Add handling of output_bam param

conf/modules.config

@@ -41,7 +41,7 @@ process {
 
     // Files to be used for pretext, likely to be deleted once the hic workflow is complete.
     // .bed, .hr.pretext, .lr.pretext, needs centromere
-    withName: 'REFORMAT_INTERSECT|SEQTK_CUTN|GAP_LENGTH|PRETEXT_INGEST_HIRES|PRETEXT_INGEST_SNDRD|COOLER_ZOOMIFY|COV_FOLDER|UCSC_BEDGRAPHTOBIGWIG|BED2BW_NORMAL|BED2BW_AVGCOV|EXTRACT_TELO|JUICER_TOOLS_PRE|SNAPSHOT_SRES|PRETEXT_GRAPH' {
+    withName: 'REFORMAT_INTERSECT|SEQTK_CUTN|GAP_LENGTH|PRETEXT_INGEST_HIRES|PRETEXT_INGEST_SNDRD|COOLER_ZOOMIFY|COV_FOLDER|UCSC_BEDGRAPHTOBIGWIG|BED2BW_NORMAL|BED2BW_AVGCOV|EXTRACT_TELO|JUICER_TOOLS_PRE|SNAPSHOT_SRES|PRETEXT_GRAPH|SAMTOOLS_MERGE_OUTPUT_BAM' {
         publishDir = [
             path: { "${params.outdir}/hic_files" },
             mode: params.publish_dir_mode,
@@ -366,6 +366,10 @@ process {
         ext.prefix      = { "${meta.id}_hic_bwamem2_merge" }
     }
 
+    withName: ".*:.*:HIC_BWAMEM2:SAMTOOLS_MERGE_OUTPUT_BAM" {
+        ext.prefix      = { "${meta.id}_hic_bwamem2_merge" }
+    }
+
     withName: ".*:.*:HIC_MINIMAP2:CRAM_FILTER_MINIMAP2_FILTER5END_FIXMATE_SORT" {
         ext.args        = ""
         ext.args1       = ""
@@ -378,6 +382,10 @@ process {
         ext.prefix      = { "${meta.id}_hic_minimap2_merge" }
     }
 
+    withName: ".*:.*:HIC_MINIMAP2:SAMTOOLS_MERGE_OUTPUT_BAM" {
+        ext.prefix      = { "${meta.id}_hic_minimap2_merge" }
+    }
+
     withName: ".*:.*:GENERATE_SORTED_GENOME:GNU_SORT" {
         ext.prefix      = { "${meta.id}_len_sorted" }
         ext.suffix      = { "genome" }

subworkflows/local/hic_bwamem2.nf

@@ -10,13 +10,15 @@
 //
 include { BWAMEM2_INDEX                                   } from '../../modules/nf-core/bwamem2/index/main'
 include { CRAM_FILTER_ALIGN_BWAMEM2_FIXMATE_SORT          } from '../../modules/local/cram_filter_align_bwamem2_fixmate_sort'
+include { SAMTOOLS_MERGE_OUTPUT_BAM                        } from '../../modules/nf-core/samtools/merge/main'
 include { SAMTOOLS_MERGE                                  } from '../../modules/nf-core/samtools/merge/main'
 
 workflow HIC_BWAMEM2 {
     take:
     reference_tuple     // Channel: tuple [ val(meta), path( file )      ]
     csv_ch
     reference_index
+    output_bam
 
     main:
     ch_versions         = Channel.empty()
@@ -73,21 +75,34 @@ workflow HIC_BWAMEM2 {
                 ],
                 file
             )
+        }        
+        .branch{
+            output      : it[0].output_bam == "true"
+            no_output    : it[0].output_bam != "true"
         }
         .set { collected_files_for_merge }
 
     //
     // MODULE: MERGE POSITION SORTED BAM FILES AND MARK DUPLICATES
     //
     SAMTOOLS_MERGE (
-        collected_files_for_merge,
+        collected_files_for_merge.no_output,
         reference_tuple,
         reference_index
     )
     ch_versions         = ch_versions.mix ( SAMTOOLS_MERGE.out.versions.first() )
+    ch_mergedbam       = SAMTOOLS_MERGE.out.bam
 
 
+    SAMTOOLS_MERGE_OUTPUT_BAM (
+        collected_files_for_merge.output,
+        reference_tuple,
+        reference_index
+    )
+    ch_versions        = ch_versions.mix ( SAMTOOLS_MERGE_OUTPUT_BAM.out.versions.first() )
+    ch_mergedbam       = ch_mergedbam.mix( SAMTOOLS_MERGE_OUTPUT_BAM.out.bam )
+
     emit:
-    mergedbam           = SAMTOOLS_MERGE.out.bam
+    mergedbam           = ch_mergedbam
     versions            = ch_versions.ifEmpty(null)
 }

subworkflows/local/hic_mapping.nf

@@ -35,6 +35,7 @@ workflow HIC_MAPPING {
     avgcoverage_file    // Channel: tuple [ val(meta), path( file )      ]
     telo_file           // Channel: tuple [ val(meta), path( file )      ]
     repeat_density_file // Channel: tuple [ val(meta), path( file )      ]
+    output_bam          // Channel: val
     workflow_setting    // Channel: val( { RAPID | FULL | RAPID_TOL } )
 
