Add subsample and branch hic_mapping #192
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,43 @@ | ||
| process SUBSAMPLE_BAM { | ||
| tag "${meta.id}" | ||
| label 'process_tiny' | ||
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| conda "bioconda::samtools=1.17" | ||
| container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? | ||
| 'https://depot.galaxyproject.org/singularity/samtools:1.17--h00cdaf9_0' : | ||
| 'biocontainers/samtools:1.17--h00cdaf9_0' }" | ||
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| input: | ||
| tuple val(meta), path(mergedbam) | ||
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| output: | ||
| tuple val(meta), path('*.bam'), emit: subsampled_bam | ||
| path "versions.yml", emit: versions | ||
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| shell: | ||
| def prefix = task.ext.prefix ?: "${meta.id}" | ||
| ''' | ||
| percentage=`wc -c !{mergedbam} | cut -d$' ' -f1 | awk '{printf "%.2f\\n", 50000000000 / $0}'` | ||
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| if awk "BEGIN {exit !($percentage <= 1 )}"; then | ||
| samtools view -s $percentage -b !{mergedbam} > !{meta.id}_subsampled.bam | ||
| else | ||
| mv !{mergedbam} !{meta.id}_subsampled.bam | ||
| fi | ||
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| cat <<-END_VERSIONS > versions.yml | ||
| "!{task.process}": | ||
| samtools: \$(echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//' ) | ||
| END_VERSIONS | ||
| ''' | ||
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| stub: | ||
| """ | ||
| touch ${meta.id}_subsampled.bam | ||
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| cat <<-END_VERSIONS > versions.yml | ||
| "${task.process}": | ||
| samtools: \$(echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//' ) | ||
| END_VERSIONS | ||
| """ | ||
| } | ||
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,64 @@ | ||
| #!/usr/bin/env nextflow | ||
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| // This subworkflow takes converts .bam to .bed for the hic_mapping subworkflow. | ||
| // It runs markdup, sort and get paired contacts. | ||
| // Input - Assembled genomic fasta file, .bam file | ||
| // Output - sorted .bed and paired contact .bed | ||
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| // | ||
| // MODULE IMPORT BLOCK | ||
| // | ||
| include { SAMTOOLS_MARKDUP } from '../../modules/nf-core/samtools/markdup/main' | ||
| include { BAMTOBED_SORT } from '../../modules/local/bamtobed_sort.nf' | ||
| include { GET_PAIRED_CONTACT_BED } from '../../modules/local/get_paired_contact_bed' | ||
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| workflow HIC_BAMTOBED { | ||
| take: | ||
| bam_file // Channel: tuple [ val(meta), path( file ) ] | ||
| reference_tuple // Channel: tuple [ val(meta), path( file ) ] | ||
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| main: | ||
| ch_versions = Channel.empty() | ||
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| // | ||
| // LOGIC: PREPARE MARKDUP INPUT | ||
| // | ||
| bam_file | ||
| .combine( reference_tuple ) | ||
| .multiMap { meta_bam, bam_file, meta_ref, ref -> | ||
| bam : tuple(meta_bam, bam_file ) | ||
| reference : ref | ||
| } | ||
| .set { markdup_input } | ||
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| // | ||
| // MODULE: MERGE POSITION SORTED BAM FILES AND MARK DUPLICATES | ||
| // | ||
| SAMTOOLS_MARKDUP ( | ||
| markdup_input.bam, | ||
| markdup_input.reference | ||
| ) | ||
| ch_versions = ch_versions.mix ( SAMTOOLS_MARKDUP.out.versions ) | ||
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| // | ||
| // MODULE: SAMTOOLS FILTER OUT DUPLICATE READS | BAMTOBED | SORT BED FILE | ||
| // | ||
| BAMTOBED_SORT( | ||
| SAMTOOLS_MARKDUP.out.bam | ||
| ) | ||
| ch_versions = ch_versions.mix( BAMTOBED_SORT.out.versions ) | ||
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| // | ||
| // MODULE: GENERATE CONTACT PAIRS | ||
| // | ||
| GET_PAIRED_CONTACT_BED( | ||
| BAMTOBED_SORT.out.sorted_bed | ||
| ) | ||
| ch_versions = ch_versions.mix( GET_PAIRED_CONTACT_BED.out.versions ) | ||
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| emit: | ||
| paired_contacts_bed = GET_PAIRED_CONTACT_BED.out.bed | ||
| sorted_bed = BAMTOBED_SORT.out.sorted_bed | ||
| versions = ch_versions.ifEmpty(null) | ||
| } |
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${percentage}
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which to change? The one in the if is being removed. The samtools parameter is referencing a shell variable, whilst {mergedbam} is a nextflow.