Resolve warnings

CHANGELOG.md

@@ -17,6 +17,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 - Changed valid values for sex according to the PED file format [#550](https://github.com/nf-core/raredisease/pull/550)
 - Refactored config files [#538](https://github.com/nf-core/raredisease/pull/538)
 - Refactored mobile element annotation subworkflow files [#538](https://github.com/nf-core/raredisease/pull/538)
+- Refactored to remove "a process is defined more than once" warning [#557](https://github.com/nf-core/raredisease/pull/557)
 
 ### `Fixed`
 

conf/modules/align_bwa_bwamem2_bwameme.config

@@ -36,7 +36,7 @@ process {
         ext.when = { params.aligner.equals("bwameme") }
     }
 
-    withName: '.*ALIGN:ALIGN_BWA_BWAMEM2_BWAMEME:BWA_MEM' {
+    withName: '.*ALIGN:ALIGN_BWA_BWAMEM2_BWAMEME:BWA' {
         ext.args = { "-M -K 100000000 -R ${meta.read_group}" }
         ext.args2 = { "-T ./samtools_sort_tmp" }
         ext.prefix = { "${meta.id}_sorted" }

conf/modules/annotate_rhocallviz.config

@@ -17,7 +17,7 @@
 
 process {
 
-    withName: '.*ANNOTATE_GENOME_SNVS:ANNOTATE_RHOCALLVIZ:BCFTOOLS_VIEW' {
+    withName: '.*ANNOTATE_GENOME_SNVS:ANNOTATE_RHOCALLVIZ:BCFTOOLS_VIEW_RHOCALL' {
         ext.prefix = { "${meta.sample}" }
         ext.args   = { "--output-type z --min-ac 1 --samples ${meta.sample}" }
     }

conf/modules/qc_bam.config

@@ -72,7 +72,7 @@ process {
         ]
     }
 
-    withName: '.*QC_BAM:PICARD_COLLECTWGSMETRICS' {
+    withName: '.*QC_BAM:PICARD_COLLECTWGSMETRICS_WG' {
         ext.args = "--TMP_DIR ."
         ext.when = { !params.aligner.equals("sentieon") }
         ext.prefix = { "${meta.id}_wgsmetrics" }
@@ -84,7 +84,7 @@ process {
         ext.prefix = { "${meta.id}_wgsmetrics_y" }
     }
 
-    withName: '.*QC_BAM:SENTIEON_WGSMETRICS' {
+    withName: '.*QC_BAM:SENTIEON_WGSMETRICS_WG' {
         ext.when = { params.aligner.equals("sentieon") }
         ext.prefix = { "${meta.id}_wgsmetrics" }
     }

subworkflows/local/alignment/align_bwa_bwamem2_bwameme.nf

@@ -2,7 +2,7 @@
 // Map to reference, fetch stats for each demultiplexed read pair, merge, mark duplicates, and index.
 //
 
-include { BWA_MEM                                  } from '../../../modules/nf-core/bwa/mem/main'
+include { BWA_MEM as BWA                           } from '../../../modules/nf-core/bwa/mem/main'
 include { BWA_MEM as BWAMEM_FALLBACK               } from '../../../modules/nf-core/bwa/mem/main'
 include { BWAMEM2_MEM                              } from '../../../modules/nf-core/bwamem2/mem/main'
 include { BWAMEME_MEM                              } from '../../../modules/nf-core/bwameme/mem/main'
@@ -28,9 +28,9 @@ workflow ALIGN_BWA_BWAMEM2_BWAMEME {
 
