add versions to filter pcr picard subworkflow

modules/local/filterbam/main.nf

@@ -12,6 +12,7 @@ process FILTER_PAIR {
 
     output:
     tuple val(meta1), path("*_1paired.bam"), val(meta2), path("*_2paired.bam"), emit: bam
+    path  "versions.yml"          , emit: versions
 
     script:
     """
@@ -21,5 +22,9 @@ process FILTER_PAIR {
     samtools view -h -N common_reads.txt ${bam1} -O BAM > ${meta1.id}_1paired.bam
     samtools view -h -N common_reads.txt ${bam2} -O BAM > ${meta2.id}_2paired.bam
 
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        samtools: \$(echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//')
+    END_VERSIONS
     """
 }

subworkflows/local/filter_pcr_dup.nf

@@ -16,16 +16,19 @@ workflow FILTER_PCR_DUP {
     index
 
     main:
+    ch_versions = Channel.empty()
 
     SAMTOOLS_SORT(
         bam
     )
+    ch_versions = ch_versions.mix(SAMTOOLS_SORT.out.versions)
 
     PICARD_MARKDUPLICATES(
         SAMTOOLS_SORT.out.bam,
         fasta.collect(),
         index.collect()
     )
+    ch_versions = ch_versions.mix(PICARD_MARKDUPLICATES.out.versions)
 
     SAMTOOLS_SORT_N(
         PICARD_MARKDUPLICATES.out.bam
@@ -40,9 +43,11 @@ workflow FILTER_PCR_DUP {
                 meta1.id == meta2.id && meta1.chunk == meta2.chunk && meta1.mates == "R1" && meta2.mates == "R2" ? [ meta1,  bam1,  meta2, bam2 ] : null
     })
     FILTER_PAIR.out.bam.set{ new_ch_bam }
-
+    ch_versions = ch_versions.mix(FILTER_PAIR.out.versions)
 
 
     emit:
     bam = new_ch_bam
+    versions = ch_versions
+
 }

subworkflows/local/hicpro_mapping.nf

@@ -92,8 +92,6 @@ workflow HICPRO_MAPPING {
     MERGE_BOWTIE2.out.bam
         .set{ ch_bowtie2_merged }
 
-    ch_bowtie2_merged.view()
-
     ch_versions = ch_versions.mix(MERGE_BOWTIE2.out.versions)
     ch_mapping_stats = MERGE_BOWTIE2.out.stats
 
@@ -113,9 +111,9 @@ workflow HICPRO_MAPPING {
             .flatten()
             .buffer( size: 2 )
             .set {ch_bowtie2_merged}
+
+        ch_versions = ch_versions.mix(FILTER_PCR_DUP.out.versions)
     }
-    //TODO add versions
-    ch_bowtie2_merged.view()
 
     // Combine mates
     ch_bowtie2_merged
@@ -123,7 +121,6 @@ workflow HICPRO_MAPPING {
       .groupTuple()
       .set {ch_bams}
 
-      ch_bams.view()
 
   }else{