remove samtools index+merge subworkflows in Nextflow

structuralvariants/nextflow/main.nf

@@ -78,8 +78,8 @@ include { SUB_TRIMMED_FASTQ } from './subworkflows/trimmed_fastq'
 include { SUB_BWA_MEM } from './subworkflows/bwa_mem'
 include { SUB_SAMTOOLS_VIEW_SAM2BAM } from './subworkflows/samtools_view_sam2bam'
 include { SUB_SAMTOOLS_SORT } from './subworkflows/samtools_sort'
-include { SUB_SAMTOOLS_MERGE } from './subworkflows/samtools_merge'
-include { SUB_SAMTOOLS_INDEX } from './subworkflows/samtools_index'
+include { SAMTOOLS_MERGE } from './modules/samtools_merge'
+include { SAMTOOLS_INDEX } from './modules/samtools_index'
 include { SUB_PICARD_MARKDUPLICATES } from './subworkflows/picard_markduplicates'
 include { SUB_BAM_FILTERING } from './subworkflows/bam_filtering'
 include { SUB_CNV_MANTA } from './subworkflows/cnv_manta'
@@ -88,7 +88,7 @@ include { SUB_CNV_EXOMEDEPTH } from './subworkflows/cnv_exomedepth'
 include { SUB_CNV_CODEX } from './subworkflows/cnv_codex'
 include { SUB_FINAL_FILTERING } from './subworkflows/final_filtering'
 
-workflow{
+workflow {
   if( params.generate_bwa_indexes ) {
     output_bwa_index = SUB_BWA_INDEX(reference_fasta)
     indexFiles = output_bwa_index.indexs.combine(output_bwa_index.fai).collect()
@@ -100,52 +100,65 @@ workflow{
 
   SUB_TRIMMED_FASTQ(fastq)
 
-  SUB_BWA_MEM(SUB_TRIMMED_FASTQ.out.reads, indexFiles)
+  SUB_BWA_MEM(
+    SUB_TRIMMED_FASTQ.out.reads,
+    indexFiles
+  )
 
   SUB_SAMTOOLS_VIEW_SAM2BAM(
-    SUB_BWA_MEM.out.output_paired,
-    SUB_BWA_MEM.out.output_unpairedR1,
-    SUB_BWA_MEM.out.output_unpairedR2
+    SUB_BWA_MEM.out.paired,
+    SUB_BWA_MEM.out.unpairedR1,
+    SUB_BWA_MEM.out.unpairedR2
   )
+
   SUB_SAMTOOLS_SORT(
-    SUB_SAMTOOLS_VIEW_SAM2BAM.out.reads,
+    SUB_SAMTOOLS_VIEW_SAM2BAM.out.paired,
     SUB_SAMTOOLS_VIEW_SAM2BAM.out.unpairedR1,
     SUB_SAMTOOLS_VIEW_SAM2BAM.out.unpairedR2
   )
 
-  SUB_SAMTOOLS_MERGE(
+  SAMTOOLS_MERGE(
     SUB_SAMTOOLS_SORT.out.paired,
     SUB_SAMTOOLS_SORT.out.unpairedR1,
     SUB_SAMTOOLS_SORT.out.unpairedR2
   )
 
-  SUB_SAMTOOLS_INDEX(
-    SUB_SAMTOOLS_MERGE.out.output
+  SAMTOOLS_INDEX(
+    SAMTOOLS_MERGE.out.output
+  )
+
+  SUB_PICARD_MARKDUPLICATES(
+    SUB_SAMTOOLS_INDEX.out.output
+  )
+
+  SUB_BAM_FILTERING(
+    SUB_PICARD_MARKDUPLICATES.out.alignments
+  )
+
+  SUB_CNV_MANTA (
+      SUB_BAM_FILTERING.out,
+      samples,
+      indexFiles,
+      bed
+  )
+
+  SUB_CNV_GRIDSS (
+      SUB_BAM_FILTERING.out,
+      samples,
+      indexFiles
+  )
+
+  SUB_CNV_EXOMEDEPTH (
+      SUB_BAM_FILTERING.out,
+      samples,
+      indexFiles
+  )
+
+  SUB_CNV_CODEX(
+      SUB_BAM_FILTERING.out,
+      samples,
+      bed
   )
 
-  SUB_PICARD_MARKDUPLICATES( SUB_SAMTOOLS_INDEX.out.output )
-  SUB_BAM_FILTERING( SUB_PICARD_MARKDUPLICATES.out.alignments )
-  
-  // SUB_CNV_MANTA (
-  //     SUB_BAM_FILTERING.out,
-  //     samples,
-  //     indexFiles,
-  //     bed
-  // )
-  // SUB_CNV_GRIDSS (
-  //     SUB_BAM_FILTERING.out,
-  //     samples,
-  //     indexFiles
-  // )
-  // SUB_CNV_EXOMEDEPTH (
-  //     SUB_BAM_FILTERING.out,
-  //     samples,
-  //     indexFiles
-  // )
-  // SUB_CNV_CODEX (
-  //     SUB_BAM_FILTERING.out,
-  //     samples,
-  //     bed
-  // )
-  // SUB_FINAL_FILTERING ( final_filtering )
+  SUB_FINAL_FILTERING(final_filtering)
 }

structuralvariants/nextflow/modules/samtools_index.nf

 process SAMTOOLS_INDEX {
-  tag "samtools index"
+  tag { "samtools index" }
   container 'quay.io/biocontainers/samtools:1.5--2'
 
   input:
     path input
 
   output:
-    tuple path(input), path("*.sorted*.bai")
+    tuple path(input), path("*.sorted*.bai"), emit: output
 
   script:
   """
   samtools index -b $input
   """
-}
\ No newline at end of file
+}

structuralvariants/nextflow/modules/samtools_merge.nf

 process SAMTOOLS_MERGE {
-  tag "samtools merge"
+  tag { "samtools merge" }
   container 'quay.io/biocontainers/samtools:1.5--2'
 
   input:
     path paired
     path unpairedR1
     path unpairedR2
-    
+
   output:
-    path "${paired.simpleName}.sorted.bam", emit: output_samtools_merge
-        
+    path "${paired.simpleName}.sorted.bam", emit: output
+
   script:
   def threadsArgument = params.threads_samtools ? "--threads $params.threads_samtools" : ""
   """
   samtools merge -f $threadsArgument ${paired.simpleName}.sorted.bam $paired $unpairedR1 $unpairedR2
   """
-}
\ No newline at end of file
+}

structuralvariants/nextflow/subworkflows/samtools_index.nf

-/*
- * Include for samtools_index
-*/
-include {
-    SAMTOOLS_INDEX
-} from "../modules/samtools_index"
-
-/*
-* Subworkflow samtools_index
-*/
-workflow SUB_SAMTOOLS_INDEX {
-  take:
-    input
-
-  main:
-    SAMTOOLS_INDEX(input)
-
-  emit:
-    output = SAMTOOLS_INDEX.out
-}
\ No newline at end of file

structuralvariants/nextflow/subworkflows/samtools_merge.nf

-/*
- * Include for samtools_merge
-*/
-include {
-    SAMTOOLS_MERGE
-} from "../modules/samtools_merge"
-
-/*
-* Subworkflow samtools_merge
-*/
-workflow SUB_SAMTOOLS_MERGE {
-  take:
-    paired
-    unpaired_R1
-    unpaired_R2
-
-  main:
-    SAMTOOLS_MERGE(paired,
-                   unpaired_R1,
-                   unpaired_R2)
-  
-  emit:
-    output = SAMTOOLS_MERGE.out
-}
\ No newline at end of file