illumina HiSeq 2500 sequencing: qiita_ptid_1263:10317.BLANK.93.3E.r22",
+                    "fastq_1": "ERX1234253_ERR1160846.fastq.gz:md5,b1de59f829fbd2d60a1ed4bc3da55709",
+                    "fastq_2": "",
+                    "fastq_aspera": "fasp.sra.ebi.ac.uk:/vol1/fastq/ERR116/006/ERR1160846/ERR1160846.fastq.gz",
+                    "fastq_bytes": "18077",
+                    "fastq_ftp": "ftp.sra.ebi.ac.uk/vol1/fastq/ERR116/006/ERR1160846/ERR1160846.fastq.gz",
+                    "fastq_galaxy": "ftp.sra.ebi.ac.uk/vol1/fastq/ERR116/006/ERR1160846/ERR1160846.fastq.gz",
+                    "fastq_md5": "5924f20ef547ebdfed7cad795bbab6e6",
+                    "id": "ERX1234253_ERR1160846",
+                    "instrument_model": "Illumina HiSeq 2500",
+                    "instrument_platform": "ILLUMINA",
+                    "library_layout": "SINGLE",
+                    "library_name": "10317.BLANK.93.3E.r22",
+                    "library_selection": "PCR",
+                    "library_source": "METAGENOMIC",
+                    "library_strategy": "AMPLICON",
+                    "md5_1": "5924f20ef547ebdfed7cad795bbab6e6",
+                    "md5_2": "",
+                    "read_count": "283",
+                    "run_accession": "ERR1160846",
+                    "run_alias": "qiita_ppdid_706:10317.BLANK.93.3E.r22",
+                    "sample_accession": "SAMEA3687214",
+                    "sample_alias": "qiita_sid_10317:10317.BLANK.93.3E.r22",
+                    "sample_description": "American Gut control",
+                    "sample_title": "10317.BLANK.93.3E.r22",
+                    "scientific_name": "metagenome",
+                    "secondary_sample_accession": "ERS994363",
+                    "secondary_study_accession": "ERP012803",
+                    "single_end": true,
+                    "study_accession": "PRJEB11419",
+                    "study_alias": "qiita_sid_10317",
+                    "study_title": "American Gut Project",
+                    "submission_accession": "ERA541392",
+                    "tax_id": "256318"
+                }
+            ],
+            [
+                "versions.yml:md5,1496d1cbc9041e07ab8a0c25f0b054d9",
+                "versions.yml:md5,9b17045ca8bdc272cb3f9d349a81d206",
+                "versions.yml:md5,b52279f7d6b891a6523d9321f3f85b47",
+                "versions.yml:md5,c19fc0f920e57875881761cc944a46d7"
+            ]
         ],
         "meta": {
             "nf-test": "0.9.0",
             "nextflow": "24.09.2"
         },
-        "timestamp": "2024-10-15T13:05:13.825847"
+        "timestamp": "2024-10-15T13:37:15.784692"
     }
 }
\ No newline at end of file
diff --git a/workflows/sra/tests/sra_nf_core_pipeline_rnaseq.nf.test b/workflows/sra/tests/sra_nf_core_pipeline_rnaseq.nf.test
index 7f67aefb..f82b1755 100644
--- a/workflows/sra/tests/sra_nf_core_pipeline_rnaseq.nf.test
+++ b/workflows/sra/tests/sra_nf_core_pipeline_rnaseq.nf.test
@@ -29,7 +29,13 @@ nextflow_workflow {
         then {
             assertAll(
                 { assert workflow.success},
-                { assert snapshot(workflow.out).match() }
+                { assert snapshot(
+                    file(workflow.out.samplesheet[0]).name,
+                    workflow.out.mappings,
+                    workflow.out.sample_mappings,
+                    workflow.out.sra_metadata,
+                    workflow.out.versions
+                ).match() }
             )
         }
     }
diff --git a/workflows/sra/tests/sra_nf_core_pipeline_rnaseq.nf.test.snap b/workflows/sra/tests/sra_nf_core_pipeline_rnaseq.nf.test.snap
index 61f6cd12..397c85c3 100644
--- a/workflows/sra/tests/sra_nf_core_pipeline_rnaseq.nf.test.snap
+++ b/workflows/sra/tests/sra_nf_core_pipeline_rnaseq.nf.test.snap
@@ -1,281 +1,143 @@
 {
     "Parameters: --nf_core_pipeline rnaseq": {
         "content": [
-            {
-                "0": [
-                    "samplesheet.csv:md5,633beb86dd3622ea86f5346425f8a574"
-                ],
-                "1": [
-                    "id_mappings.csv:md5,3e41ce6ab19feb76f2b20fa77a910ad3"
-                ],
-                "2": [
-                    "multiqc_config.yml:md5,1ac06bb95b503703430e74660bbdd768"
-                ],
-                "3": [
-                    {
-                        "base_count": "194930",
-                        "experiment_accession": "DRX026011",
-                        "experiment_alias": "DRX026011",
-                        "experiment_title": "Illumina HiSeq 2500 paired end sequencing: Illumina HiSeq 2500 paired end sequencing of SAMD00024405",
-                        "fastq_1": "DRX026011_DRR028935_1.fastq.gz:md5,f9b4a5d25aa7d6ab4050dbe0764eb04d",
-                        "fastq_2": "DRX026011_DRR028935_2.fastq.gz:md5,dc0d2e1fc46f4d4581a477f87ec3ff15",
-                        "fastq_aspera": "fasp.sra.ebi.ac.uk:/vol1/fastq/DRR028/DRR028935/DRR028935_1.fastq.gz;fasp.sra.ebi.ac.uk:/vol1/fastq/DRR028/DRR028935/DRR028935_2.fastq.gz",
-                        "fastq_bytes": "60275;61610",
-                        "fastq_ftp": "ftp.sra.ebi.ac.uk/vol1/fastq/DRR028/DRR028935/DRR028935_1.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/DRR028/DRR028935/DRR028935_2.fastq.gz",
-                        "fastq_galaxy": "ftp.sra.ebi.ac.uk/vol1/fastq/DRR028/DRR028935/DRR028935_1.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/DRR028/DRR028935/DRR028935_2.fastq.gz",
-                        "fastq_md5": "cc01df82a9354bb6b3be93483b20c35a;941c9998d746416dad53c94c480ddf30",
-                        "id": "DRX026011_DRR028935",
-                        "instrument_model": "Illumina HiSeq 2500",
-                        "instrument_platform": "ILLUMINA",
-                        "library_layout": "PAIRED",
-                        "library_name": "day0_BbSQE-I",
-                        "library_selection": "cDNA",
-                        "library_source": "TRANSCRIPTOMIC",
-                        "library_strategy": "RNA-Seq",
-                        "md5_1": "cc01df82a9354bb6b3be93483b20c35a",
-                        "md5_2": "941c9998d746416dad53c94c480ddf30",
-                        "read_count": "965",
-                        "run_accession": "DRR028935",
-                        "run_alias": "DRR028935",
-                        "sample_accession": "SAMD00024405",
-                        "sample_alias": "SAMD00024405",
-                        "sample_description": "Liquid culture",
-                        "sample_title": "Botryococcus braunii Showa at day 0 after inoculation into fresh culture medium",
-                        "scientific_name": "Botryococcus braunii Showa",
-                        "secondary_sample_accession": "DRS019431",
-                        "secondary_study_accession": "DRP002616",
-                        "single_end": false,
-                        "study_accession": "PRJDB3420",
-                        "study_alias": "DRP002616",
-                        "study_title": "Liquid culture of Botryococcus braunii, race B, Showa",
-                        "submission_accession": "DRA002949",
-                        "tax_id": "1202541"
-                    },
-                    {
-                        "base_count": "1996273",
-                        "experiment_accession": "SRX6725035",
-                        "experiment_alias": "Emb289P1_bin131",
-                        "experiment_title": "Illumina HiSeq 2500 sequencing: Binning of metagenomic reads from the P1 gut compartment of Embiratermes neotenicus",
-                        "fastq_1": "SRX6725035_SRR9984183.fastq.gz:md5,c9b4c2c4abf19da7082caf442fdefea7",
-                        "fastq_2": "",
-                        "fastq_aspera": "fasp.sra.ebi.ac.uk:/vol1/fastq/SRR998/003/SRR9984183/SRR9984183.fastq.gz",
-                        "fastq_bytes": "605358",
-                        "fastq_ftp": "ftp.sra.ebi.ac.uk/vol1/fastq/SRR998/003/SRR9984183/SRR9984183.fastq.gz",
-                        "fastq_galaxy": "ftp.sra.ebi.ac.uk/vol1/fastq/SRR998/003/SRR9984183/SRR9984183.fastq.gz",
-                        "fastq_md5": "0b512d2dc31685983456bd56fd836544",
-                        "id": "SRX6725035_SRR9984183",
-                        "instrument_model": "Illumina HiSeq 2500",
-                        "instrument_platform": "ILLUMINA",
-                        "library_layout": "SINGLE",
-                        "library_name": "Emb289P1_bin131",
-                        "library_selection": "RANDOM",
-                        "library_source": "METAGENOMIC",
-                        "library_strategy": "WGS",
-                        "md5_1": "0b512d2dc31685983456bd56fd836544",
-                        "md5_2": "",
-                        "read_count": "58",
-                        "run_accession": "SRR9984183",
-                        "run_alias": "Emb289P1_bin131.fastq",
-                        "sample_accession": "SAMN12581720",
-                        "sample_alias": "Emb289P1_bin131",
-                        "sample_description": "Keywords: GSC:MIxS MIMAG:5.0",
-                        "sample_title": "MIMAG Metagenome-assembled Genome sample from Defluviitaleaceae bacterium",
-                        "scientific_name": "Defluviitaleaceae bacterium",
-                        "secondary_sample_accession": "SRS5277011",
-                        "secondary_study_accession": "SRP218535",
-                        "single_end": true,
-                        "study_accession": "PRJNA560329",
-                        "study_alias": "PRJNA560329",
-                        "study_title": "Phylogenomic analysis of 589 metagenome-assembled genomes encompassing all major prokaryotic lineages from the gut of higher termites",
-                        "submission_accession": "SRA942061",
-                        "tax_id": "2660712"
-                    },
-                    {
-                        "base_count": "35658",
-                        "experiment_accession": "ERX1234253",
-                        "experiment_alias": "qiita_ptid_1263:10317.BLANK.93.3E.r22",
-                        "experiment_title": "Illumina HiSeq 2500 sequencing: qiita_ptid_1263:10317.BLANK.93.3E.r22",
-                        "fastq_1": "ERX1234253_ERR1160846.fastq.gz:md5,b1de59f829fbd2d60a1ed4bc3da55709",
-                        "fastq_2": "",
-                        "fastq_aspera": "fasp.sra.ebi.ac.uk:/vol1/fastq/ERR116/006/ERR1160846/ERR1160846.fastq.gz",
-                        "fastq_bytes": "18077",
-                        "fastq_ftp": "ftp.sra.ebi.ac.uk/vol1/fastq/ERR116/006/ERR1160846/ERR1160846.fastq.gz",
-                        "fastq_galaxy": "ftp.sra.ebi.ac.uk/vol1/fastq/ERR116/006/ERR1160846/ERR1160846.fastq.gz",
-                        "fastq_md5": "5924f20ef547ebdfed7cad795bbab6e6",
-                        "id": "ERX1234253_ERR1160846",
-                        "instrument_model": "Illumina HiSeq 2500",
-                        "instrument_platform": "ILLUMINA",
-                        "library_layout": "SINGLE",
-                        "library_name": "10317.BLANK.93.3E.r22",
-                        "library_selection": "PCR",
-                        "library_source": "METAGENOMIC",
-                        "library_strategy": "AMPLICON",
