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attempt to fix tests: 2
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@maxulysse
maxulysse committed Oct 15, 2024
1 parent 473d1a2 commit fafd95b
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Showing 18 changed files with 1,181 additions and 2,290 deletions.
8 changes: 7 additions & 1 deletion workflows/sra/tests/main.nf.test
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Original file line number Diff line number Diff line change
Expand Up @@ -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() }
)
}
}
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404 changes: 133 additions & 271 deletions workflows/sra/tests/main.nf.test.snap
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8 changes: 7 additions & 1 deletion workflows/sra/tests/sra_custom_ena_metadata_fields.nf.test
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Original file line number Diff line number Diff line change
Expand Up @@ -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() }
)
}
}
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170 changes: 55 additions & 115 deletions workflows/sra/tests/sra_custom_ena_metadata_fields.nf.test.snap
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Original file line number Diff line number Diff line change
@@ -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"
}
}
8 changes: 7 additions & 1 deletion workflows/sra/tests/sra_download_method_aspera.nf.test
View file
Original file line number Diff line number Diff line change
Expand Up @@ -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() }
)
}
}
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