feat merge to dev

genomic-medicine-sweden · Mar 11, 2024 · 91fb82b · 91fb82b
2 parents ad9354e + 5fd26fa
commit 91fb82b
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Showing 3 changed files with 14 additions and 21 deletions.
diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -30,6 +30,7 @@ Initial release of genomic-medicine-sweden/tomte, created with the [nf-core](htt
 - Changed name of salmon's quant.nf to include sample id [#78](https://github.com/genomic-medicine-sweden/tomte/pull/78)
 - Shortened name of DROP output files [#79](https://github.com/genomic-medicine-sweden/tomte/pull/79)
 - Merging of vcfs has been moved to after bootstrapAnn [#81](https://github.com/genomic-medicine-sweden/tomte/pull/81)
+- Substituted bgzip and tabix modules by bgzip_tabix module [#85](https://github.com/genomic-medicine-sweden/tomte/pull/85)
 
 ### `Dependencies`
 

diff --git a/conf/modules/allele_specific_calling.config b/conf/modules/allele_specific_calling.config
@@ -30,10 +30,6 @@ process {
         ext.args = { '--tbi' }
     }
 
-    withName: '.*ALLELE_SPECIFIC_CALLING:BCFTOOLS_INDEX_2' {
-        ext.args = { '--tbi' }
-    }
-
     withName: '.*ALLELE_SPECIFIC_CALLING:BCFTOOLS_MERGE' {
         ext.args = '--output-type z'
         ext.prefix = { "${meta.id}" }

diff --git a/subworkflows/local/allele_specific_calling.nf b/subworkflows/local/allele_specific_calling.nf
@@ -2,15 +2,14 @@
 // Allele specific variant calling
 //
 
-include { BCFTOOLS_VIEW                      } from '../../modules/nf-core/bcftools/view/main'
-include { BCFTOOLS_INDEX                     } from '../../modules/nf-core/bcftools/index/main'
-include { GATK4_ASEREADCOUNTER               } from '../../modules/nf-core/gatk4/asereadcounter/main'
-include { BOOTSTRAPANN                       } from '../../modules/local/bootstrapann'
-include { TABIX_BGZIP                        } from '../../modules/nf-core/tabix/bgzip/main'
-include { BCFTOOLS_INDEX as BCFTOOLS_INDEX_2 } from '../../modules/nf-core/bcftools/index/main'
-include { BCFTOOLS_MERGE                     } from '../../modules/nf-core/bcftools/merge/main'
-include { RENAME_FILES                       } from '../../modules/local/rename_files'
-include { TABIX_TABIX                        } from '../../modules/nf-core/tabix/tabix/main'
+include { BCFTOOLS_VIEW        } from '../../modules/nf-core/bcftools/view/main'
+include { BCFTOOLS_INDEX       } from '../../modules/nf-core/bcftools/index/main'
+include { GATK4_ASEREADCOUNTER } from '../../modules/nf-core/gatk4/asereadcounter/main'
+include { BOOTSTRAPANN         } from '../../modules/local/bootstrapann'
+include { TABIX_BGZIPTABIX     } from '../../modules/nf-core/tabix/bgziptabix/main'
+include { BCFTOOLS_MERGE       } from '../../modules/nf-core/bcftools/merge/main'
+include { RENAME_FILES         } from '../../modules/local/rename_files'
+include { TABIX_TABIX          } from '../../modules/nf-core/tabix/tabix/main'
 
 
 workflow ALLELE_SPECIFIC_CALLING {
@@ -53,18 +52,16 @@ workflow ALLELE_SPECIFIC_CALLING {
             GATK4_ASEREADCOUNTER.out.csv
         )
 
-        TABIX_BGZIP(BOOTSTRAPANN.out.vcf)
+        TABIX_BGZIPTABIX(BOOTSTRAPANN.out.vcf)
 
-        BCFTOOLS_INDEX_2(TABIX_BGZIP.out.output)
-
-        TABIX_BGZIP.out.output
+        TABIX_BGZIPTABIX.out.gz_tbi
                     .collect{it[1]}
                     .ifEmpty([])
                     .toList()
                     .set { file_list_vcf }
 
-        BCFTOOLS_INDEX_2.out.tbi
-                    .collect{it[1]}
+        TABIX_BGZIPTABIX.out.gz_tbi
+                    .collect{it[2]}
                     .ifEmpty([])
                     .toList()
                     .set { file_list_tbi }
@@ -101,8 +98,7 @@ workflow ALLELE_SPECIFIC_CALLING {
         ch_versions = ch_versions.mix(BCFTOOLS_INDEX.out.versions.first())
         ch_versions = ch_versions.mix(GATK4_ASEREADCOUNTER.out.versions.first())
         ch_versions = ch_versions.mix(BOOTSTRAPANN.out.versions.first())
-        ch_versions = ch_versions.mix(TABIX_BGZIP.out.versions.first())
-        ch_versions = ch_versions.mix(BCFTOOLS_INDEX_2.out.versions.first())
+        ch_versions = ch_versions.mix(TABIX_BGZIPTABIX.out.versions.first())
         ch_versions = ch_versions.mix( BCFTOOLS_MERGE.out.versions.first() )
         ch_versions = ch_versions.mix( RENAME_FILES.out.versions.first() )
         ch_versions = ch_versions.mix( TABIX_TABIX.out.versions.first() )