-                        "md5_1": "5924f20ef547ebdfed7cad795bbab6e6",
-                        "md5_2": "",
-                        "read_count": "283",
-                        "run_accession": "ERR1160846",
-                        "run_alias": "qiita_ppdid_706:10317.BLANK.93.3E.r22",
-                        "sample_accession": "SAMEA3687214",
-                        "sample_alias": "qiita_sid_10317:10317.BLANK.93.3E.r22",
-                        "sample_description": "American Gut control",
-                        "sample_title": "10317.BLANK.93.3E.r22",
-                        "scientific_name": "metagenome",
-                        "secondary_sample_accession": "ERS994363",
-                        "secondary_study_accession": "ERP012803",
-                        "single_end": true,
-                        "study_accession": "PRJEB11419",
-                        "study_alias": "qiita_sid_10317",
-                        "study_title": "American Gut Project",
-                        "submission_accession": "ERA541392",
-                        "tax_id": "256318"
-                    }
-                ],
-                "4": [
-                    "versions.yml:md5,1496d1cbc9041e07ab8a0c25f0b054d9",
-                    "versions.yml:md5,9b17045ca8bdc272cb3f9d349a81d206",
-                    "versions.yml:md5,b52279f7d6b891a6523d9321f3f85b47",
-                    "versions.yml:md5,c19fc0f920e57875881761cc944a46d7"
-                ],
-                "mappings": [
-                    "id_mappings.csv:md5,3e41ce6ab19feb76f2b20fa77a910ad3"
-                ],
-                "sample_mappings": [
-                    "multiqc_config.yml:md5,1ac06bb95b503703430e74660bbdd768"
-                ],
-                "samplesheet": [
-                    "samplesheet.csv:md5,633beb86dd3622ea86f5346425f8a574"
-                ],
-                "sra_metadata": [
-                    {
-                        "base_count": "194930",
-                        "experiment_accession": "DRX026011",
-                        "experiment_alias": "DRX026011",
-                        "experiment_title": "Illumina HiSeq 2500 paired end sequencing: Illumina HiSeq 2500 paired end sequencing of SAMD00024405",
-                        "fastq_1": "DRX026011_DRR028935_1.fastq.gz:md5,f9b4a5d25aa7d6ab4050dbe0764eb04d",
-                        "fastq_2": "DRX026011_DRR028935_2.fastq.gz:md5,dc0d2e1fc46f4d4581a477f87ec3ff15",
-                        "fastq_aspera": "fasp.sra.ebi.ac.uk:/vol1/fastq/DRR028/DRR028935/DRR028935_1.fastq.gz;fasp.sra.ebi.ac.uk:/vol1/fastq/DRR028/DRR028935/DRR028935_2.fastq.gz",
-                        "fastq_bytes": "60275;61610",
-                        "fastq_ftp": "ftp.sra.ebi.ac.uk/vol1/fastq/DRR028/DRR028935/DRR028935_1.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/DRR028/DRR028935/DRR028935_2.fastq.gz",
-                        "fastq_galaxy": "ftp.sra.ebi.ac.uk/vol1/fastq/DRR028/DRR028935/DRR028935_1.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/DRR028/DRR028935/DRR028935_2.fastq.gz",
-                        "fastq_md5": "cc01df82a9354bb6b3be93483b20c35a;941c9998d746416dad53c94c480ddf30",
-                        "id": "DRX026011_DRR028935",
-                        "instrument_model": "Illumina HiSeq 2500",
-                        "instrument_platform": "ILLUMINA",
-                        "library_layout": "PAIRED",
-                        "library_name": "day0_BbSQE-I",
-                        "library_selection": "cDNA",
-                        "library_source": "TRANSCRIPTOMIC",
-                        "library_strategy": "RNA-Seq",
-                        "md5_1": "cc01df82a9354bb6b3be93483b20c35a",
-                        "md5_2": "941c9998d746416dad53c94c480ddf30",
-                        "read_count": "965",
-                        "run_accession": "DRR028935",
-                        "run_alias": "DRR028935",
-                        "sample_accession": "SAMD00024405",
-                        "sample_alias": "SAMD00024405",
-                        "sample_description": "Liquid culture",
-                        "sample_title": "Botryococcus braunii Showa at day 0 after inoculation into fresh culture medium",
-                        "scientific_name": "Botryococcus braunii Showa",
-                        "secondary_sample_accession": "DRS019431",
-                        "secondary_study_accession": "DRP002616",
-                        "single_end": false,
-                        "study_accession": "PRJDB3420",
-                        "study_alias": "DRP002616",
-                        "study_title": "Liquid culture of Botryococcus braunii, race B, Showa",
-                        "submission_accession": "DRA002949",
-                        "tax_id": "1202541"
-                    },
-                    {
-                        "base_count": "1996273",
-                        "experiment_accession": "SRX6725035",
-                        "experiment_alias": "Emb289P1_bin131",
-                        "experiment_title": "Illumina HiSeq 2500 sequencing: Binning of metagenomic reads from the P1 gut compartment of Embiratermes neotenicus",
-                        "fastq_1": "SRX6725035_SRR9984183.fastq.gz:md5,c9b4c2c4abf19da7082caf442fdefea7",
-                        "fastq_2": "",
-                        "fastq_aspera": "fasp.sra.ebi.ac.uk:/vol1/fastq/SRR998/003/SRR9984183/SRR9984183.fastq.gz",
-                        "fastq_bytes": "605358",
-                        "fastq_ftp": "ftp.sra.ebi.ac.uk/vol1/fastq/SRR998/003/SRR9984183/SRR9984183.fastq.gz",
-                        "fastq_galaxy": "ftp.sra.ebi.ac.uk/vol1/fastq/SRR998/003/SRR9984183/SRR9984183.fastq.gz",
-                        "fastq_md5": "0b512d2dc31685983456bd56fd836544",
-                        "id": "SRX6725035_SRR9984183",
-                        "instrument_model": "Illumina HiSeq 2500",
-                        "instrument_platform": "ILLUMINA",
-                        "library_layout": "SINGLE",
-                        "library_name": "Emb289P1_bin131",
-                        "library_selection": "RANDOM",
-                        "library_source": "METAGENOMIC",
-                        "library_strategy": "WGS",
-                        "md5_1": "0b512d2dc31685983456bd56fd836544",
-                        "md5_2": "",
-                        "read_count": "58",
-                        "run_accession": "SRR9984183",
-                        "run_alias": "Emb289P1_bin131.fastq",
-                        "sample_accession": "SAMN12581720",
-                        "sample_alias": "Emb289P1_bin131",
-                        "sample_description": "Keywords: GSC:MIxS MIMAG:5.0",
-                        "sample_title": "MIMAG Metagenome-assembled Genome sample from Defluviitaleaceae bacterium",
-                        "scientific_name": "Defluviitaleaceae bacterium",
-                        "secondary_sample_accession": "SRS5277011",
-                        "secondary_study_accession": "SRP218535",
-                        "single_end": true,
-                        "study_accession": "PRJNA560329",
-                        "study_alias": "PRJNA560329",
-                        "study_title": "Phylogenomic analysis of 589 metagenome-assembled genomes encompassing all major prokaryotic lineages from the gut of higher termites",
-                        "submission_accession": "SRA942061",
-                        "tax_id": "2660712"
-                    },
-                    {
-                        "base_count": "35658",
-                        "experiment_accession": "ERX1234253",
-                        "experiment_alias": "qiita_ptid_1263:10317.BLANK.93.3E.r22",
-                        "experiment_title": "Illumina HiSeq 2500 sequencing: qiita_ptid_1263:10317.BLANK.93.3E.r22",
-                        "fastq_1": "ERX1234253_ERR1160846.fastq.gz:md5,b1de59f829fbd2d60a1ed4bc3da55709",
-                        "fastq_2": "",
-                        "fastq_aspera": "fasp.sra.ebi.ac.uk:/vol1/fastq/ERR116/006/ERR1160846/ERR1160846.fastq.gz",
-                        "fastq_bytes": "18077",
-                        "fastq_ftp": "ftp.sra.ebi.ac.uk/vol1/fastq/ERR116/006/ERR1160846/ERR1160846.fastq.gz",
-                        "fastq_galaxy": "ftp.sra.ebi.ac.uk/vol1/fastq/ERR116/006/ERR1160846/ERR1160846.fastq.gz",
-                        "fastq_md5": "5924f20ef547ebdfed7cad795bbab6e6",
-                        "id": "ERX1234253_ERR1160846",
-                        "instrument_model": "Illumina HiSeq 2500",
-                        "instrument_platform": "ILLUMINA",
-                        "library_layout": "SINGLE",
-                        "library_name": "10317.BLANK.93.3E.r22",
-                        "library_selection": "PCR",
-                        "library_source": "METAGENOMIC",
-                        "library_strategy": "AMPLICON",
-                        "md5_1": "5924f20ef547ebdfed7cad795bbab6e6",
-                        "md5_2": "",
-                        "read_count": "283",
-                        "run_accession": "ERR1160846",
-                        "run_alias": "qiita_ppdid_706:10317.BLANK.93.3E.r22",
-                        "sample_accession": "SAMEA3687214",
-                        "sample_alias": "qiita_sid_10317:10317.BLANK.93.3E.r22",
-                        "sample_description": "American Gut control",
-                        "sample_title": "10317.BLANK.93.3E.r22",
-                        "scientific_name": "metagenome",
-                        "secondary_sample_accession": "ERS994363",
-                        "secondary_study_accession": "ERP012803",
-                        "single_end": true,
-                        "study_accession": "PRJEB11419",
-                        "study_alias": "qiita_sid_10317",
-                        "study_title": "American Gut Project",
-                        "submission_accession": "ERA541392",
-                        "tax_id": "256318"
-                    }
-                ],
-                "versions": [
-                    "versions.yml:md5,1496d1cbc9041e07ab8a0c25f0b054d9",
-                    "versions.yml:md5,9b17045ca8bdc272cb3f9d349a81d206",
-                    "versions.yml:md5,b52279f7d6b891a6523d9321f3f85b47",
-                    "versions.yml:md5,c19fc0f920e57875881761cc944a46d7"
-                ]
-            }
+            "samplesheet.csv",
+            [
+                "id_mappings.csv:md5,3e41ce6ab19feb76f2b20fa77a910ad3"
+            ],
+            [
+                "multiqc_config.yml:md5,1ac06bb95b503703430e74660bbdd768"
+            ],
+            [
+                {
+                    "base_count": "194930",
+                    "experiment_accession": "DRX026011",
+                    "experiment_alias": "DRX026011",
+                    "experiment_title": "Illumina HiSeq 2500 paired end sequencing: Illumina HiSeq 2500 paired end sequencing of SAMD00024405",
+                    "fastq_1": "DRX026011_DRR028935_1.fastq.gz:md5,f9b4a5d25aa7d6ab4050dbe0764eb04d",
+                    "fastq_2": "DRX026011_DRR028935_2.fastq.gz:md5,dc0d2e1fc46f4d4581a477f87ec3ff15",
+                    "fastq_aspera": "fasp.sra.ebi.ac.uk:/vol1/fastq/DRR028/DRR028935/DRR028935_1.fastq.gz;fasp.sra.ebi.ac.uk:/vol1/fastq/DRR028/DRR028935/DRR028935_2.fastq.gz",