         // Map, sort, and index
         if (params.aligner.equals("bwa")) {
-            BWA_MEM ( ch_reads_input, ch_bwa_index, true )
-            ch_align = BWA_MEM.out.bam
-            ch_versions = ch_versions.mix(BWA_MEM.out.versions.first())
+            BWA ( ch_reads_input, ch_bwa_index, true )
+            ch_align = BWA.out.bam
+            ch_versions = ch_versions.mix(BWA.out.versions.first())
         } else if (params.aligner.equals("bwameme")) {
             BWAMEME_MEM ( ch_reads_input, ch_bwameme_index, ch_genome_fasta, true )
             ch_align = BWAMEME_MEM.out.bam

subworkflows/local/annotation/annotate_rhocallviz.nf

@@ -2,7 +2,7 @@
 // A subworkflow to plot binned zygosity and RHO-regions.
 //
 
-include { BCFTOOLS_VIEW                             } from '../../../modules/nf-core/bcftools/view/main'
+include { BCFTOOLS_VIEW as BCFTOOLS_VIEW_RHOCALL    } from '../../../modules/nf-core/bcftools/view/main'
 include { TABIX_TABIX                               } from '../../../modules/nf-core/tabix/tabix/main'
 include { BCFTOOLS_ROH                              } from '../../../modules/nf-core/bcftools/roh/main'
 include { BCFTOOLS_VIEW as BCFTOOLS_VIEW_UNCOMPRESS } from '../../../modules/nf-core/bcftools/view/main'
@@ -25,11 +25,11 @@ workflow ANNOTATE_RHOCALLVIZ {
             .map {meta, vcf, tbi, meta2 -> return [meta2,vcf,tbi]}
             .set { ch_rhocall_viz }
 
-        BCFTOOLS_VIEW(ch_rhocall_viz, [],[],[])
+        BCFTOOLS_VIEW_RHOCALL(ch_rhocall_viz, [],[],[])
 
-        TABIX_TABIX(BCFTOOLS_VIEW.out.vcf)
+        TABIX_TABIX(BCFTOOLS_VIEW_RHOCALL.out.vcf)
 
-        BCFTOOLS_VIEW.out.vcf
+        BCFTOOLS_VIEW_RHOCALL.out.vcf
             .join(TABIX_TABIX.out.tbi)
             .set {ch_roh_in }
 
@@ -43,7 +43,7 @@ workflow ANNOTATE_RHOCALLVIZ {
 
         UCSC_WIGTOBIGWIG(RHOCALL_VIZ.out.wig, ch_genome_chrsizes)
 
-        ch_versions = ch_versions.mix(BCFTOOLS_VIEW.out.versions.first())
+        ch_versions = ch_versions.mix(BCFTOOLS_VIEW_RHOCALL.out.versions.first())
         ch_versions = ch_versions.mix(CHROMOGRAPH_AUTOZYG.out.versions.first())
         ch_versions = ch_versions.mix(TABIX_TABIX.out.versions.first())
         ch_versions = ch_versions.mix(BCFTOOLS_ROH.out.versions.first())

