updating traceback subworkflow with local changes made to pass nf-cor…

modules/msk/genotypevariants/all/environment.yml

@@ -1,9 +1,7 @@
 ---
 # yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json
-name: "genotypevariants_all"
 channels:
   - conda-forge
   - bioconda
-  - defaults
 dependencies:
-  - "YOUR-TOOL-HERE"
+  - "YOUR-TOOL=HERE"

modules/msk/genotypevariants/all/main.nf

@@ -1,12 +1,12 @@
 process GENOTYPEVARIANTS_ALL {
     tag "$meta.id"
-    label 'process_single'
+    label 'process_medium'
 
 
     conda "${moduleDir}/environment.yml"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'ghcr.io/msk-access/genotype_variants:0.3.8':
-        'ghcr.io/msk-access/genotype_variants:0.3.8' }"
+        'ghcr.io/msk-access/genotype_variants:0.3.9':
+        'ghcr.io/msk-access/genotype_variants:0.3.9' }"
 
     input:
     // [[patient:null, id:'sample'], standard.bam, standard.bam.bai, [], [], [], []]
@@ -55,7 +55,10 @@ process GENOTYPEVARIANTS_ALL {
     def patient = "${meta.patient}"
 
     """
-    touch ${prefix}.maf
+    touch ${prefix}-DUPLEX_genotyped.maf
+    touch ${prefix}-ORG-SIMPLEX-DUPLEX_genotyped.maf
+    touch ${prefix}-SIMPLEX-DUPLEX_genotyped.maf
+    touch ${prefix}-SIMPLEX_genotyped.maf
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":

modules/msk/genotypevariants/all/tests/main.nf.test.snap

@@ -8,7 +8,12 @@
                             "id": "197",
                             "patient": "c-id"
                         },
-                        "197.maf:md5,d41d8cd98f00b204e9800998ecf8427e"
+                        [
+                            "197-DUPLEX_genotyped.maf:md5,d41d8cd98f00b204e9800998ecf8427e",
+                            "197-ORG-SIMPLEX-DUPLEX_genotyped.maf:md5,d41d8cd98f00b204e9800998ecf8427e",
+                            "197-SIMPLEX-DUPLEX_genotyped.maf:md5,d41d8cd98f00b204e9800998ecf8427e",
+                            "197-SIMPLEX_genotyped.maf:md5,d41d8cd98f00b204e9800998ecf8427e"
+                        ]
                     ]
                 ],
                 "1": [
@@ -20,17 +25,26 @@
                             "id": "197",
                             "patient": "c-id"
                         },
-                        "197.maf:md5,d41d8cd98f00b204e9800998ecf8427e"
+                        [
+                            "197-DUPLEX_genotyped.maf:md5,d41d8cd98f00b204e9800998ecf8427e",
+                            "197-ORG-SIMPLEX-DUPLEX_genotyped.maf:md5,d41d8cd98f00b204e9800998ecf8427e",
+                            "197-SIMPLEX-DUPLEX_genotyped.maf:md5,d41d8cd98f00b204e9800998ecf8427e",
+                            "197-SIMPLEX_genotyped.maf:md5,d41d8cd98f00b204e9800998ecf8427e"
+                        ]
                     ]
                 ],
                 "versions": [
                     "versions.yml:md5,55fd807cb50fcc6611e6d352b86e4704"
                 ]
             }
         ],
-        "timestamp": "2024-06-18T14:18:45.350503"
+        "meta": {
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.2"
+        },
+        "timestamp": "2024-09-10T18:33:45.583973403"
     },
-    "illumina - duplex and simplex, msk - maf": {
+    "illumina - bam, msk - maf": {
         "content": [
             {
                 "0": [
@@ -40,10 +54,8 @@
                             "patient": "c-id"
                         },
                         [
-                            "197-DUPLEX_genotyped.maf:md5,6c0649cfd70ceb0587827f48bf93caf7",
-                            "197-ORG-SIMPLEX-DUPLEX_genotyped.maf:md5,6f37d4e00ab92ce623bd286f6804f30a",
-                            "197-SIMPLEX-DUPLEX_genotyped.maf:md5,6d6c71cdf73e74c10fcb68e477a4455f",
-                            "197-SIMPLEX_genotyped.maf:md5,6c0649cfd70ceb0587827f48bf93caf7"
+                            "197-ORG-STD_genotyped.maf:md5,e430edb08476cf771fdb608b646ccfb7",
+                            "197-STANDARD_genotyped.maf:md5,6c0649cfd70ceb0587827f48bf93caf7"
                         ]
                     ]
                 ],
@@ -57,10 +69,8 @@
                             "patient": "c-id"
                         },
                         [
-                            "197-DUPLEX_genotyped.maf:md5,6c0649cfd70ceb0587827f48bf93caf7",
-                            "197-ORG-SIMPLEX-DUPLEX_genotyped.maf:md5,6f37d4e00ab92ce623bd286f6804f30a",
-                            "197-SIMPLEX-DUPLEX_genotyped.maf:md5,6d6c71cdf73e74c10fcb68e477a4455f",
-                            "197-SIMPLEX_genotyped.maf:md5,6c0649cfd70ceb0587827f48bf93caf7"
+                            "197-ORG-STD_genotyped.maf:md5,e430edb08476cf771fdb608b646ccfb7",
+                            "197-STANDARD_genotyped.maf:md5,6c0649cfd70ceb0587827f48bf93caf7"
                         ]
                     ]
                 ],
@@ -69,9 +79,13 @@
                 ]
             }
         ],
-        "timestamp": "2024-06-18T14:18:39.109687"
+        "meta": {
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.2"
+        },
+        "timestamp": "2024-09-10T18:33:27.603672746"
     },
-    "illumina - bam, msk - maf": {
+    "illumina - duplex and simplex, msk - maf": {
         "content": [
             {
                 "0": [
@@ -81,8 +95,10 @@
                             "patient": "c-id"
                         },
                         [
-                            "197-ORG-STD_genotyped.maf:md5,8a140bbb7af1c291e8597866fb9d6bb9",
-                            "197-STANDARD_genotyped.maf:md5,6c0649cfd70ceb0587827f48bf93caf7"
+                            "197-DUPLEX_genotyped.maf:md5,6c0649cfd70ceb0587827f48bf93caf7",
+                            "197-ORG-SIMPLEX-DUPLEX_genotyped.maf:md5,6f37d4e00ab92ce623bd286f6804f30a",
+                            "197-SIMPLEX-DUPLEX_genotyped.maf:md5,6d6c71cdf73e74c10fcb68e477a4455f",
+                            "197-SIMPLEX_genotyped.maf:md5,6c0649cfd70ceb0587827f48bf93caf7"
                         ]
                     ]
                 ],
@@ -96,8 +112,10 @@
                             "patient": "c-id"
                         },
                         [
-                            "197-ORG-STD_genotyped.maf:md5,8a140bbb7af1c291e8597866fb9d6bb9",
-                            "197-STANDARD_genotyped.maf:md5,6c0649cfd70ceb0587827f48bf93caf7"
+                            "197-DUPLEX_genotyped.maf:md5,6c0649cfd70ceb0587827f48bf93caf7",
+                            "197-ORG-SIMPLEX-DUPLEX_genotyped.maf:md5,6f37d4e00ab92ce623bd286f6804f30a",
+                            "197-SIMPLEX-DUPLEX_genotyped.maf:md5,6d6c71cdf73e74c10fcb68e477a4455f",
+                            "197-SIMPLEX_genotyped.maf:md5,6c0649cfd70ceb0587827f48bf93caf7"
                         ]
                     ]
                 ],
@@ -106,6 +124,10 @@
                 ]
             }
         ],
-        "timestamp": "2024-06-18T14:18:29.181063"
+        "meta": {
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.2"
+        },
+        "timestamp": "2024-09-10T18:33:37.478400329"
     }
 }