+                    "fastq_bytes": "60275;61610",
+                    "fastq_ftp": "ftp.sra.ebi.ac.uk/vol1/fastq/DRR028/DRR028935/DRR028935_1.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/DRR028/DRR028935/DRR028935_2.fastq.gz",
+                    "fastq_galaxy": "ftp.sra.ebi.ac.uk/vol1/fastq/DRR028/DRR028935/DRR028935_1.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/DRR028/DRR028935/DRR028935_2.fastq.gz",
+                    "fastq_md5": "cc01df82a9354bb6b3be93483b20c35a;941c9998d746416dad53c94c480ddf30",
+                    "id": "DRX026011_DRR028935",
+                    "instrument_model": "Illumina HiSeq 2500",
+                    "instrument_platform": "ILLUMINA",
+                    "library_layout": "PAIRED",
+                    "library_name": "day0_BbSQE-I",
+                    "library_selection": "cDNA",
+                    "library_source": "TRANSCRIPTOMIC",
+                    "library_strategy": "RNA-Seq",
+                    "md5_1": "cc01df82a9354bb6b3be93483b20c35a",
+                    "md5_2": "941c9998d746416dad53c94c480ddf30",
+                    "read_count": "965",
+                    "run_accession": "DRR028935",
+                    "run_alias": "DRR028935",
+                    "sample_accession": "SAMD00024405",
+                    "sample_alias": "SAMD00024405",
+                    "sample_description": "Liquid culture",
+                    "sample_title": "Botryococcus braunii Showa at day 0 after inoculation into fresh culture medium",
+                    "scientific_name": "Botryococcus braunii Showa",
+                    "secondary_sample_accession": "DRS019431",
+                    "secondary_study_accession": "DRP002616",
+                    "single_end": false,
+                    "study_accession": "PRJDB3420",
+                    "study_alias": "DRP002616",
+                    "study_title": "Liquid culture of Botryococcus braunii, race B, Showa",
+                    "submission_accession": "DRA002949",
+                    "tax_id": "1202541"
+                },
+                {
+                    "base_count": "1996273",
+                    "experiment_accession": "SRX6725035",
+                    "experiment_alias": "Emb289P1_bin131",
+                    "experiment_title": "Illumina HiSeq 2500 sequencing: Binning of metagenomic reads from the P1 gut compartment of Embiratermes neotenicus",
+                    "fastq_1": "SRX6725035_SRR9984183.fastq.gz:md5,c9b4c2c4abf19da7082caf442fdefea7",
+                    "fastq_2": "",
+                    "fastq_aspera": "fasp.sra.ebi.ac.uk:/vol1/fastq/SRR998/003/SRR9984183/SRR9984183.fastq.gz",
+                    "fastq_bytes": "605358",
+                    "fastq_ftp": "ftp.sra.ebi.ac.uk/vol1/fastq/SRR998/003/SRR9984183/SRR9984183.fastq.gz",
+                    "fastq_galaxy": "ftp.sra.ebi.ac.uk/vol1/fastq/SRR998/003/SRR9984183/SRR9984183.fastq.gz",
+                    "fastq_md5": "0b512d2dc31685983456bd56fd836544",
+                    "id": "SRX6725035_SRR9984183",
+                    "instrument_model": "Illumina HiSeq 2500",
+                    "instrument_platform": "ILLUMINA",
+                    "library_layout": "SINGLE",
+                    "library_name": "Emb289P1_bin131",
+                    "library_selection": "RANDOM",
+                    "library_source": "METAGENOMIC",
+                    "library_strategy": "WGS",
+                    "md5_1": "0b512d2dc31685983456bd56fd836544",
+                    "md5_2": "",
+                    "read_count": "58",
+                    "run_accession": "SRR9984183",
+                    "run_alias": "Emb289P1_bin131.fastq",
+                    "sample_accession": "SAMN12581720",
+                    "sample_alias": "Emb289P1_bin131",
+                    "sample_description": "Keywords: GSC:MIxS MIMAG:5.0",
+                    "sample_title": "MIMAG Metagenome-assembled Genome sample from Defluviitaleaceae bacterium",
+                    "scientific_name": "Defluviitaleaceae bacterium",
+                    "secondary_sample_accession": "SRS5277011",
+                    "secondary_study_accession": "SRP218535",
+                    "single_end": true,
+                    "study_accession": "PRJNA560329",
+                    "study_alias": "PRJNA560329",
+                    "study_title": "Phylogenomic analysis of 589 metagenome-assembled genomes encompassing all major prokaryotic lineages from the gut of higher termites",
+                    "submission_accession": "SRA942061",
+                    "tax_id": "2660712"
+                },
+                {
+                    "base_count": "35658",
+                    "experiment_accession": "ERX1234253",
+                    "experiment_alias": "qiita_ptid_1263:10317.BLANK.93.3E.r22",
+                    "experiment_title": "Illumina HiSeq 2500 sequencing: qiita_ptid_1263:10317.BLANK.93.3E.r22",
+                    "fastq_1": "ERX1234253_ERR1160846.fastq.gz:md5,b1de59f829fbd2d60a1ed4bc3da55709",
+                    "fastq_2": "",
+                    "fastq_aspera": "fasp.sra.ebi.ac.uk:/vol1/fastq/ERR116/006/ERR1160846/ERR1160846.fastq.gz",
+                    "fastq_bytes": "18077",
+                    "fastq_ftp": "ftp.sra.ebi.ac.uk/vol1/fastq/ERR116/006/ERR1160846/ERR1160846.fastq.gz",
+                    "fastq_galaxy": "ftp.sra.ebi.ac.uk/vol1/fastq/ERR116/006/ERR1160846/ERR1160846.fastq.gz",
+                    "fastq_md5": "5924f20ef547ebdfed7cad795bbab6e6",
+                    "id": "ERX1234253_ERR1160846",
+                    "instrument_model": "Illumina HiSeq 2500",
+                    "instrument_platform": "ILLUMINA",
+                    "library_layout": "SINGLE",
+                    "library_name": "10317.BLANK.93.3E.r22",
+                    "library_selection": "PCR",
+                    "library_source": "METAGENOMIC",
+                    "library_strategy": "AMPLICON",
+                    "md5_1": "5924f20ef547ebdfed7cad795bbab6e6",
+                    "md5_2": "",
+                    "read_count": "283",
+                    "run_accession": "ERR1160846",
+                    "run_alias": "qiita_ppdid_706:10317.BLANK.93.3E.r22",
+                    "sample_accession": "SAMEA3687214",
+                    "sample_alias": "qiita_sid_10317:10317.BLANK.93.3E.r22",
+                    "sample_description": "American Gut control",
+                    "sample_title": "10317.BLANK.93.3E.r22",
+                    "scientific_name": "metagenome",
+                    "secondary_sample_accession": "ERS994363",
+                    "secondary_study_accession": "ERP012803",
+                    "single_end": true,
+                    "study_accession": "PRJEB11419",
+                    "study_alias": "qiita_sid_10317",
+                    "study_title": "American Gut Project",
+                    "submission_accession": "ERA541392",
+                    "tax_id": "256318"
+                }
+            ],
+            [
+                "versions.yml:md5,1496d1cbc9041e07ab8a0c25f0b054d9",
+                "versions.yml:md5,9b17045ca8bdc272cb3f9d349a81d206",
+                "versions.yml:md5,b52279f7d6b891a6523d9321f3f85b47",
+                "versions.yml:md5,c19fc0f920e57875881761cc944a46d7"
+            ]
         ],
         "meta": {
             "nf-test": "0.9.0",
             "nextflow": "24.09.2"
         },
-        "timestamp": "2024-10-15T13:05:35.712529"
+        "timestamp": "2024-10-15T13:37:33.713018"
     }
 }
\ No newline at end of file
diff --git a/workflows/sra/tests/sra_nf_core_pipeline_taxprofiler.nf.test b/workflows/sra/tests/sra_nf_core_pipeline_taxprofiler.nf.test
index 257afef5..da15ed22 100644
--- a/workflows/sra/tests/sra_nf_core_pipeline_taxprofiler.nf.test
+++ b/workflows/sra/tests/sra_nf_core_pipeline_taxprofiler.nf.test
@@ -29,7 +29,13 @@ nextflow_workflow {
         then {
             assertAll(
                 { assert workflow.success},
-                { assert snapshot(workflow.out).match() }
+                { assert snapshot(
+                    file(workflow.out.samplesheet[0]).name,
+                    workflow.out.mappings,
+                    workflow.out.sample_mappings,
+                    workflow.out.sra_metadata,
+                    workflow.out.versions
+                ).match() }
             )
         }
     }
diff --git a/workflows/sra/tests/sra_nf_core_pipeline_taxprofiler.nf.test.snap b/workflows/sra/tests/sra_nf_core_pipeline_taxprofiler.nf.test.snap
index d4d7047e..bb4306bb 100644
--- a/workflows/sra/tests/sra_nf_core_pipeline_taxprofiler.nf.test.snap
+++ b/workflows/sra/tests/sra_nf_core_pipeline_taxprofiler.nf.test.snap
@@ -1,281 +1,143 @@
 {
     "Parameters: --nf_core_pipeline taxprofiler": {
         "content": [
-            {
-                "0": [
-                    "samplesheet.csv:md5,790f0cad9d01e35e0d1e03f199851770"
-                ],
-                "1": [
-                    "id_mappings.csv:md5,3e41ce6ab19feb76f2b20fa77a910ad3"
-                ],
-                "2": [
-                    "multiqc_config.yml:md5,1ac06bb95b503703430e74660bbdd768"
-                ],
-                "3": [
-                    {
-                        "base_count": "194930",
-                        "experiment_accession": "DRX026011",
-                        "experiment_alias": "DRX026011",
-                        "experiment_title": "Illumina HiSeq 2500 paired end sequencing: Illumina HiSeq 2500 paired end sequencing of SAMD00024405",
-                        "fastq_1": "DRX026011_DRR028935_1.fastq.gz:md5,f9b4a5d25aa7d6ab4050dbe0764eb04d",
-                        "fastq_2": "DRX026011_DRR028935_2.fastq.gz:md5,dc0d2e1fc46f4d4581a477f87ec3ff15",
-                        "fastq_aspera": "fasp.sra.ebi.ac.uk:/vol1/fastq/DRR028/DRR028935/DRR028935_1.fastq.gz;fasp.sra.ebi.ac.uk:/vol1/fastq/DRR028/DRR028935/DRR028935_2.fastq.gz",
-                        "fastq_bytes": "60275;61610",
-                        "fastq_ftp": "ftp.sra.ebi.ac.uk/vol1/fastq/DRR028/DRR028935/DRR028935_1.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/DRR028/DRR028935/DRR028935_2.fastq.gz",
-                        "fastq_galaxy": "ftp.sra.ebi.ac.uk/vol1/fastq/DRR028/DRR028935/DRR028935_1.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/DRR028/DRR028935/DRR028935_2.fastq.gz",
-                        "fastq_md5": "cc01df82a9354bb6b3be93483b20c35a;941c9998d746416dad53c94c480ddf30",
-                        "id": "DRX026011_DRR028935",
-                        "instrument_model": "Illumina HiSeq 2500",
-                        "instrument_platform": "ILLUMINA",
-                        "library_layout": "PAIRED",
-                        "library_name": "day0_BbSQE-I",
-                        "library_selection": "cDNA",
-                        "library_source": "TRANSCRIPTOMIC",
-                        "library_strategy": "RNA-Seq",
-                        "md5_1": "cc01df82a9354bb6b3be93483b20c35a",
-                        "md5_2": "941c9998d746416dad53c94c480ddf30",
-                        "read_count": "965",
-                        "run_accession": "DRR028935",
-                        "run_alias": "DRR028935",
-                        "sample_accession": "SAMD00024405",
-                        "sample_alias": "SAMD00024405",
-                        "sample_description": "Liquid culture",
