Merge pull request #7 from mskcc-omics-workflows/feature/call_variant…

…s_type adding filloutype for traceback
mskcc-omics-workflows · Jul 11, 2024 · cff0019 · cff0019
2 parents 1a44f23 + 73fd141
commit cff0019
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Showing 35 changed files with 52 additions and 936 deletions.
diff --git a/modules.json b/modules.json
@@ -7,7 +7,7 @@
                 "msk": {
                     "genotypevariants/all": {
                         "branch": "Subworkflow-traceback",
-                        "git_sha": "5abcf40301834adb05cbc826f8f3e582bea2e769",
+                        "git_sha": "64aa65cb2dc476607b93a3d5f161528891ba5e34",
                         "installed_by": [
                             "traceback"
                         ]
@@ -21,16 +21,16 @@
                     },
                     "pvmaf/concat": {
                         "branch": "Subworkflow-traceback",
-                        "git_sha": "5abcf40301834adb05cbc826f8f3e582bea2e769",
+                        "git_sha": "82bc8976b36a187ddcd48be1f516e5f8a5faa09b",
                         "installed_by": [
                             "traceback"
                         ]
                     },
-                    "pvmaf/tag": {
+                    "pvmaf/tagtraceback": {
                         "branch": "Subworkflow-traceback",
-                        "git_sha": "5abcf40301834adb05cbc826f8f3e582bea2e769",
+                        "git_sha": "a9e056a4bd1c7d5974013972ed26414d867d28a3",
                         "installed_by": [
-                            "traceback"
+                            "modules"
                         ]
                     }
                 }
@@ -39,7 +39,7 @@
                 "msk": {
                     "traceback": {
                         "branch": "Subworkflow-traceback",
-                        "git_sha": "601f6f4d95162f922ae7df87d96a361a420d5cf3",
+                        "git_sha": "a0d608c00b9421ac35ae6f12699588115b741ed4",
                         "installed_by": [
                             "subworkflows"
                         ]

diff --git a/modules/msk/genotypevariants/all/main.nf b/modules/msk/genotypevariants/all/main.nf
@@ -5,8 +5,8 @@ process GENOTYPEVARIANTS_ALL {
 
     conda "${moduleDir}/environment.yml"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'ghcr.io/msk-access/genotype_variants:sha-7e2c3c8a':
-        'ghcr.io/msk-access/genotype_variants:sha-7e2c3c8a' }"
+        'ghcr.io/msk-access/genotype_variants:0.3.8':
+        'ghcr.io/msk-access/genotype_variants:0.3.8' }"
 
     input:
     tuple val(meta), path(bam_standard), path(bai_standard), path(bam_duplex), path(bai_duplex), path(bam_simplex), path(bai_simplex), path(maf)
@@ -59,4 +59,4 @@ process GENOTYPEVARIANTS_ALL {
         genotypevariants: \$(genotype_variants --version)
     END_VERSIONS
     """
-}
+}
diff --git a/modules/msk/genotypevariants/all/meta.yml b/modules/msk/genotypevariants/all/meta.yml
@@ -65,7 +65,7 @@ output:
         e.g. `[ id:'sample1', patient:'patient_1' ]`
   - maf:
       type: file
-      description: Genotyped mafs for each bam type (simplex, duplex, standard) provided and a merged genotyped maf. The maf(s) will be labelled with patient identifier or sample identifier as the prefix, and end with their type (standard, simplex, duplex). The sample identifier is prioritized.
+      description: Genotyped mafs for each bam provided and a merged genotyped maf. The maf(s) will be labelled with patient identifier or sample identifier as the prefix, and end with the type of bam (duplex, simplex, or standard). The sample identifier is prioritized.
       pattern: "*.{mafs}"
   - versions:
       type: file

diff --git a/modules/msk/genotypevariants/all/tests/main.nf.test b/modules/msk/genotypevariants/all/tests/main.nf.test
@@ -7,6 +7,7 @@ nextflow_process {
 
     tag "modules"
     tag "modules_nfcore"
+    tag "modules_msk"
     tag "genotypevariants"
     tag "genotypevariants/all"
 