modules/msk/pvmaf/concat/environment.yml

@@ -1,9 +1,7 @@
 ---
 # yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json
-name: "pvmaf_concat"
 channels:
   - conda-forge
   - bioconda
-  - defaults
 dependencies:
-  - "YOUR-TOOL-HERE"
+  - "YOUR-TOOL=HERE"

modules/msk/pvmaf/concat/main.nf

@@ -8,7 +8,7 @@ process PVMAF_CONCAT {
         'ghcr.io/msk-access/postprocessing_variant_calls:0.3.0' }"
 
     input:
-    tuple val(meta), path(maf_files) // [ id:'sample1', patient:'patient1' ], [maf_1, ... maf_n]
+    tuple val(meta), path(maf_files, stageAs: "*?-ORG-SIMPLEX-DUPLEX_genotyped.maf")// [ id:'sample1', patient:'patient1' ], [maf_1, ... maf_n]
 
 
     output:

subworkflows/msk/traceback/main.nf

@@ -53,6 +53,8 @@ workflow TRACEBACK {
         }
     .set{split_genotype_xs}
 
+
+
     // Combine impact and access mafs
     split_genotype_imp
     .concat(split_genotype_xs.genotyped)
@@ -61,12 +63,14 @@ workflow TRACEBACK {
     .set{all_genotype}
     individual_genotype = all_genotype.collect()
 
+
     // concat gentoyped mafs, per patient if provided
     PVMAFCONCAT_GENOTYPE(all_genotype)
     ch_versions = ch_versions.mix(PVMAFCONCAT_GENOTYPE.out.versions.first())
 
     genotyped_maf = PVMAFCONCAT_GENOTYPE.out.maf
 
+
     emit:
     individual_genotyped_mafs = individual_genotype
     genotyped_maf = genotyped_maf                         // channel:[[patient:''], genotyped.maf]

subworkflows/msk/traceback/tests/main.nf.test

@@ -40,7 +40,7 @@ nextflow_workflow {
         then {
             assertAll(
                 { assert workflow.success},
-                { assert snapshot(workflow.out).match()}
+                { assert snapshot(path("$outputDir").list()).match()}
             )
         }
     }

subworkflows/msk/traceback/tests/main.nf.test.snap

@@ -1,29 +1,12 @@
 {
     "standard and access bams - stub": {
         "content": [
-            {
-                "0": [
-
-                ],
-                "1": [
-
-                ],
-                "2": [
-                    "versions.yml:md5,bb5f5880ef3572733a2349212e8ab549",
-                    "versions.yml:md5,f31415b0aae41057f59e929b99af930f"
-                ],
-                "genotyped_maf": [
-
-                ],
-                "individual_genotyped_mafs": [
-
-                ],
-                "versions": [
-                    "versions.yml:md5,bb5f5880ef3572733a2349212e8ab549",
-                    "versions.yml:md5,f31415b0aae41057f59e929b99af930f"
-                ]
-            }
+
         ],
-        "timestamp": "2024-06-18T13:38:00.215685"
+        "meta": {
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.2"
+        },
+        "timestamp": "2024-09-10T18:59:54.138840673"
     }
 }