     main:
@@ -90,7 +91,8 @@ workflow HIC_MAPPING {
     HIC_MINIMAP2 (
         ch_aligner.minimap2,
         GENERATE_CRAM_CSV.out.csv,
-        reference_index
+        reference_index,
+        output_bam
     )
     ch_versions         = ch_versions.mix( HIC_MINIMAP2.out.versions )
     mergedbam           = HIC_MINIMAP2.out.mergedbam
@@ -101,7 +103,8 @@ workflow HIC_MAPPING {
     HIC_BWAMEM2 (
         ch_aligner.bwamem2,
         GENERATE_CRAM_CSV.out.csv,
-        reference_index
+        reference_index,
+        output_bam
     )
     ch_versions         = ch_versions.mix( HIC_BWAMEM2.out.versions )
     mergedbam           = mergedbam.mix(HIC_BWAMEM2.out.mergedbam)

subworkflows/local/hic_minimap2.nf

@@ -10,6 +10,7 @@
 //
 include { CRAM_FILTER_MINIMAP2_FILTER5END_FIXMATE_SORT    } from '../../modules/local/cram_filter_minimap2_filter5end_fixmate_sort'
 include { SAMTOOLS_MERGE                                  } from '../../modules/nf-core/samtools/merge/main'
+include { SAMTOOLS_MERGE_OUTPUT_BAM                        } from '../../modules/nf-core/samtools/merge/main'
 include { MINIMAP2_INDEX                                   } from '../../modules/nf-core/minimap2/index/main'
 
 
@@ -19,6 +20,7 @@ workflow HIC_MINIMAP2 {
     reference_tuple     // Channel: tuple [ val(meta), path( file )      ]
     csv_ch
     reference_index
+    output_bam
 
     main:
     ch_versions         = Channel.empty()
@@ -83,20 +85,33 @@ workflow HIC_MINIMAP2 {
                 file
             )
         }
+        .branch{
+            output      : it[0].output_bam == "true"
+            no_output    : it[0].output_bam != "true"
+        }
         .set { collected_files_for_merge }
 
     //
     // MODULE: MERGE POSITION SORTED BAM FILES AND MARK DUPLICATES
     //
     SAMTOOLS_MERGE (
-        collected_files_for_merge,
+        collected_files_for_merge.no_output,
         reference_tuple,
         reference_index
     )
     ch_versions         = ch_versions.mix ( SAMTOOLS_MERGE.out.versions.first() )
+    ch_mergedbam       = SAMTOOLS_MERGE.out.bam
+
 
+    SAMTOOLS_MERGE_OUTPUT_BAM (
+        collected_files_for_merge.output,
+        reference_tuple,
+        reference_index
+    )
+    ch_versions        = ch_versions.mix ( SAMTOOLS_MERGE_OUTPUT_BAM.out.versions.first() )
+    ch_mergedbam       = ch_mergedbam.mix( SAMTOOLS_MERGE_OUTPUT_BAM.out.bam )
 
     emit:
-    mergedbam               = SAMTOOLS_MERGE.out.bam
+    mergedbam           = ch_mergedbam
     versions            = ch_versions.ifEmpty(null)
 }

subworkflows/local/yaml_input.nf

@@ -36,6 +36,7 @@ workflow YAML_INPUT {
                 busco_gene:             ( data.busco )
                 teloseq:                ( data.telomere )
                 map_order:              ( data.map_order)
+                output_bam:             ( data.output_bam)
         }
         .set{ group }
 
@@ -217,6 +218,7 @@ workflow YAML_INPUT {
     assembly_id                      = tolid_version
     reference_ch                     = ref_ch
     map_order_ch                     = group.map_order
+    output_bam_ch                    = group.output_bam
 
     read_ch                          = read_ch
 

workflows/treeval.nf

@@ -241,6 +241,7 @@ workflow TREEVAL {
         READ_COVERAGE.out.ch_covbw_avg,
         TELO_FINDER.out.bedgraph_file,
         REPEAT_DENSITY.out.repeat_density,
+        YAML_INPUT.out.output_bam_ch,
         params.entry
     )
     ch_versions     = ch_versions.mix( HIC_MAPPING.out.versions )

workflows/treeval_rapid.nf

@@ -121,6 +121,7 @@ workflow TREEVAL_RAPID {
         READ_COVERAGE.out.ch_covbw_avg,
         TELO_FINDER.out.bedgraph_file,
         REPEAT_DENSITY.out.repeat_density,
+        YAML_INPUT.out.output_bam_ch,
         params.entry
     )
     ch_versions     = ch_versions.mix( HIC_MAPPING.out.versions )

workflows/treeval_rapid_tol.nf

@@ -130,6 +130,7 @@ workflow TREEVAL_RAPID_TOL {
         READ_COVERAGE.out.ch_covbw_avg,
         TELO_FINDER.out.bedgraph_file,
         REPEAT_DENSITY.out.repeat_density,
+        YAML_INPUT.out.output_bam_ch,
         params.entry
     )
     ch_versions     = ch_versions.mix( HIC_MAPPING.out.versions )