diff --git a/modules/msk/genotypevariants/all/tests/main.nf.test.snap b/modules/msk/genotypevariants/all/tests/main.nf.test.snap
@@ -12,7 +12,7 @@
                     ]
                 ],
                 "1": [
-                    "versions.yml:md5,b7680b263124563b4efc85c69b23ce3b"
+                    "versions.yml:md5,55fd807cb50fcc6611e6d352b86e4704"
                 ],
                 "maf": [
                     [
@@ -24,11 +24,11 @@
                     ]
                 ],
                 "versions": [
-                    "versions.yml:md5,b7680b263124563b4efc85c69b23ce3b"
+                    "versions.yml:md5,55fd807cb50fcc6611e6d352b86e4704"
                 ]
             }
         ],
-        "timestamp": "2024-02-12T11:27:25.169131"
+        "timestamp": "2024-06-18T14:18:45.350503"
     },
     "illumina - duplex and simplex, msk - maf": {
         "content": [
@@ -48,7 +48,7 @@
                     ]
                 ],
                 "1": [
-                    "versions.yml:md5,b7680b263124563b4efc85c69b23ce3b"
+                    "versions.yml:md5,55fd807cb50fcc6611e6d352b86e4704"
                 ],
                 "maf": [
                     [
@@ -65,11 +65,11 @@
                     ]
                 ],
                 "versions": [
-                    "versions.yml:md5,b7680b263124563b4efc85c69b23ce3b"
+                    "versions.yml:md5,55fd807cb50fcc6611e6d352b86e4704"
                 ]
             }
         ],
-        "timestamp": "2024-02-12T11:27:17.612126"
+        "timestamp": "2024-06-18T14:18:39.109687"
     },
     "illumina - bam, msk - maf": {
         "content": [
@@ -87,7 +87,7 @@
                     ]
                 ],
                 "1": [
-                    "versions.yml:md5,b7680b263124563b4efc85c69b23ce3b"
+                    "versions.yml:md5,55fd807cb50fcc6611e6d352b86e4704"
                 ],
                 "maf": [
                     [
@@ -102,10 +102,10 @@
                     ]
                 ],
                 "versions": [
-                    "versions.yml:md5,b7680b263124563b4efc85c69b23ce3b"
+                    "versions.yml:md5,55fd807cb50fcc6611e6d352b86e4704"
                 ]
             }
         ],
-        "timestamp": "2024-02-12T11:27:06.821575"
+        "timestamp": "2024-06-18T14:18:29.181063"
     }
 }
diff --git a/modules/msk/pvmaf/concat/main.nf b/modules/msk/pvmaf/concat/main.nf
@@ -1,11 +1,11 @@
 process PVMAF_CONCAT {
     tag "$meta.id"
     label 'process_single'
-    //ghcr.io/msk-access/postprocessing_variant_calls:0.3.0
+
     conda "${moduleDir}/environment.yml"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'ghcr.io/msk-access/postprocessing_variant_calls:remove_variant_by_annot_0.0.05':
-        'ghcr.io/msk-access/postprocessing_variant_calls:remove_variant_by_annot_0.0.05' }"
+        'ghcr.io/msk-access/postprocessing_variant_calls:0.3.0':
+        'ghcr.io/msk-access/postprocessing_variant_calls:0.3.0' }"
 
     input:
     tuple val(meta), path(maf_files)
@@ -49,4 +49,4 @@ process PVMAF_CONCAT {
         pv: \$( pv --version )
     END_VERSIONS
     """
-}
+}
diff --git a/modules/msk/pvmaf/concat/meta.yml b/modules/msk/pvmaf/concat/meta.yml
@@ -24,10 +24,6 @@ input:
       type: file
       description: list of maf files to concatenate
       pattern: "*.{maf}"
-  - header:
-      type: file
-      description: header file indicating the columns by which the mafs should be concatenated
-      pattern: "*.{txt}"
 
 output:
   #Only when we have meta

diff --git a/modules/msk/pvmaf/concat/tests/main.nf.test b/modules/msk/pvmaf/concat/tests/main.nf.test
@@ -20,7 +20,6 @@ nextflow_process {
                             file(params.test_data_mskcc['chr22']['chr22maf'], checkIfExists: true),
                             file(params.test_data_mskcc['chr22']['chr22maf'], checkIfExists: true)
                         ]
-                input[1] = []
                 """
             }
         }
@@ -45,7 +44,6 @@ nextflow_process {
                 input[0] = [
                         [ id:'chr22', patient:'test'], file(params.test_data_mskcc['chr22']['chr22maf'], checkIfExists: true), file(params.test_data_mskcc['chr22']['chr22maf'], checkIfExists: true)
                         ]
-                input[1] = []
                 """
             }
         }

diff --git a/modules/msk/pvmaf/concat/tests/nextflow.config b/modules/msk/pvmaf/concat/tests/nextflow.config
@@ -4,4 +4,4 @@ process {
     withName: "PVMAF_CONCAT" {
         ext.args = ''
     }
-}
+}
diff --git a/modules/msk/pvmaf/tag/environment.yml b/modules/msk/pvmaf/tag/environment.yml
diff --git a/modules/msk/pvmaf/tag/main.nf b/modules/msk/pvmaf/tag/main.nf
diff --git a/modules/msk/pvmaf/tag/meta.yml b/modules/msk/pvmaf/tag/meta.yml
diff --git a/modules/msk/pvmaf/tag/tests/main.nf.test b/modules/msk/pvmaf/tag/tests/main.nf.test
-Original file line number
+Diff line change
@@ Expand Up / @@ -4,4 +4,4 @@ process { @@
         withName: "PVMAF_CONCAT" {
             ext.args = ''
         }
-    }
+    }