Merge pull request nf-core#732 from nf-core/mscsq_mspli_update

Switch local most severe consequence & pli scripts for the nf-core ones

Author: ramprasadn

CHANGELOG.md

@@ -12,6 +12,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 ### `Changed`
 
 - Use distinct output filenames for bcfools (in call_mobile_elements subworkflow) and svdb (in call_sv_tiddit subworkflow) [#716](https://github.com/nf-core/raredisease/pull/716)
+- Use nf-core's most severe consequence & pli scripts instead of local ones [#732](https://github.com/nf-core/raredisease/pull/732)
 
 ### `Fixed`
 

conf/modules/annotate_consequence_pli.config

@@ -14,61 +14,55 @@
 
 process {
 
-    withName: '.*ANN_CSQ_PLI_SV:ADD_MOST_SEVERE_CSQ' {
+    withName: '.*ANN_CSQ_PLI_SV:CUSTOM_ADDMOSTSEVERECONSEQUENCE' {
         ext.prefix = { "${meta.id}_sv_csq_${meta.set}" }
     }
 
-    withName: '.*ANN_CSQ_PLI_SV:ADD_MOST_SEVERE_PLI' {
+    withName: '.*ANN_CSQ_PLI_SV:CUSTOM_ADDMOSTSEVEREPLI' {
         ext.prefix = { "${meta.id}_sv_csq_pli_${meta.set}" }
     }
 
-    withName: '.*ANN_CSQ_PLI_SV:TABIX_BGZIPTABIX' {
-        ext.prefix = { "${meta.id}_sv_csq_pli_${meta.set}" }
-    }
 }
 
 process {
 
-    withName: '.*ANN_CSQ_PLI_SNV:ADD_MOST_SEVERE_CSQ' {
+    withName: '.*ANN_CSQ_PLI_SNV:CUSTOM_ADDMOSTSEVERECONSEQUENCE' {
         ext.prefix = { "${meta.id}_snv_csq_${meta.set}" }
     }
 
-    withName: '.*ANN_CSQ_PLI_SNV:ADD_MOST_SEVERE_PLI' {
+    withName: '.*ANN_CSQ_PLI_SNV:CUSTOM_ADDMOSTSEVEREPLI' {
         ext.prefix = { "${meta.id}_snv_csq_pli_${meta.set}" }
     }
 
-    withName: '.*ANN_CSQ_PLI_SNV:TABIX_BGZIPTABIX' {
-        ext.prefix = { "${meta.id}_snv_csq_pli_${meta.set}" }
-    }
 }
 
 process {
 
-    withName: '.*ANN_CSQ_PLI_MT:ADD_MOST_SEVERE_CSQ' {
+    withName: '.*ANN_CSQ_PLI_MT:CUSTOM_ADDMOSTSEVERECONSEQUENCE' {
         ext.prefix = { "${meta.id}_mt_csq_${meta.set}" }
     }
 
-    withName: '.*ANN_CSQ_PLI_MT:ADD_MOST_SEVERE_PLI' {
+    withName: '.*ANN_CSQ_PLI_MT:CUSTOM_ADDMOSTSEVEREPLI' {
         ext.prefix = { "${meta.id}_mt_csq_pli_${meta.set}" }
     }
 
-    withName: '.*ANN_CSQ_PLI_MT:TABIX_BGZIPTABIX' {
-        ext.prefix = { "${meta.id}_mt_csq_pli_${meta.set}" }
-    }
 }
 
 process {
 
-    withName: '.*ANN_CSQ_PLI_ME:ADD_MOST_SEVERE_CSQ' {
+    withName: '.*ANN_CSQ_PLI_ME:CUSTOM_ADDMOSTSEVERECONSEQUENCE' {
         ext.prefix = { "${meta.id}_me_csq_${meta.set}" }
     }
 
-    withName: '.*ANN_CSQ_PLI_ME:ADD_MOST_SEVERE_PLI' {
+    withName: '.*ANN_CSQ_PLI_ME:CUSTOM_ADDMOSTSEVEREPLI' {
         ext.prefix = { "${meta.id}_me_pli_${meta.set}" }
+        publishDir = [
+            path: { "${params.outdir}/annotate_mobile_elements" },
+            mode: params.publish_dir_mode,
+            saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
+        ]
     }
-
-    withName: '.*ANN_CSQ_PLI_ME:TABIX_BGZIPTABIX' {
-        ext.prefix = { "${meta.id}_me_annotated_${meta.set}" }
+    withName: '.*ANN_CSQ_PLI_ME:TABIX_TABIX' {
         publishDir = [
             path: { "${params.outdir}/annotate_mobile_elements" },
             mode: params.publish_dir_mode,

conf/test.config

@@ -37,7 +37,7 @@ params {
     pipelines_testdata_base_path    = 'https://raw.githubusercontent.com/nf-core/test-datasets/raredisease'
 
     skip_tools                      = 'fastp,gens,haplogrep3,peddy,germlinecnvcaller,qualimap,eklipse,ngsbits'
-    skip_subworkflows               = "mt_annotation,mt_subsample,me_calling,me_annotation,sv_annotation"
+    skip_subworkflows               = "mt_annotation,mt_subsample,sv_annotation"
 
     input                           = params.pipelines_testdata_base_path + '/testdata/samplesheet_fq_spring.csv'
     fasta                           = params.pipelines_testdata_base_path + '/reference/reference.fasta'

modules.json

@@ -116,6 +116,16 @@
                         "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
                         "installed_by": ["modules"]
                     },
+                    "custom/addmostsevereconsequence": {
+                        "branch": "master",
+                        "git_sha": "56f5268d044a61636f55c3935e2d5b23b65437e1",
+                        "installed_by": ["modules"]
+                    },
+                    "custom/addmostseverepli": {
+                        "branch": "master",
+                        "git_sha": "56f5268d044a61636f55c3935e2d5b23b65437e1",
+                        "installed_by": ["modules"]
+                    },
                     "deepvariant/rundeepvariant": {
                         "branch": "master",
                         "git_sha": "470ac76fb4fbba2a9284c8b65191119c8bfe5a69",