-                        "sample_title": "Botryococcus braunii Showa at day 0 after inoculation into fresh culture medium",
-                        "scientific_name": "Botryococcus braunii Showa",
-                        "secondary_sample_accession": "DRS019431",
-                        "secondary_study_accession": "DRP002616",
-                        "single_end": false,
-                        "study_accession": "PRJDB3420",
-                        "study_alias": "DRP002616",
-                        "study_title": "Liquid culture of Botryococcus braunii, race B, Showa",
-                        "submission_accession": "DRA002949",
-                        "tax_id": "1202541"
-                    },
-                    {
-                        "base_count": "1996273",
-                        "experiment_accession": "SRX6725035",
-                        "experiment_alias": "Emb289P1_bin131",
-                        "experiment_title": "Illumina HiSeq 2500 sequencing: Binning of metagenomic reads from the P1 gut compartment of Embiratermes neotenicus",
-                        "fastq_1": "SRX6725035_SRR9984183.fastq.gz:md5,c9b4c2c4abf19da7082caf442fdefea7",
-                        "fastq_2": "",
-                        "fastq_aspera": "fasp.sra.ebi.ac.uk:/vol1/fastq/SRR998/003/SRR9984183/SRR9984183.fastq.gz",
-                        "fastq_bytes": "605358",
-                        "fastq_ftp": "ftp.sra.ebi.ac.uk/vol1/fastq/SRR998/003/SRR9984183/SRR9984183.fastq.gz",
-                        "fastq_galaxy": "ftp.sra.ebi.ac.uk/vol1/fastq/SRR998/003/SRR9984183/SRR9984183.fastq.gz",
-                        "fastq_md5": "0b512d2dc31685983456bd56fd836544",
-                        "id": "SRX6725035_SRR9984183",
-                        "instrument_model": "Illumina HiSeq 2500",
-                        "instrument_platform": "ILLUMINA",
-                        "library_layout": "SINGLE",
-                        "library_name": "Emb289P1_bin131",
-                        "library_selection": "RANDOM",
-                        "library_source": "METAGENOMIC",
-                        "library_strategy": "WGS",
-                        "md5_1": "0b512d2dc31685983456bd56fd836544",
-                        "md5_2": "",
-                        "read_count": "58",
-                        "run_accession": "SRR9984183",
-                        "run_alias": "Emb289P1_bin131.fastq",
-                        "sample_accession": "SAMN12581720",
-                        "sample_alias": "Emb289P1_bin131",
-                        "sample_description": "Keywords: GSC:MIxS MIMAG:5.0",
-                        "sample_title": "MIMAG Metagenome-assembled Genome sample from Defluviitaleaceae bacterium",
-                        "scientific_name": "Defluviitaleaceae bacterium",
-                        "secondary_sample_accession": "SRS5277011",
-                        "secondary_study_accession": "SRP218535",
-                        "single_end": true,
-                        "study_accession": "PRJNA560329",
-                        "study_alias": "PRJNA560329",
-                        "study_title": "Phylogenomic analysis of 589 metagenome-assembled genomes encompassing all major prokaryotic lineages from the gut of higher termites",
-                        "submission_accession": "SRA942061",
-                        "tax_id": "2660712"
-                    },
-                    {
-                        "base_count": "35658",
-                        "experiment_accession": "ERX1234253",
-                        "experiment_alias": "qiita_ptid_1263:10317.BLANK.93.3E.r22",
-                        "experiment_title": "Illumina HiSeq 2500 sequencing: qiita_ptid_1263:10317.BLANK.93.3E.r22",
-                        "fastq_1": "ERX1234253_ERR1160846.fastq.gz:md5,b1de59f829fbd2d60a1ed4bc3da55709",
-                        "fastq_2": "",
-                        "fastq_aspera": "fasp.sra.ebi.ac.uk:/vol1/fastq/ERR116/006/ERR1160846/ERR1160846.fastq.gz",
-                        "fastq_bytes": "18077",
-                        "fastq_ftp": "ftp.sra.ebi.ac.uk/vol1/fastq/ERR116/006/ERR1160846/ERR1160846.fastq.gz",
-                        "fastq_galaxy": "ftp.sra.ebi.ac.uk/vol1/fastq/ERR116/006/ERR1160846/ERR1160846.fastq.gz",
-                        "fastq_md5": "5924f20ef547ebdfed7cad795bbab6e6",
-                        "id": "ERX1234253_ERR1160846",
-                        "instrument_model": "Illumina HiSeq 2500",
-                        "instrument_platform": "ILLUMINA",
-                        "library_layout": "SINGLE",
-                        "library_name": "10317.BLANK.93.3E.r22",
-                        "library_selection": "PCR",
-                        "library_source": "METAGENOMIC",
-                        "library_strategy": "AMPLICON",
-                        "md5_1": "5924f20ef547ebdfed7cad795bbab6e6",
-                        "md5_2": "",
-                        "read_count": "283",
-                        "run_accession": "ERR1160846",
-                        "run_alias": "qiita_ppdid_706:10317.BLANK.93.3E.r22",
-                        "sample_accession": "SAMEA3687214",
-                        "sample_alias": "qiita_sid_10317:10317.BLANK.93.3E.r22",
-                        "sample_description": "American Gut control",
-                        "sample_title": "10317.BLANK.93.3E.r22",
-                        "scientific_name": "metagenome",
-                        "secondary_sample_accession": "ERS994363",
-                        "secondary_study_accession": "ERP012803",
-                        "single_end": true,
-                        "study_accession": "PRJEB11419",
-                        "study_alias": "qiita_sid_10317",
-                        "study_title": "American Gut Project",
-                        "submission_accession": "ERA541392",
-                        "tax_id": "256318"
-                    }
-                ],
-                "4": [
-                    "versions.yml:md5,1496d1cbc9041e07ab8a0c25f0b054d9",
-                    "versions.yml:md5,9b17045ca8bdc272cb3f9d349a81d206",
-                    "versions.yml:md5,b52279f7d6b891a6523d9321f3f85b47",
-                    "versions.yml:md5,c19fc0f920e57875881761cc944a46d7"
-                ],
-                "mappings": [
-                    "id_mappings.csv:md5,3e41ce6ab19feb76f2b20fa77a910ad3"
-                ],
-                "sample_mappings": [
-                    "multiqc_config.yml:md5,1ac06bb95b503703430e74660bbdd768"
-                ],
-                "samplesheet": [
-                    "samplesheet.csv:md5,790f0cad9d01e35e0d1e03f199851770"
-                ],
-                "sra_metadata": [
-                    {
-                        "base_count": "194930",
-                        "experiment_accession": "DRX026011",
-                        "experiment_alias": "DRX026011",
-                        "experiment_title": "Illumina HiSeq 2500 paired end sequencing: Illumina HiSeq 2500 paired end sequencing of SAMD00024405",
-                        "fastq_1": "DRX026011_DRR028935_1.fastq.gz:md5,f9b4a5d25aa7d6ab4050dbe0764eb04d",
-                        "fastq_2": "DRX026011_DRR028935_2.fastq.gz:md5,dc0d2e1fc46f4d4581a477f87ec3ff15",
-                        "fastq_aspera": "fasp.sra.ebi.ac.uk:/vol1/fastq/DRR028/DRR028935/DRR028935_1.fastq.gz;fasp.sra.ebi.ac.uk:/vol1/fastq/DRR028/DRR028935/DRR028935_2.fastq.gz",
-                        "fastq_bytes": "60275;61610",
-                        "fastq_ftp": "ftp.sra.ebi.ac.uk/vol1/fastq/DRR028/DRR028935/DRR028935_1.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/DRR028/DRR028935/DRR028935_2.fastq.gz",
-                        "fastq_galaxy": "ftp.sra.ebi.ac.uk/vol1/fastq/DRR028/DRR028935/DRR028935_1.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/DRR028/DRR028935/DRR028935_2.fastq.gz",
-                        "fastq_md5": "cc01df82a9354bb6b3be93483b20c35a;941c9998d746416dad53c94c480ddf30",
-                        "id": "DRX026011_DRR028935",
-                        "instrument_model": "Illumina HiSeq 2500",
-                        "instrument_platform": "ILLUMINA",
-                        "library_layout": "PAIRED",
-                        "library_name": "day0_BbSQE-I",
-                        "library_selection": "cDNA",
-                        "library_source": "TRANSCRIPTOMIC",
-                        "library_strategy": "RNA-Seq",
-                        "md5_1": "cc01df82a9354bb6b3be93483b20c35a",
-                        "md5_2": "941c9998d746416dad53c94c480ddf30",
-                        "read_count": "965",
-                        "run_accession": "DRR028935",
-                        "run_alias": "DRR028935",
-                        "sample_accession": "SAMD00024405",
-                        "sample_alias": "SAMD00024405",
-                        "sample_description": "Liquid culture",
-                        "sample_title": "Botryococcus braunii Showa at day 0 after inoculation into fresh culture medium",
-                        "scientific_name": "Botryococcus braunii Showa",
-                        "secondary_sample_accession": "DRS019431",
-                        "secondary_study_accession": "DRP002616",
-                        "single_end": false,
-                        "study_accession": "PRJDB3420",
-                        "study_alias": "DRP002616",
-                        "study_title": "Liquid culture of Botryococcus braunii, race B, Showa",
-                        "submission_accession": "DRA002949",
-                        "tax_id": "1202541"
-                    },
-                    {
-                        "base_count": "1996273",
-                        "experiment_accession": "SRX6725035",
-                        "experiment_alias": "Emb289P1_bin131",
-                        "experiment_title": "Illumina HiSeq 2500 sequencing: Binning of metagenomic reads from the P1 gut compartment of Embiratermes neotenicus",
-                        "fastq_1": "SRX6725035_SRR9984183.fastq.gz:md5,c9b4c2c4abf19da7082caf442fdefea7",
-                        "fastq_2": "",
-                        "fastq_aspera": "fasp.sra.ebi.ac.uk:/vol1/fastq/SRR998/003/SRR9984183/SRR9984183.fastq.gz",
-                        "fastq_bytes": "605358",
-                        "fastq_ftp": "ftp.sra.ebi.ac.uk/vol1/fastq/SRR998/003/SRR9984183/SRR9984183.fastq.gz",
-                        "fastq_galaxy": "ftp.sra.ebi.ac.uk/vol1/fastq/SRR998/003/SRR9984183/SRR9984183.fastq.gz",
-                        "fastq_md5": "0b512d2dc31685983456bd56fd836544",
-                        "id": "SRX6725035_SRR9984183",
-                        "instrument_model": "Illumina HiSeq 2500",
-                        "instrument_platform": "ILLUMINA",
-                        "library_layout": "SINGLE",
-                        "library_name": "Emb289P1_bin131",
-                        "library_selection": "RANDOM",
-                        "library_source": "METAGENOMIC",
-                        "library_strategy": "WGS",
-                        "md5_1": "0b512d2dc31685983456bd56fd836544",
-                        "md5_2": "",
-                        "read_count": "58",
-                        "run_accession": "SRR9984183",
-                        "run_alias": "Emb289P1_bin131.fastq",
