Merge pull request #21 from LaurenGonsalves/check-modules

Check modules and biobakerymgx pipeline
HoffLab · Apr 25, 2024 · cf4aca6 · cf4aca6
2 parents 77f86bd + 3758edd
commit cf4aca6
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Showing 6 changed files with 52 additions and 12 deletions.
diff --git a/modules/local/kneaddata/kneaddata/main.nf b/modules/local/kneaddata/kneaddata/main.nf
@@ -34,7 +34,7 @@ process KNEADDATA_KNEADDATA {
     kneaddata \\
         --input1 ${fastq_gz[0]} \\
         --input2 ${fastq_gz[1]} \\
-        --output . \\
+        --output ./ \\
         --output-prefix ${prefix}_kneaddata \\
         --reference-db ${kneaddata_db} \\
         --threads ${task.cpus} \\

diff --git a/modules/nf-core/metaphlan/mergemetaphlantables/nextflow.config b/modules/nf-core/metaphlan/mergemetaphlantables/nextflow.config
diff --git a/subworkflows/local/fastq_read_preprocessing_kneaddata/tests/main.nf.test.snap b/subworkflows/local/fastq_read_preprocessing_kneaddata/tests/main.nf.test.snap
@@ -3,21 +3,61 @@
         "content": [
             {
                 "0": [
-
+                    [
+                        {
+                            "id": "test2"
+                        },
+                        [
+                            "test2_kneaddata_paired_1.fastq.gz:md5,acba94fdc94d1e4229beec12086a93af",
+                            "test2_kneaddata_paired_2.fastq.gz:md5,7c8a08782ad6705eced33d11d5032859"
+                        ]
+                    ],
+                    [
+                        {
+                            "id": "test"
+                        },
+                        [
+                            "test_kneaddata_paired_1.fastq.gz:md5,acba94fdc94d1e4229beec12086a93af",
+                            "test_kneaddata_paired_2.fastq.gz:md5,7c8a08782ad6705eced33d11d5032859"
+                        ]
+                    ]
                 ],
                 "1": [
-
+                    "all_samples_kneaddata_read_counts.tsv:md5,0cbc1c285d40c25876ce0675fe36f34b"
                 ],
                 "2": [
+                    "versions.yml:md5,78fbce8ab53a0d6fb8dbf43cd7624846",
+                    "versions.yml:md5,78fbce8ab53a0d6fb8dbf43cd7624846",
+                    "versions.yml:md5,bb0ae5552fe7c380606c211bcf91f2c8",
                     "versions.yml:md5,c97c9af1b0da5c6c85c297ad365653cc"
                 ],
                 "preprocessed_fastq_gz": [
-
+                    [
+                        {
+                            "id": "test2"
+                        },
+                        [
+                            "test2_kneaddata_paired_1.fastq.gz:md5,acba94fdc94d1e4229beec12086a93af",
+                            "test2_kneaddata_paired_2.fastq.gz:md5,7c8a08782ad6705eced33d11d5032859"
+                        ]
+                    ],
+                    [
+                        {
+                            "id": "test"
+                        },
+                        [
+                            "test_kneaddata_paired_1.fastq.gz:md5,acba94fdc94d1e4229beec12086a93af",
+                            "test_kneaddata_paired_2.fastq.gz:md5,7c8a08782ad6705eced33d11d5032859"
+                        ]
+                    ]
                 ],
                 "read_counts_tsv": [
-
+                    "all_samples_kneaddata_read_counts.tsv:md5,0cbc1c285d40c25876ce0675fe36f34b"
                 ],
                 "versions": [
+                    "versions.yml:md5,78fbce8ab53a0d6fb8dbf43cd7624846",
+                    "versions.yml:md5,78fbce8ab53a0d6fb8dbf43cd7624846",
+                    "versions.yml:md5,bb0ae5552fe7c380606c211bcf91f2c8",
                     "versions.yml:md5,c97c9af1b0da5c6c85c297ad365653cc"
                 ]
             }
@@ -26,6 +66,6 @@
             "nf-test": "0.8.4",
             "nextflow": "23.10.1"
         },
-        "timestamp": "2024-04-24T11:21:29.845724761"
+        "timestamp": "2024-04-25T21:47:34.07117763"
     }
 }
diff --git a/subworkflows/local/fastq_read_taxonomy_metaphlan/main.nf b/subworkflows/local/fastq_read_taxonomy_metaphlan/main.nf
@@ -43,14 +43,14 @@ workflow FASTQ_READ_TAXONOMY_METAPHLAN {
     ch_versions = ch_versions.mix(METAPHLAN_SGBTOGTDBPROFILE.out.versions)
 
     // combine metaphlan profiles for merging
-    ch_gtdb_profiles_combined_tsv = ch_gtdb_profile_tsv
+    ch_metaphlan_profiles_combined_tsv = ch_metaphlan_profile_txt
     .map { [ [ id:'all_samples' ], it[1] ] }
     .groupTuple( sort: 'deep' )
 
     //
     // MODULE: Merge Metaphlan profiles
     //
-    ch_metaphlan_profiles_merged_tsv = METAPHLAN_MERGEMETAPHLANTABLES ( ch_gtdb_profiles_combined_tsv ).txt
+    ch_metaphlan_profiles_merged_tsv = METAPHLAN_MERGEMETAPHLANTABLES ( ch_metaphlan_profiles_combined_tsv ).txt
     ch_versions = ch_versions.mix(METAPHLAN_MERGEMETAPHLANTABLES.out.versions)
 
     emit:

diff --git a/subworkflows/local/fastq_read_taxonomy_metaphlan/tests/main.nf.test.snap b/subworkflows/local/fastq_read_taxonomy_metaphlan/tests/main.nf.test.snap
@@ -28,6 +28,6 @@
             "nf-test": "0.8.4",
             "nextflow": "23.10.1"
         },
-        "timestamp": "2024-04-24T10:29:04.201964325"
+        "timestamp": "2024-04-25T21:55:37.113549813"
     }
 }
diff --git a/workflows/biobakerymgx/tests/main.nf.test.snap b/workflows/biobakerymgx/tests/main.nf.test.snap
@@ -28,13 +28,13 @@
 
             ],
             [
-
+                "versions.yml:md5,d9f2edf37349457eccb7644ee1db2ae7"
             ]
         ],
         "meta": {
             "nf-test": "0.8.4",
             "nextflow": "23.10.1"
         },
-        "timestamp": "2024-04-24T22:51:47.767796873"
+        "timestamp": "2024-04-25T22:21:11.648598038"
     }
 }