feat: add picard qc modules

mskilab-org · Oct 10, 2024 · c09d46a · c09d46a
1 parent d00058c
commit c09d46a
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Showing 16 changed files with 697 additions and 2 deletions.
diff --git a/conf/base.config b/conf/base.config
@@ -236,3 +236,5 @@ process {
         cache = false
     }
 }
+
+
diff --git a/conf/modules.config b/conf/modules.config
@@ -37,6 +37,22 @@ process {
         ]
     }
 
+    withName: 'PICARD_COLLECTMULTIPLEMETRICS' {
+        publishDir = [
+            mode: params.publish_dir_mode,
+            path: { "${params.outdir}/qc_reports/picard/${meta.id}" },
+            saveAs: { filename -> filename.equals('versions.yml') ? null : filename },
+        ]
+    }
+
+    withName: 'PICARD_COLLECTWGSMETRICS' {
+        publishDir = [
+            mode: params.publish_dir_mode,
+            path: { "${params.outdir}/qc_reports/picard/${meta.id}" },
+            saveAs: { filename -> filename.equals('versions.yml') ? null : filename },
+        ]
+    }
+
     withName: 'SAMTOOLS_STATS' {
         ext.when         = { !(params.skip_tools && params.skip_tools.split(',').contains('samtools')) }
         ext.prefix       = { "${meta.id}.sorted.cram" }

diff --git a/modules.json b/modules.json
@@ -125,6 +125,16 @@
                         "git_sha": "3e52a04aa60e0cb5cea0487b9ae2fdd04f874027",
                         "installed_by": ["modules"]
                     },
+                    "picard/collectmultiplemetrics": {
+                        "branch": "master",
+                        "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
+                        "installed_by": ["modules"]
+                    },
+                    "picard/collectwgsmetrics": {
+                        "branch": "master",
+                        "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
+                        "installed_by": ["modules"]
+                    },
                     "samtools/collatefastq": {
                         "branch": "master",
                         "git_sha": "911696ea0b62df80e900ef244d7867d177971f73",

diff --git a/modules/nf-core/picard/collectmultiplemetrics/environment.yml b/modules/nf-core/picard/collectmultiplemetrics/environment.yml
diff --git a/modules/nf-core/picard/collectmultiplemetrics/main.nf b/modules/nf-core/picard/collectmultiplemetrics/main.nf
diff --git a/modules/nf-core/picard/collectmultiplemetrics/meta.yml b/modules/nf-core/picard/collectmultiplemetrics/meta.yml
diff --git a/modules/nf-core/picard/collectmultiplemetrics/tests/main.nf.test b/modules/nf-core/picard/collectmultiplemetrics/tests/main.nf.test
diff --git a/modules/nf-core/picard/collectmultiplemetrics/tests/main.nf.test.snap b/modules/nf-core/picard/collectmultiplemetrics/tests/main.nf.test.snap