Adding Picard tools for QC metrics

.nf-core.yml

@@ -4,6 +4,7 @@ lint:
     - .github/CONTRIBUTING.md
   files_exist:
     - .github/workflows/ci.yml
+    - tests/default.nf.test
   nextflow_config:
     - config_defaults:
         - params.fastq_screen_references

conf/modules.config

@@ -49,6 +49,32 @@ process {
             saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
         ]
     }
+    withName: 'PICARD_COLLECTMULTIPLEMETRICS' {
+        ext.args   =  ''
+        publishDir = [
+            path: { "${params.outdir}/picard_collectmultiplemetrics" },
+            mode: params.publish_dir_mode,
+            saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
+        ]
+    }
+
+    withName: 'SAMTOOLS_FAIDX' {
+        ext.args   = ''
+        publishDir = [
+            path: { "${params.outdir}/samtools_faidx" },
+            mode: params.publish_dir_mode,
+            saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
+        ]
+    }
+
+    withName: 'SAMTOOLS_INDEX' {
+        ext.args   = ''
+        publishDir = [
+            path: { "${params.outdir}/samtools_index" },
+            mode: params.publish_dir_mode,
+            saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
+        ]
+    }
 
     withName: 'MULTIQC_GLOBAL' {
         ext.args   = { params.multiqc_title ? "--title \"$params.multiqc_title\"" : '' }

modules.json

@@ -42,6 +42,21 @@
                         "git_sha": "7b50cb7be890e4b28cffb82e438cc6a8d7805d3f",
                         "installed_by": ["modules"]
                     },
+                    "picard/collectmultiplemetrics": {
+                        "branch": "master",
+                        "git_sha": "df124e87c74d8b40285199f8cc20151f5aa57255",
+                        "installed_by": ["modules"]
+                    },
+                    "samtools/faidx": {
+                        "branch": "master",
+                        "git_sha": "c8be52dba1166c678e74cda9c3a3c221635c8bb1",
+                        "installed_by": ["modules"]
+                    },
+                    "samtools/index": {
+                        "branch": "master",
+                        "git_sha": "c8be52dba1166c678e74cda9c3a3c221635c8bb1",
+                        "installed_by": ["modules"]
+                    },
                     "seqfu/stats": {
                         "branch": "master",
                         "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",