-                        "sample_accession": "SAMN12581720",
-                        "sample_alias": "Emb289P1_bin131",
-                        "sample_description": "Keywords: GSC:MIxS MIMAG:5.0",
-                        "sample_title": "MIMAG Metagenome-assembled Genome sample from Defluviitaleaceae bacterium",
-                        "scientific_name": "Defluviitaleaceae bacterium",
-                        "secondary_sample_accession": "SRS5277011",
-                        "secondary_study_accession": "SRP218535",
-                        "single_end": true,
-                        "study_accession": "PRJNA560329",
-                        "study_alias": "PRJNA560329",
-                        "study_title": "Phylogenomic analysis of 589 metagenome-assembled genomes encompassing all major prokaryotic lineages from the gut of higher termites",
-                        "submission_accession": "SRA942061",
-                        "tax_id": "2660712"
-                    },
-                    {
-                        "base_count": "35658",
-                        "experiment_accession": "ERX1234253",
-                        "experiment_alias": "qiita_ptid_1263:10317.BLANK.93.3E.r22",
-                        "experiment_title": "Illumina HiSeq 2500 sequencing: qiita_ptid_1263:10317.BLANK.93.3E.r22",
-                        "fastq_1": "ERX1234253_ERR1160846.fastq.gz:md5,b1de59f829fbd2d60a1ed4bc3da55709",
-                        "fastq_2": "",
-                        "fastq_aspera": "fasp.sra.ebi.ac.uk:/vol1/fastq/ERR116/006/ERR1160846/ERR1160846.fastq.gz",
-                        "fastq_bytes": "18077",
-                        "fastq_ftp": "ftp.sra.ebi.ac.uk/vol1/fastq/ERR116/006/ERR1160846/ERR1160846.fastq.gz",
-                        "fastq_galaxy": "ftp.sra.ebi.ac.uk/vol1/fastq/ERR116/006/ERR1160846/ERR1160846.fastq.gz",
-                        "fastq_md5": "5924f20ef547ebdfed7cad795bbab6e6",
-                        "id": "ERX1234253_ERR1160846",
-                        "instrument_model": "Illumina HiSeq 2500",
-                        "instrument_platform": "ILLUMINA",
-                        "library_layout": "SINGLE",
-                        "library_name": "10317.BLANK.93.3E.r22",
-                        "library_selection": "PCR",
-                        "library_source": "METAGENOMIC",
-                        "library_strategy": "AMPLICON",
-                        "md5_1": "5924f20ef547ebdfed7cad795bbab6e6",
-                        "md5_2": "",
-                        "read_count": "283",
-                        "run_accession": "ERR1160846",
-                        "run_alias": "qiita_ppdid_706:10317.BLANK.93.3E.r22",
-                        "sample_accession": "SAMEA3687214",
-                        "sample_alias": "qiita_sid_10317:10317.BLANK.93.3E.r22",
-                        "sample_description": "American Gut control",
-                        "sample_title": "10317.BLANK.93.3E.r22",
-                        "scientific_name": "metagenome",
-                        "secondary_sample_accession": "ERS994363",
-                        "secondary_study_accession": "ERP012803",
-                        "single_end": true,
-                        "study_accession": "PRJEB11419",
-                        "study_alias": "qiita_sid_10317",
-                        "study_title": "American Gut Project",
-                        "submission_accession": "ERA541392",
-                        "tax_id": "256318"
-                    }
-                ],
-                "versions": [
-                    "versions.yml:md5,1496d1cbc9041e07ab8a0c25f0b054d9",
-                    "versions.yml:md5,9b17045ca8bdc272cb3f9d349a81d206",
-                    "versions.yml:md5,b52279f7d6b891a6523d9321f3f85b47",
-                    "versions.yml:md5,c19fc0f920e57875881761cc944a46d7"
-                ]
-            }
+            "samplesheet.csv",
+            [
+                "id_mappings.csv:md5,3e41ce6ab19feb76f2b20fa77a910ad3"
+            ],
+            [
+                "multiqc_config.yml:md5,1ac06bb95b503703430e74660bbdd768"
+            ],
+            [
+                {
+                    "base_count": "194930",
+                    "experiment_accession": "DRX026011",
+                    "experiment_alias": "DRX026011",
+                    "experiment_title": "Illumina HiSeq 2500 paired end sequencing: Illumina HiSeq 2500 paired end sequencing of SAMD00024405",
+                    "fastq_1": "DRX026011_DRR028935_1.fastq.gz:md5,f9b4a5d25aa7d6ab4050dbe0764eb04d",
+                    "fastq_2": "DRX026011_DRR028935_2.fastq.gz:md5,dc0d2e1fc46f4d4581a477f87ec3ff15",
+                    "fastq_aspera": "fasp.sra.ebi.ac.uk:/vol1/fastq/DRR028/DRR028935/DRR028935_1.fastq.gz;fasp.sra.ebi.ac.uk:/vol1/fastq/DRR028/DRR028935/DRR028935_2.fastq.gz",
+                    "fastq_bytes": "60275;61610",
+                    "fastq_ftp": "ftp.sra.ebi.ac.uk/vol1/fastq/DRR028/DRR028935/DRR028935_1.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/DRR028/DRR028935/DRR028935_2.fastq.gz",
+                    "fastq_galaxy": "ftp.sra.ebi.ac.uk/vol1/fastq/DRR028/DRR028935/DRR028935_1.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/DRR028/DRR028935/DRR028935_2.fastq.gz",
+                    "fastq_md5": "cc01df82a9354bb6b3be93483b20c35a;941c9998d746416dad53c94c480ddf30",
+                    "id": "DRX026011_DRR028935",
+                    "instrument_model": "Illumina HiSeq 2500",
+                    "instrument_platform": "ILLUMINA",
+                    "library_layout": "PAIRED",
+                    "library_name": "day0_BbSQE-I",
+                    "library_selection": "cDNA",
+                    "library_source": "TRANSCRIPTOMIC",
+                    "library_strategy": "RNA-Seq",
+                    "md5_1": "cc01df82a9354bb6b3be93483b20c35a",
+                    "md5_2": "941c9998d746416dad53c94c480ddf30",
+                    "read_count": "965",
+                    "run_accession": "DRR028935",
+                    "run_alias": "DRR028935",
+                    "sample_accession": "SAMD00024405",
+                    "sample_alias": "SAMD00024405",
+                    "sample_description": "Liquid culture",
+                    "sample_title": "Botryococcus braunii Showa at day 0 after inoculation into fresh culture medium",
+                    "scientific_name": "Botryococcus braunii Showa",
+                    "secondary_sample_accession": "DRS019431",
+                    "secondary_study_accession": "DRP002616",
+                    "single_end": false,
+                    "study_accession": "PRJDB3420",
+                    "study_alias": "DRP002616",
+                    "study_title": "Liquid culture of Botryococcus braunii, race B, Showa",
+                    "submission_accession": "DRA002949",
+                    "tax_id": "1202541"
+                },
+                {
+                    "base_count": "1996273",
+                    "experiment_accession": "SRX6725035",
+                    "experiment_alias": "Emb289P1_bin131",
+                    "experiment_title": "Illumina HiSeq 2500 sequencing: Binning of metagenomic reads from the P1 gut compartment of Embiratermes neotenicus",
+                    "fastq_1": "SRX6725035_SRR9984183.fastq.gz:md5,c9b4c2c4abf19da7082caf442fdefea7",
+                    "fastq_2": "",
+                    "fastq_aspera": "fasp.sra.ebi.ac.uk:/vol1/fastq/SRR998/003/SRR9984183/SRR9984183.fastq.gz",
+                    "fastq_bytes": "605358",
+                    "fastq_ftp": "ftp.sra.ebi.ac.uk/vol1/fastq/SRR998/003/SRR9984183/SRR9984183.fastq.gz",
+                    "fastq_galaxy": "ftp.sra.ebi.ac.uk/vol1/fastq/SRR998/003/SRR9984183/SRR9984183.fastq.gz",
+                    "fastq_md5": "0b512d2dc31685983456bd56fd836544",
+                    "id": "SRX6725035_SRR9984183",
+                    "instrument_model": "Illumina HiSeq 2500",
+                    "instrument_platform": "ILLUMINA",
+                    "library_layout": "SINGLE",
+                    "library_name": "Emb289P1_bin131",
+                    "library_selection": "RANDOM",
+                    "library_source": "METAGENOMIC",
+                    "library_strategy": "WGS",
+                    "md5_1": "0b512d2dc31685983456bd56fd836544",
+                    "md5_2": "",
+                    "read_count": "58",
+                    "run_accession": "SRR9984183",
+                    "run_alias": "Emb289P1_bin131.fastq",
+                    "sample_accession": "SAMN12581720",
+                    "sample_alias": "Emb289P1_bin131",
+                    "sample_description": "Keywords: GSC:MIxS MIMAG:5.0",
+                    "sample_title": "MIMAG Metagenome-assembled Genome sample from Defluviitaleaceae bacterium",
+                    "scientific_name": "Defluviitaleaceae bacterium",
+                    "secondary_sample_accession": "SRS5277011",
+                    "secondary_study_accession": "SRP218535",
+                    "single_end": true,
+                    "study_accession": "PRJNA560329",
+                    "study_alias": "PRJNA560329",
+                    "study_title": "Phylogenomic analysis of 589 metagenome-assembled genomes encompassing all major prokaryotic lineages from the gut of higher termites",
+                    "submission_accession": "SRA942061",
+                    "tax_id": "2660712"
+                },
+                {
+                    "base_count": "35658",
+                    "experiment_accession": "ERX1234253",
+                    "experiment_alias": "qiita_ptid_1263:10317.BLANK.93.3E.r22",
+                    "experiment_title": "Illumina HiSeq 2500 sequencing: qiita_ptid_1263:10317.BLANK.93.3E.r22",
+                    "fastq_1": "ERX1234253_ERR1160846.fastq.gz:md5,b1de59f829fbd2d60a1ed4bc3da55709",
+                    "fastq_2": "",
+                    "fastq_aspera": "fasp.sra.ebi.ac.uk:/vol1/fastq/ERR116/006/ERR1160846/ERR1160846.fastq.gz",
+                    "fastq_bytes": "18077",
+                    "fastq_ftp": "ftp.sra.ebi.ac.uk/vol1/fastq/ERR116/006/ERR1160846/ERR1160846.fastq.gz",
+                    "fastq_galaxy": "ftp.sra.ebi.ac.uk/vol1/fastq/ERR116/006/ERR1160846/ERR1160846.fastq.gz",
+                    "fastq_md5": "5924f20ef547ebdfed7cad795bbab6e6",
+                    "id": "ERX1234253_ERR1160846",
+                    "instrument_model": "Illumina HiSeq 2500",
+                    "instrument_platform": "ILLUMINA",
+                    "library_layout": "SINGLE",
+                    "library_name": "10317.BLANK.93.3E.r22",
+                    "library_selection": "PCR",
+                    "library_source": "METAGENOMIC",
+                    "library_strategy": "AMPLICON",
+                    "md5_1": "5924f20ef547ebdfed7cad795bbab6e6",
+                    "md5_2": "",
+                    "read_count": "283",
+                    "run_accession": "ERR1160846",
+                    "run_alias": "qiita_ppdid_706:10317.BLANK.93.3E.r22",
+                    "sample_accession": "SAMEA3687214",
+                    "sample_alias": "qiita_sid_10317:10317.BLANK.93.3E.r22",
+                    "sample_description": "American Gut control",
+                    "sample_title": "10317.BLANK.93.3E.r22",
+                    "scientific_name": "metagenome",
