Merge pull request #62 from sanger-tol/vcftools_site_pi_het

VCFTOOLs site_pi and het options
sanger-tol · Nov 16, 2023 · 3b3a745 · 3b3a745
2 parents aa99735 + 1882fef
commit 3b3a745
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Showing 12 changed files with 569 additions and 9 deletions.
diff --git a/conf/modules.config b/conf/modules.config
@@ -51,6 +51,29 @@ process {
         ]
     }
 
+    withName: '.*:PROCESS_VCF:VCFTOOLS_SITE_PI' {
+        ext.args = '--site-pi'
+        if( params.include_positions ){
+            ext.args += ' --positions'
+        } else if ( params.exclude_positions ){
+            ext.args += ' --exclude-positions'
+        }
+        publishDir = [
+            path: { "${params.outdir}/variant_calling" },
+            mode: params.publish_dir_mode,
+            saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
+        ]
+    }
+
+    withName: '.*:PROCESS_VCF:VCFTOOLS_HET' {
+        ext.args = '--het'
+        publishDir = [
+            path: { "${params.outdir}/variant_calling" },
+            mode: params.publish_dir_mode,
+            saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
+        ]
+    }
+
     withName: CUSTOM_DUMPSOFTWAREVERSIONS {
         publishDir = [
             path: { "${params.outdir}/pipeline_info/variantcalling" },

diff --git a/modules.json b/modules.json
@@ -22,7 +22,7 @@
                     },
                     "deepvariant": {
                         "branch": "master",
-                        "git_sha": "ed67f2fadd6d2a155b296f728e6b1f8c92ddc1a6",
+                        "git_sha": "516189e968feb4ebdd9921806988b4c12b4ac2dc",
                         "installed_by": ["modules"]
                     },
                     "samtools/faidx": {
@@ -45,6 +45,12 @@
                         "branch": "master",
                         "git_sha": "3ffae3598260a99e8db3207dead9f73f87f90d1f",
                         "installed_by": ["modules"]
+                    },
+                    "vcftools": {
+                        "branch": "master",
+                        "git_sha": "8fc1d24c710ebe1d5de0f2447ec9439fd3d9d66a",
+                        "installed_by": ["modules"],
+                        "patch": "modules/nf-core/vcftools/vcftools.diff"
                     }
                 }
             }

diff --git a/modules/nf-core/deepvariant/environment.yml b/modules/nf-core/deepvariant/environment.yml
diff --git a/modules/nf-core/deepvariant/meta.yml b/modules/nf-core/deepvariant/meta.yml
diff --git a/modules/nf-core/vcftools/environment.yml b/modules/nf-core/vcftools/environment.yml
diff --git a/modules/nf-core/vcftools/main.nf b/modules/nf-core/vcftools/main.nf