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Add handling of output_bam param
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@weaglesBio
weaglesBio committed Aug 22, 2024
1 parent b7475b7 commit 20892da
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Showing 8 changed files with 53 additions and 7 deletions.
10 changes: 9 additions & 1 deletion conf/modules.config
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Original file line number Diff line number Diff line change
Expand Up @@ -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: { "${params.outdir}/hic_files" },
mode: params.publish_dir_mode,
Expand Down Expand Up @@ -366,6 +366,10 @@ process {
ext.prefix = { "${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 = ""
Expand All @@ -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" }
Expand Down
19 changes: 17 additions & 2 deletions subworkflows/local/hic_bwamem2.nf
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Expand Up @@ -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()
Expand Down Expand Up @@ -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)
}
7 changes: 5 additions & 2 deletions subworkflows/local/hic_mapping.nf
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Expand Up @@ -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:
Expand Down Expand Up @@ -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
Expand All @@ -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)
Expand Down
19 changes: 17 additions & 2 deletions subworkflows/local/hic_minimap2.nf
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Original file line number Diff line number Diff line change
Expand Up @@ -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'


Expand All @@ -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()
Expand Down Expand Up @@ -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)
}
2 changes: 2 additions & 0 deletions subworkflows/local/yaml_input.nf
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Expand Up @@ -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 }

Expand Down Expand Up @@ -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

Expand Down
1 change: 1 addition & 0 deletions workflows/treeval.nf
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Expand Up @@ -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 )
Expand Down
1 change: 1 addition & 0 deletions workflows/treeval_rapid.nf
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Expand Up @@ -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 )
Expand Down
1 change: 1 addition & 0 deletions workflows/treeval_rapid_tol.nf
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Original file line number Diff line number Diff line change
Expand Up @@ -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 )
Expand Down

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