+                    "secondary_sample_accession": "ERS994363",
+                    "secondary_study_accession": "ERP012803",
+                    "single_end": true,
+                    "study_accession": "PRJEB11419",
+                    "study_alias": "qiita_sid_10317",
+                    "study_title": "American Gut Project",
+                    "submission_accession": "ERA541392",
+                    "tax_id": "256318"
+                }
+            ],
+            [
+                "versions.yml:md5,1496d1cbc9041e07ab8a0c25f0b054d9",
+                "versions.yml:md5,9b17045ca8bdc272cb3f9d349a81d206",
+                "versions.yml:md5,b52279f7d6b891a6523d9321f3f85b47",
+                "versions.yml:md5,c19fc0f920e57875881761cc944a46d7"
+            ]
         ],
         "meta": {
             "nf-test": "0.9.0",
             "nextflow": "24.09.2"
         },
-        "timestamp": "2024-10-15T13:05:55.50559"
+        "timestamp": "2024-10-15T13:37:49.813745"
     }
 }
\ No newline at end of file
diff --git a/workflows/sra/tests/sra_nf_core_pipeline_viralrecon.nf.test b/workflows/sra/tests/sra_nf_core_pipeline_viralrecon.nf.test
index 77ab9e2a..fb9a5bdb 100644
--- a/workflows/sra/tests/sra_nf_core_pipeline_viralrecon.nf.test
+++ b/workflows/sra/tests/sra_nf_core_pipeline_viralrecon.nf.test
@@ -29,7 +29,13 @@ nextflow_workflow {
         then {
             assertAll(
                 { assert workflow.success},
-                { assert snapshot(workflow.out).match() }
+                { assert snapshot(
+                    file(workflow.out.samplesheet[0]).name,
+                    workflow.out.mappings,
+                    workflow.out.sample_mappings,
+                    workflow.out.sra_metadata,
+                    workflow.out.versions
+                ).match() }
             )
         }
     }
diff --git a/workflows/sra/tests/sra_nf_core_pipeline_viralrecon.nf.test.snap b/workflows/sra/tests/sra_nf_core_pipeline_viralrecon.nf.test.snap
index a9b14b4d..715cf6b8 100644
--- a/workflows/sra/tests/sra_nf_core_pipeline_viralrecon.nf.test.snap
+++ b/workflows/sra/tests/sra_nf_core_pipeline_viralrecon.nf.test.snap
@@ -1,281 +1,143 @@
 {
     "Parameters: --nf_core_pipeline viralrecon": {
         "content": [
-            {
-                "0": [
-                    "samplesheet.csv:md5,d81fe6175afaa01183475a6e28c7caa9"
-                ],
-                "1": [
-                    "id_mappings.csv:md5,3e41ce6ab19feb76f2b20fa77a910ad3"
-                ],
-                "2": [
-                    "multiqc_config.yml:md5,1ac06bb95b503703430e74660bbdd768"
-                ],
-                "3": [
-                    {
-                        "base_count": "194930",
-                        "experiment_accession": "DRX026011",
-                        "experiment_alias": "DRX026011",
-                        "experiment_title": "Illumina HiSeq 2500 paired end sequencing: Illumina HiSeq 2500 paired end sequencing of SAMD00024405",
-                        "fastq_1": "DRX026011_DRR028935_1.fastq.gz:md5,f9b4a5d25aa7d6ab4050dbe0764eb04d",
-                        "fastq_2": "DRX026011_DRR028935_2.fastq.gz:md5,dc0d2e1fc46f4d4581a477f87ec3ff15",
-                        "fastq_aspera": "fasp.sra.ebi.ac.uk:/vol1/fastq/DRR028/DRR028935/DRR028935_1.fastq.gz;fasp.sra.ebi.ac.uk:/vol1/fastq/DRR028/DRR028935/DRR028935_2.fastq.gz",
-                        "fastq_bytes": "60275;61610",
-                        "fastq_ftp": "ftp.sra.ebi.ac.uk/vol1/fastq/DRR028/DRR028935/DRR028935_1.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/DRR028/DRR028935/DRR028935_2.fastq.gz",
-                        "fastq_galaxy": "ftp.sra.ebi.ac.uk/vol1/fastq/DRR028/DRR028935/DRR028935_1.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/DRR028/DRR028935/DRR028935_2.fastq.gz",
-                        "fastq_md5": "cc01df82a9354bb6b3be93483b20c35a;941c9998d746416dad53c94c480ddf30",
-                        "id": "DRX026011_DRR028935",
-                        "instrument_model": "Illumina HiSeq 2500",
-                        "instrument_platform": "ILLUMINA",
-                        "library_layout": "PAIRED",
-                        "library_name": "day0_BbSQE-I",
-                        "library_selection": "cDNA",
-                        "library_source": "TRANSCRIPTOMIC",
-                        "library_strategy": "RNA-Seq",
-                        "md5_1": "cc01df82a9354bb6b3be93483b20c35a",
-                        "md5_2": "941c9998d746416dad53c94c480ddf30",
-                        "read_count": "965",
-                        "run_accession": "DRR028935",
-                        "run_alias": "DRR028935",
-                        "sample_accession": "SAMD00024405",
-                        "sample_alias": "SAMD00024405",
-                        "sample_description": "Liquid culture",
-                        "sample_title": "Botryococcus braunii Showa at day 0 after inoculation into fresh culture medium",
-                        "scientific_name": "Botryococcus braunii Showa",
-                        "secondary_sample_accession": "DRS019431",
-                        "secondary_study_accession": "DRP002616",
-                        "single_end": false,
-                        "study_accession": "PRJDB3420",
-                        "study_alias": "DRP002616",
-                        "study_title": "Liquid culture of Botryococcus braunii, race B, Showa",
-                        "submission_accession": "DRA002949",
-                        "tax_id": "1202541"
-                    },
-                    {
-                        "base_count": "1996273",
-                        "experiment_accession": "SRX6725035",
-                        "experiment_alias": "Emb289P1_bin131",
-                        "experiment_title": "Illumina HiSeq 2500 sequencing: Binning of metagenomic reads from the P1 gut compartment of Embiratermes neotenicus",
-                        "fastq_1": "SRX6725035_SRR9984183.fastq.gz:md5,c9b4c2c4abf19da7082caf442fdefea7",
-                        "fastq_2": "",
-                        "fastq_aspera": "fasp.sra.ebi.ac.uk:/vol1/fastq/SRR998/003/SRR9984183/SRR9984183.fastq.gz",
-                        "fastq_bytes": "605358",
-                        "fastq_ftp": "ftp.sra.ebi.ac.uk/vol1/fastq/SRR998/003/SRR9984183/SRR9984183.fastq.gz",
-                        "fastq_galaxy": "ftp.sra.ebi.ac.uk/vol1/fastq/SRR998/003/SRR9984183/SRR9984183.fastq.gz",
-                        "fastq_md5": "0b512d2dc31685983456bd56fd836544",
-                        "id": "SRX6725035_SRR9984183",
-                        "instrument_model": "Illumina HiSeq 2500",
-                        "instrument_platform": "ILLUMINA",
-                        "library_layout": "SINGLE",
-                        "library_name": "Emb289P1_bin131",
-                        "library_selection": "RANDOM",
-                        "library_source": "METAGENOMIC",
-                        "library_strategy": "WGS",
-                        "md5_1": "0b512d2dc31685983456bd56fd836544",
-                        "md5_2": "",
-                        "read_count": "58",
-                        "run_accession": "SRR9984183",
-                        "run_alias": "Emb289P1_bin131.fastq",
-                        "sample_accession": "SAMN12581720",
-                        "sample_alias": "Emb289P1_bin131",
-                        "sample_description": "Keywords: GSC:MIxS MIMAG:5.0",
-                        "sample_title": "MIMAG Metagenome-assembled Genome sample from Defluviitaleaceae bacterium",
-                        "scientific_name": "Defluviitaleaceae bacterium",
-                        "secondary_sample_accession": "SRS5277011",
-                        "secondary_study_accession": "SRP218535",
-                        "single_end": true,
-                        "study_accession": "PRJNA560329",
-                        "study_alias": "PRJNA560329",
-                        "study_title": "Phylogenomic analysis of 589 metagenome-assembled genomes encompassing all major prokaryotic lineages from the gut of higher termites",
-                        "submission_accession": "SRA942061",
-                        "tax_id": "2660712"
-                    },
-                    {
-                        "base_count": "35658",
-                        "experiment_accession": "ERX1234253",
-                        "experiment_alias": "qiita_ptid_1263:10317.BLANK.93.3E.r22",
-                        "experiment_title": "Illumina HiSeq 2500 sequencing: qiita_ptid_1263:10317.BLANK.93.3E.r22",
-                        "fastq_1": "ERX1234253_ERR1160846.fastq.gz:md5,b1de59f829fbd2d60a1ed4bc3da55709",
-                        "fastq_2": "",
-                        "fastq_aspera": "fasp.sra.ebi.ac.uk:/vol1/fastq/ERR116/006/ERR1160846/ERR1160846.fastq.gz",
-                        "fastq_bytes": "18077",
-                        "fastq_ftp": "ftp.sra.ebi.ac.uk/vol1/fastq/ERR116/006/ERR1160846/ERR1160846.fastq.gz",
-                        "fastq_galaxy": "ftp.sra.ebi.ac.uk/vol1/fastq/ERR116/006/ERR1160846/ERR1160846.fastq.gz",
-                        "fastq_md5": "5924f20ef547ebdfed7cad795bbab6e6",
-                        "id": "ERX1234253_ERR1160846",
-                        "instrument_model": "Illumina HiSeq 2500",
-                        "instrument_platform": "ILLUMINA",
-                        "library_layout": "SINGLE",
-                        "library_name": "10317.BLANK.93.3E.r22",
-                        "library_selection": "PCR",
-                        "library_source": "METAGENOMIC",
-                        "library_strategy": "AMPLICON",
-                        "md5_1": "5924f20ef547ebdfed7cad795bbab6e6",
-                        "md5_2": "",
-                        "read_count": "283",
-                        "run_accession": "ERR1160846",
-                        "run_alias": "qiita_ppdid_706:10317.BLANK.93.3E.r22",
-                        "sample_accession": "SAMEA3687214",
-                        "sample_alias": "qiita_sid_10317:10317.BLANK.93.3E.r22",
-                        "sample_description": "American Gut control",
-                        "sample_title": "10317.BLANK.93.3E.r22",
-                        "scientific_name": "metagenome",
-                        "secondary_sample_accession": "ERS994363",
-                        "secondary_study_accession": "ERP012803",
-                        "single_end": true,
-                        "study_accession": "PRJEB11419",
-                        "study_alias": "qiita_sid_10317",
-                        "study_title": "American Gut Project",
-                        "submission_accession": "ERA541392",
-                        "tax_id": "256318"
-                    }
-                ],
-                "4": [
-                    "versions.yml:md5,1496d1cbc9041e07ab8a0c25f0b054d9",
-                    "versions.yml:md5,9b17045ca8bdc272cb3f9d349a81d206",
-                    "versions.yml:md5,b52279f7d6b891a6523d9321f3f85b47",
-                    "versions.yml:md5,c19fc0f920e57875881761cc944a46d7"
-                ],
-                "mappings": [
-                    "id_mappings.csv:md5,3e41ce6ab19feb76f2b20fa77a910ad3"
-                ],
-                "sample_mappings": [