subworkflows/local/qc_bam.nf

@@ -2,18 +2,18 @@
 // A quality check subworkflow for processed bams.
 //
 
-include { PICARD_COLLECTMULTIPLEMETRICS                          } from '../../modules/nf-core/picard/collectmultiplemetrics/main'
-include { PICARD_COLLECTHSMETRICS                                } from '../../modules/nf-core/picard/collecthsmetrics/main'
-include { CHROMOGRAPH as CHROMOGRAPH_COV                         } from '../../modules/nf-core/chromograph/main'
-include { QUALIMAP_BAMQC                                         } from '../../modules/nf-core/qualimap/bamqc/main'
-include { TIDDIT_COV                                             } from '../../modules/nf-core/tiddit/cov/main'
-include { MOSDEPTH                                               } from '../../modules/nf-core/mosdepth/main'
-include { UCSC_WIGTOBIGWIG                                       } from '../../modules/nf-core/ucsc/wigtobigwig/main'
-include { PICARD_COLLECTWGSMETRICS as PICARD_COLLECTWGSMETRICS   } from '../../modules/nf-core/picard/collectwgsmetrics/main'
-include { PICARD_COLLECTWGSMETRICS as PICARD_COLLECTWGSMETRICS_Y } from '../../modules/nf-core/picard/collectwgsmetrics/main'
-include { SENTIEON_WGSMETRICS                                    } from '../../modules/nf-core/sentieon/wgsmetrics/main'
-include { SENTIEON_WGSMETRICS as SENTIEON_WGSMETRICS_Y           } from '../../modules/nf-core/sentieon/wgsmetrics/main'
-include { NGSBITS_SAMPLEGENDER                                   } from '../../modules/nf-core/ngsbits/samplegender/main'
+include { PICARD_COLLECTMULTIPLEMETRICS                            } from '../../modules/nf-core/picard/collectmultiplemetrics/main'
+include { PICARD_COLLECTHSMETRICS                                  } from '../../modules/nf-core/picard/collecthsmetrics/main'
+include { CHROMOGRAPH as CHROMOGRAPH_COV                           } from '../../modules/nf-core/chromograph/main'
+include { QUALIMAP_BAMQC                                           } from '../../modules/nf-core/qualimap/bamqc/main'
+include { TIDDIT_COV                                               } from '../../modules/nf-core/tiddit/cov/main'
+include { MOSDEPTH                                                 } from '../../modules/nf-core/mosdepth/main'
+include { UCSC_WIGTOBIGWIG                                         } from '../../modules/nf-core/ucsc/wigtobigwig/main'
+include { PICARD_COLLECTWGSMETRICS as PICARD_COLLECTWGSMETRICS_WG  } from '../../modules/nf-core/picard/collectwgsmetrics/main'
+include { PICARD_COLLECTWGSMETRICS as PICARD_COLLECTWGSMETRICS_Y   } from '../../modules/nf-core/picard/collectwgsmetrics/main'
+include { SENTIEON_WGSMETRICS as SENTIEON_WGSMETRICS_WG            } from '../../modules/nf-core/sentieon/wgsmetrics/main'
+include { SENTIEON_WGSMETRICS as SENTIEON_WGSMETRICS_Y             } from '../../modules/nf-core/sentieon/wgsmetrics/main'
+include { NGSBITS_SAMPLEGENDER                                     } from '../../modules/nf-core/ngsbits/samplegender/main'
 
 workflow QC_BAM {
 
@@ -61,13 +61,13 @@ workflow QC_BAM {
 
         // COLLECT WGS METRICS
         if (!params.analysis_type.equals("wes")) {
-            PICARD_COLLECTWGSMETRICS ( ch_bam_bai, ch_genome_fasta, ch_genome_fai, ch_intervals_wgs )
+            PICARD_COLLECTWGSMETRICS_WG ( ch_bam_bai, ch_genome_fasta, ch_genome_fai, ch_intervals_wgs )
             PICARD_COLLECTWGSMETRICS_Y ( ch_bam_bai, ch_genome_fasta, ch_genome_fai, ch_intervals_y )
-            SENTIEON_WGSMETRICS ( ch_bam_bai, ch_genome_fasta, ch_genome_fai, ch_intervals_wgs.map{ interval -> [[:], interval]} )
+            SENTIEON_WGSMETRICS_WG ( ch_bam_bai, ch_genome_fasta, ch_genome_fai, ch_intervals_wgs.map{ interval -> [[:], interval]} )
             SENTIEON_WGSMETRICS_Y ( ch_bam_bai, ch_genome_fasta, ch_genome_fai, ch_intervals_y.map{ interval -> [[:], interval]} )
-            ch_cov   = Channel.empty().mix(PICARD_COLLECTWGSMETRICS.out.metrics, SENTIEON_WGSMETRICS.out.wgs_metrics)
+            ch_cov   = Channel.empty().mix(PICARD_COLLECTWGSMETRICS_WG.out.metrics, SENTIEON_WGSMETRICS_WG.out.wgs_metrics)
             ch_cov_y = Channel.empty().mix(PICARD_COLLECTWGSMETRICS_Y.out.metrics, SENTIEON_WGSMETRICS_Y.out.wgs_metrics)
-            ch_versions = ch_versions.mix(PICARD_COLLECTWGSMETRICS.out.versions.first(), SENTIEON_WGSMETRICS.out.versions.first())
+            ch_versions = ch_versions.mix(PICARD_COLLECTWGSMETRICS_WG.out.versions.first(), SENTIEON_WGSMETRICS_WG.out.versions.first())
             ch_versions = ch_versions.mix(PICARD_COLLECTWGSMETRICS_Y.out.versions.first(), SENTIEON_WGSMETRICS_Y.out.versions.first())
         }
         // Check sex