Merge pull request #147 from IntGenomicsLab/whatshap_stats

Whatshap stats

Author: robert-a-forsyth

conf/modules.config

@@ -96,6 +96,16 @@ process {
         ]
     }
 
+    withName: '.*:WHATSHAP_STATS' {
+        ext.prefix = { "${meta.id}_whatshap_stats" }
+        ext.args = { "--sample ${meta.id}" }
+        publishDir = [
+            path: { "${params.outdir}/${meta.id}/qc/whatshap_stats" },
+            mode: params.publish_dir_mode,
+            saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
+        ]
+    }
+
     //
     // Preprocessing and other processes
     //
@@ -209,7 +219,7 @@ process {
     //
 
     withName: '.*:LONGPHASE_PHASE' {
-        ext.prefix = { "somatic_smallvariants" }
+        ext.prefix = { "germline_smallvariants" }
         ext.args   = {
                 [
                     meta.platform == 'pb' ? '--pb' : '--ont',
@@ -222,6 +232,7 @@ process {
             saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
         ]
     }
+
     withName: '.*:LONGPHASE_HAPLOTAG' {
         ext.prefix = { "${meta.id}_${meta.type}" }
         publishDir = [
@@ -262,6 +273,7 @@ process {
         ]
     }
     withName: '.*:CLAIRSTO' {
+        ext.args = { "--sample_name ${meta.id}" }
         publishDir = [
             path: { "${params.outdir}/${meta.id}/variants/clairsto" },
             mode: params.publish_dir_mode,
@@ -279,6 +291,7 @@ process {
     }
 
     withName: '.*:CLAIR3' {
+        ext.args = { "--sample_name=${meta.id}" }
         publishDir = [
             path: { "${params.outdir}/${meta.id}/variants/clair3" },
             mode: params.publish_dir_mode,

modules.json

@@ -90,6 +90,11 @@
                         "git_sha": "2c73cc8fa92cf48de3da0b643fdf357a8a290b36",
                         "installed_by": ["modules"]
                     },
+                    "nanoplot": {
+                        "branch": "master",
+                        "git_sha": "682f789f93070bd047868300dd018faf3d434e7c",
+                        "installed_by": ["modules"]
+                    },
                     "pigz/uncompress": {
                         "branch": "master",
                         "git_sha": "f84336b7fa91a65aa61d215b8c109fbb8e4b4ac6",
@@ -146,6 +151,11 @@
                         "branch": "master",
                         "git_sha": "41dfa3f7c0ffabb96a6a813fe321c6d1cc5b6e46",
                         "installed_by": ["modules"]
+                    },
+                    "whatshap/stats": {
+                        "branch": "master",
+                        "git_sha": "bfab71f4d68c1aaff09335a3433e7b2836918b2a",
+                        "installed_by": ["modules"]
                     }
                 }
             },