-                    "multiqc_config.yml:md5,1ac06bb95b503703430e74660bbdd768"
-                ],
-                "samplesheet": [
-                    "samplesheet.csv:md5,d81fe6175afaa01183475a6e28c7caa9"
-                ],
-                "sra_metadata": [
-                    {
-                        "base_count": "194930",
-                        "experiment_accession": "DRX026011",
-                        "experiment_alias": "DRX026011",
-                        "experiment_title": "Illumina HiSeq 2500 paired end sequencing: Illumina HiSeq 2500 paired end sequencing of SAMD00024405",
-                        "fastq_1": "DRX026011_DRR028935_1.fastq.gz:md5,f9b4a5d25aa7d6ab4050dbe0764eb04d",
-                        "fastq_2": "DRX026011_DRR028935_2.fastq.gz:md5,dc0d2e1fc46f4d4581a477f87ec3ff15",
-                        "fastq_aspera": "fasp.sra.ebi.ac.uk:/vol1/fastq/DRR028/DRR028935/DRR028935_1.fastq.gz;fasp.sra.ebi.ac.uk:/vol1/fastq/DRR028/DRR028935/DRR028935_2.fastq.gz",
-                        "fastq_bytes": "60275;61610",
-                        "fastq_ftp": "ftp.sra.ebi.ac.uk/vol1/fastq/DRR028/DRR028935/DRR028935_1.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/DRR028/DRR028935/DRR028935_2.fastq.gz",
-                        "fastq_galaxy": "ftp.sra.ebi.ac.uk/vol1/fastq/DRR028/DRR028935/DRR028935_1.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/DRR028/DRR028935/DRR028935_2.fastq.gz",
-                        "fastq_md5": "cc01df82a9354bb6b3be93483b20c35a;941c9998d746416dad53c94c480ddf30",
-                        "id": "DRX026011_DRR028935",
-                        "instrument_model": "Illumina HiSeq 2500",
-                        "instrument_platform": "ILLUMINA",
-                        "library_layout": "PAIRED",
-                        "library_name": "day0_BbSQE-I",
-                        "library_selection": "cDNA",
-                        "library_source": "TRANSCRIPTOMIC",
-                        "library_strategy": "RNA-Seq",
-                        "md5_1": "cc01df82a9354bb6b3be93483b20c35a",
-                        "md5_2": "941c9998d746416dad53c94c480ddf30",
-                        "read_count": "965",
-                        "run_accession": "DRR028935",
-                        "run_alias": "DRR028935",
-                        "sample_accession": "SAMD00024405",
-                        "sample_alias": "SAMD00024405",
-                        "sample_description": "Liquid culture",
-                        "sample_title": "Botryococcus braunii Showa at day 0 after inoculation into fresh culture medium",
-                        "scientific_name": "Botryococcus braunii Showa",
-                        "secondary_sample_accession": "DRS019431",
-                        "secondary_study_accession": "DRP002616",
-                        "single_end": false,
-                        "study_accession": "PRJDB3420",
-                        "study_alias": "DRP002616",
-                        "study_title": "Liquid culture of Botryococcus braunii, race B, Showa",
-                        "submission_accession": "DRA002949",
-                        "tax_id": "1202541"
-                    },
-                    {
-                        "base_count": "1996273",
-                        "experiment_accession": "SRX6725035",
-                        "experiment_alias": "Emb289P1_bin131",
-                        "experiment_title": "Illumina HiSeq 2500 sequencing: Binning of metagenomic reads from the P1 gut compartment of Embiratermes neotenicus",
-                        "fastq_1": "SRX6725035_SRR9984183.fastq.gz:md5,c9b4c2c4abf19da7082caf442fdefea7",
-                        "fastq_2": "",
-                        "fastq_aspera": "fasp.sra.ebi.ac.uk:/vol1/fastq/SRR998/003/SRR9984183/SRR9984183.fastq.gz",
-                        "fastq_bytes": "605358",
-                        "fastq_ftp": "ftp.sra.ebi.ac.uk/vol1/fastq/SRR998/003/SRR9984183/SRR9984183.fastq.gz",
-                        "fastq_galaxy": "ftp.sra.ebi.ac.uk/vol1/fastq/SRR998/003/SRR9984183/SRR9984183.fastq.gz",
-                        "fastq_md5": "0b512d2dc31685983456bd56fd836544",
-                        "id": "SRX6725035_SRR9984183",
-                        "instrument_model": "Illumina HiSeq 2500",
-                        "instrument_platform": "ILLUMINA",
-                        "library_layout": "SINGLE",
-                        "library_name": "Emb289P1_bin131",
-                        "library_selection": "RANDOM",
-                        "library_source": "METAGENOMIC",
-                        "library_strategy": "WGS",
-                        "md5_1": "0b512d2dc31685983456bd56fd836544",
-                        "md5_2": "",
-                        "read_count": "58",
-                        "run_accession": "SRR9984183",
-                        "run_alias": "Emb289P1_bin131.fastq",
-                        "sample_accession": "SAMN12581720",
-                        "sample_alias": "Emb289P1_bin131",
-                        "sample_description": "Keywords: GSC:MIxS MIMAG:5.0",
-                        "sample_title": "MIMAG Metagenome-assembled Genome sample from Defluviitaleaceae bacterium",
-                        "scientific_name": "Defluviitaleaceae bacterium",
-                        "secondary_sample_accession": "SRS5277011",
-                        "secondary_study_accession": "SRP218535",
-                        "single_end": true,
-                        "study_accession": "PRJNA560329",
-                        "study_alias": "PRJNA560329",
-                        "study_title": "Phylogenomic analysis of 589 metagenome-assembled genomes encompassing all major prokaryotic lineages from the gut of higher termites",
-                        "submission_accession": "SRA942061",
-                        "tax_id": "2660712"
-                    },
-                    {
-                        "base_count": "35658",
-                        "experiment_accession": "ERX1234253",
-                        "experiment_alias": "qiita_ptid_1263:10317.BLANK.93.3E.r22",
-                        "experiment_title": "Illumina HiSeq 2500 sequencing: qiita_ptid_1263:10317.BLANK.93.3E.r22",
-                        "fastq_1": "ERX1234253_ERR1160846.fastq.gz:md5,b1de59f829fbd2d60a1ed4bc3da55709",
-                        "fastq_2": "",
-                        "fastq_aspera": "fasp.sra.ebi.ac.uk:/vol1/fastq/ERR116/006/ERR1160846/ERR1160846.fastq.gz",
-                        "fastq_bytes": "18077",
-                        "fastq_ftp": "ftp.sra.ebi.ac.uk/vol1/fastq/ERR116/006/ERR1160846/ERR1160846.fastq.gz",
-                        "fastq_galaxy": "ftp.sra.ebi.ac.uk/vol1/fastq/ERR116/006/ERR1160846/ERR1160846.fastq.gz",
-                        "fastq_md5": "5924f20ef547ebdfed7cad795bbab6e6",
-                        "id": "ERX1234253_ERR1160846",
-                        "instrument_model": "Illumina HiSeq 2500",
-                        "instrument_platform": "ILLUMINA",
-                        "library_layout": "SINGLE",
-                        "library_name": "10317.BLANK.93.3E.r22",
-                        "library_selection": "PCR",
-                        "library_source": "METAGENOMIC",
-                        "library_strategy": "AMPLICON",
-                        "md5_1": "5924f20ef547ebdfed7cad795bbab6e6",
-                        "md5_2": "",
-                        "read_count": "283",
-                        "run_accession": "ERR1160846",
-                        "run_alias": "qiita_ppdid_706:10317.BLANK.93.3E.r22",
-                        "sample_accession": "SAMEA3687214",
-                        "sample_alias": "qiita_sid_10317:10317.BLANK.93.3E.r22",
-                        "sample_description": "American Gut control",
-                        "sample_title": "10317.BLANK.93.3E.r22",
-                        "scientific_name": "metagenome",
-                        "secondary_sample_accession": "ERS994363",
-                        "secondary_study_accession": "ERP012803",
-                        "single_end": true,
-                        "study_accession": "PRJEB11419",
-                        "study_alias": "qiita_sid_10317",
-                        "study_title": "American Gut Project",
-                        "submission_accession": "ERA541392",
-                        "tax_id": "256318"
-                    }
-                ],
-                "versions": [
-                    "versions.yml:md5,1496d1cbc9041e07ab8a0c25f0b054d9",
-                    "versions.yml:md5,9b17045ca8bdc272cb3f9d349a81d206",
-                    "versions.yml:md5,b52279f7d6b891a6523d9321f3f85b47",
-                    "versions.yml:md5,c19fc0f920e57875881761cc944a46d7"
-                ]
-            }
+            "samplesheet.csv",
+            [
+                "id_mappings.csv:md5,3e41ce6ab19feb76f2b20fa77a910ad3"
+            ],
+            [
+                "multiqc_config.yml:md5,1ac06bb95b503703430e74660bbdd768"
+            ],
+            [
+                {
+                    "base_count": "194930",
+                    "experiment_accession": "DRX026011",
+                    "experiment_alias": "DRX026011",
+                    "experiment_title": "Illumina HiSeq 2500 paired end sequencing: Illumina HiSeq 2500 paired end sequencing of SAMD00024405",
+                    "fastq_1": "DRX026011_DRR028935_1.fastq.gz:md5,f9b4a5d25aa7d6ab4050dbe0764eb04d",
+                    "fastq_2": "DRX026011_DRR028935_2.fastq.gz:md5,dc0d2e1fc46f4d4581a477f87ec3ff15",
+                    "fastq_aspera": "fasp.sra.ebi.ac.uk:/vol1/fastq/DRR028/DRR028935/DRR028935_1.fastq.gz;fasp.sra.ebi.ac.uk:/vol1/fastq/DRR028/DRR028935/DRR028935_2.fastq.gz",
+                    "fastq_bytes": "60275;61610",
+                    "fastq_ftp": "ftp.sra.ebi.ac.uk/vol1/fastq/DRR028/DRR028935/DRR028935_1.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/DRR028/DRR028935/DRR028935_2.fastq.gz",
+                    "fastq_galaxy": "ftp.sra.ebi.ac.uk/vol1/fastq/DRR028/DRR028935/DRR028935_1.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/DRR028/DRR028935/DRR028935_2.fastq.gz",
+                    "fastq_md5": "cc01df82a9354bb6b3be93483b20c35a;941c9998d746416dad53c94c480ddf30",
+                    "id": "DRX026011_DRR028935",
+                    "instrument_model": "Illumina HiSeq 2500",
+                    "instrument_platform": "ILLUMINA",
+                    "library_layout": "PAIRED",
+                    "library_name": "day0_BbSQE-I",
+                    "library_selection": "cDNA",
+                    "library_source": "TRANSCRIPTOMIC",
+                    "library_strategy": "RNA-Seq",
+                    "md5_1": "cc01df82a9354bb6b3be93483b20c35a",
+                    "md5_2": "941c9998d746416dad53c94c480ddf30",
+                    "read_count": "965",
+                    "run_accession": "DRR028935",
+                    "run_alias": "DRR028935",
+                    "sample_accession": "SAMD00024405",
+                    "sample_alias": "SAMD00024405",
+                    "sample_description": "Liquid culture",
+                    "sample_title": "Botryococcus braunii Showa at day 0 after inoculation into fresh culture medium",
+                    "scientific_name": "Botryococcus braunii Showa",
+                    "secondary_sample_accession": "DRS019431",
+                    "secondary_study_accession": "DRP002616",
+                    "single_end": false,
+                    "study_accession": "PRJDB3420",
+                    "study_alias": "DRP002616",
+                    "study_title": "Liquid culture of Botryococcus braunii, race B, Showa",
+                    "submission_accession": "DRA002949",
+                    "tax_id": "1202541"
+                },
+                {
+                    "base_count": "1996273",
+                    "experiment_accession": "SRX6725035",
+                    "experiment_alias": "Emb289P1_bin131",
+                    "experiment_title": "Illumina HiSeq 2500 sequencing: Binning of metagenomic reads from the P1 gut compartment of Embiratermes neotenicus",
+                    "fastq_1": "SRX6725035_SRR9984183.fastq.gz:md5,c9b4c2c4abf19da7082caf442fdefea7",
+                    "fastq_2": "",
+                    "fastq_aspera": "fasp.sra.ebi.ac.uk:/vol1/fastq/SRR998/003/SRR9984183/SRR9984183.fastq.gz",
+                    "fastq_bytes": "605358",
+                    "fastq_ftp": "ftp.sra.ebi.ac.uk/vol1/fastq/SRR998/003/SRR9984183/SRR9984183.fastq.gz",
+                    "fastq_galaxy": "ftp.sra.ebi.ac.uk/vol1/fastq/SRR998/003/SRR9984183/SRR9984183.fastq.gz",
+                    "fastq_md5": "0b512d2dc31685983456bd56fd836544",
+                    "id": "SRX6725035_SRR9984183",
+                    "instrument_model": "Illumina HiSeq 2500",
+                    "instrument_platform": "ILLUMINA",
+                    "library_layout": "SINGLE",
+                    "library_name": "Emb289P1_bin131",
+                    "library_selection": "RANDOM",
+                    "library_source": "METAGENOMIC",
+                    "library_strategy": "WGS",
+                    "md5_1": "0b512d2dc31685983456bd56fd836544",
+                    "md5_2": "",
+                    "read_count": "58",
+                    "run_accession": "SRR9984183",
+                    "run_alias": "Emb289P1_bin131.fastq",
+                    "sample_accession": "SAMN12581720",
+                    "sample_alias": "Emb289P1_bin131",
+                    "sample_description": "Keywords: GSC:MIxS MIMAG:5.0",
+                    "sample_title": "MIMAG Metagenome-assembled Genome sample from Defluviitaleaceae bacterium",
+                    "scientific_name": "Defluviitaleaceae bacterium",
+                    "secondary_sample_accession": "SRS5277011",
+                    "secondary_study_accession": "SRP218535",
+                    "single_end": true,
+                    "study_accession": "PRJNA560329",
+                    "study_alias": "PRJNA560329",
+                    "study_title": "Phylogenomic analysis of 589 metagenome-assembled genomes encompassing all major prokaryotic lineages from the gut of higher termites",
+                    "submission_accession": "SRA942061",
+                    "tax_id": "2660712"
+                },
+                {
+                    "base_count": "35658",
+                    "experiment_accession": "ERX1234253",
+                    "experiment_alias": "qiita_ptid_1263:10317.BLANK.93.3E.r22",
+                    "experiment_title": "Illumina HiSeq 2500 sequencing: qiita_ptid_1263:10317.BLANK.93.3E.r22",
+                    "fastq_1": "ERX1234253_ERR1160846.fastq.gz:md5,b1de59f829fbd2d60a1ed4bc3da55709",
+                    "fastq_2": "",
+                    "fastq_aspera": "fasp.sra.ebi.ac.uk:/vol1/fastq/ERR116/006/ERR1160846/ERR1160846.fastq.gz",
+                    "fastq_bytes": "18077",
+                    "fastq_ftp": "ftp.sra.ebi.ac.uk/vol1/fastq/ERR116/006/ERR1160846/ERR1160846.fastq.gz",
+                    "fastq_galaxy": "ftp.sra.ebi.ac.uk/vol1/fastq/ERR116/006/ERR1160846/ERR1160846.fastq.gz",
+                    "fastq_md5": "5924f20ef547ebdfed7cad795bbab6e6",
+                    "id": "ERX1234253_ERR1160846",
+                    "instrument_model": "Illumina HiSeq 2500",
+                    "instrument_platform": "ILLUMINA",
+                    "library_layout": "SINGLE",
+                    "library_name": "10317.BLANK.93.3E.r22",
+                    "library_selection": "PCR",
+                    "library_source": "METAGENOMIC",
+                    "library_strategy": "AMPLICON",
+                    "md5_1": "5924f20ef547ebdfed7cad795bbab6e6",
+                    "md5_2": "",
+                    "read_count": "283",
+                    "run_accession": "ERR1160846",
+                    "run_alias": "qiita_ppdid_706:10317.BLANK.93.3E.r22",
+                    "sample_accession": "SAMEA3687214",
+                    "sample_alias": "qiita_sid_10317:10317.BLANK.93.3E.r22",
+                    "sample_description": "American Gut control",
+                    "sample_title": "10317.BLANK.93.3E.r22",
+                    "scientific_name": "metagenome",
+                    "secondary_sample_accession": "ERS994363",
+                    "secondary_study_accession": "ERP012803",
+                    "single_end": true,
+                    "study_accession": "PRJEB11419",
+                    "study_alias": "qiita_sid_10317",
+                    "study_title": "American Gut Project",
+                    "submission_accession": "ERA541392",
+                    "tax_id": "256318"
+                }
+            ],
+            [
+                "versions.yml:md5,1496d1cbc9041e07ab8a0c25f0b054d9",
+                "versions.yml:md5,9b17045ca8bdc272cb3f9d349a81d206",
+                "versions.yml:md5,b52279f7d6b891a6523d9321f3f85b47",
+                "versions.yml:md5,c19fc0f920e57875881761cc944a46d7"
+            ]
         ],
         "meta": {
             "nf-test": "0.9.0",
             "nextflow": "24.09.2"
         },
-        "timestamp": "2024-10-15T13:06:17.713513"
+        "timestamp": "2024-10-15T13:38:08.969914"
     }
 }
\ No newline at end of file
diff --git a/workflows/sra/tests/sra_skip_fastq_download.nf.test b/workflows/sra/tests/sra_skip_fastq_download.nf.test
index 4b7080d9..a467f59b 100644
--- a/workflows/sra/tests/sra_skip_fastq_download.nf.test
+++ b/workflows/sra/tests/sra_skip_fastq_download.nf.test
@@ -28,7 +28,13 @@ nextflow_workflow {
         then {
             assertAll(
                 { assert workflow.success},
-                { assert snapshot(workflow.out).match() }
+                { assert snapshot(
+                    file(workflow.out.samplesheet[0]).name,
+                    workflow.out.mappings,
+                    workflow.out.sample_mappings,
+                    workflow.out.sra_metadata,
+                    workflow.out.versions
+                ).match() }
             )
         }
     }
diff --git a/workflows/sra/tests/sra_skip_fastq_download.nf.test.snap b/workflows/sra/tests/sra_skip_fastq_download.nf.test.snap
index 34ee72c1..436769c1 100644
--- a/workflows/sra/tests/sra_skip_fastq_download.nf.test.snap
+++ b/workflows/sra/tests/sra_skip_fastq_download.nf.test.snap
@@ -1,279 +1,142 @@
 {
     "Parameters: --skip_fastq_download": {
         "content": [
-            {
-                "0": [
-                    "samplesheet.csv:md5,0788cf0fed166518e5d1399532f8068f"
-                ],
-                "1": [
-                    "id_mappings.csv:md5,3e41ce6ab19feb76f2b20fa77a910ad3"
-                ],
-                "2": [
-                    "multiqc_config.yml:md5,1ac06bb95b503703430e74660bbdd768"
-                ],
-                "3": [
-                    {
-                        "base_count": "194930",
-                        "experiment_accession": "DRX026011",
-                        "experiment_alias": "DRX026011",
-                        "experiment_title": "Illumina HiSeq 2500 paired end sequencing: Illumina HiSeq 2500 paired end sequencing of SAMD00024405",
-                        "fastq_1": "ftp.sra.ebi.ac.uk/vol1/fastq/DRR028/DRR028935/DRR028935_1.fastq.gz",
-                        "fastq_2": "ftp.sra.ebi.ac.uk/vol1/fastq/DRR028/DRR028935/DRR028935_2.fastq.gz",
-                        "fastq_aspera": "fasp.sra.ebi.ac.uk:/vol1/fastq/DRR028/DRR028935/DRR028935_1.fastq.gz;fasp.sra.ebi.ac.uk:/vol1/fastq/DRR028/DRR028935/DRR028935_2.fastq.gz",
-                        "fastq_bytes": "60275;61610",
-                        "fastq_ftp": "ftp.sra.ebi.ac.uk/vol1/fastq/DRR028/DRR028935/DRR028935_1.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/DRR028/DRR028935/DRR028935_2.fastq.gz",
-                        "fastq_galaxy": "ftp.sra.ebi.ac.uk/vol1/fastq/DRR028/DRR028935/DRR028935_1.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/DRR028/DRR028935/DRR028935_2.fastq.gz",
-                        "fastq_md5": "cc01df82a9354bb6b3be93483b20c35a;941c9998d746416dad53c94c480ddf30",
-                        "id": "DRX026011_DRR028935",
-                        "instrument_model": "Illumina HiSeq 2500",
-                        "instrument_platform": "ILLUMINA",
-                        "library_layout": "PAIRED",
-                        "library_name": "day0_BbSQE-I",
-                        "library_selection": "cDNA",
-                        "library_source": "TRANSCRIPTOMIC",
-                        "library_strategy": "RNA-Seq",
-                        "md5_1": "cc01df82a9354bb6b3be93483b20c35a",
-                        "md5_2": "941c9998d746416dad53c94c480ddf30",
-                        "read_count": "965",
-                        "run_accession": "DRR028935",
-                        "run_alias": "DRR028935",
-                        "sample_accession": "SAMD00024405",
-                        "sample_alias": "SAMD00024405",
-                        "sample_description": "Liquid culture",
-                        "sample_title": "Botryococcus braunii Showa at day 0 after inoculation into fresh culture medium",
-                        "scientific_name": "Botryococcus braunii Showa",
-                        "secondary_sample_accession": "DRS019431",
-                        "secondary_study_accession": "DRP002616",
-                        "single_end": false,
-                        "study_accession": "PRJDB3420",
-                        "study_alias": "DRP002616",
-                        "study_title": "Liquid culture of Botryococcus braunii, race B, Showa",
-                        "submission_accession": "DRA002949",
-                        "tax_id": "1202541"
-                    },
-                    {
-                        "base_count": "1996273",
-                        "experiment_accession": "SRX6725035",
-                        "experiment_alias": "Emb289P1_bin131",
-                        "experiment_title": "Illumina HiSeq 2500 sequencing: Binning of metagenomic reads from the P1 gut compartment of Embiratermes neotenicus",
-                        "fastq_1": "ftp.sra.ebi.ac.uk/vol1/fastq/SRR998/003/SRR9984183/SRR9984183.fastq.gz",
-                        "fastq_2": "",
-                        "fastq_aspera": "fasp.sra.ebi.ac.uk:/vol1/fastq/SRR998/003/SRR9984183/SRR9984183.fastq.gz",
-                        "fastq_bytes": "605358",
-                        "fastq_ftp": "ftp.sra.ebi.ac.uk/vol1/fastq/SRR998/003/SRR9984183/SRR9984183.fastq.gz",
-                        "fastq_galaxy": "ftp.sra.ebi.ac.uk/vol1/fastq/SRR998/003/SRR9984183/SRR9984183.fastq.gz",
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