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bedtools/genomecov updated to allow for providing a per-sample scale factor (#799)
* hifiasm copied from fastqc * hifiasm tests init from fastqc * meta.yml init; test.yml and main.nf for printing version * Add hifiasm version printing * Removed spaced on an empty line * Reverted hifiasm from main * Added genomecov scale module * Updated tagging * Removed extra module - began merging * Removed extra module tests * Updated genomecov to take a scale value * Updated line endings * Removed redundant test * Update tests/modules/bedtools/genomecov/main.nf Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> * Added checking for existing -bg arg * Update modules/bedtools/genomecov/main.nf Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> * Update modules/bedtools/genomecov/main.nf Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> Co-authored-by: Sviatoslav Sidorov <sviatoslav.sidorov@crick.ac.uk> Co-authored-by: Svyatoslav Sidorov <svet.sidorov@gmail.com> Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
This commit is contained in:
Chris Cheshire
GitHub
parent
1662201102
commit
e8b33e6eb1
4 changed files with 70 additions and 12 deletions
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@ -19,7 +19,7 @@ process BEDTOOLS_GENOMECOV {
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}
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input:
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tuple val(meta), path(intervals)
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tuple val(meta), path(intervals), val(scale)
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path sizes
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val extension
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@ -28,13 +28,21 @@ process BEDTOOLS_GENOMECOV {
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path "versions.yml" , emit: versions
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script:
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def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
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def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
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def args_token = options.args.tokenize()
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def args = options.args
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args += (scale > 0 && scale != 1) ? " -scale $scale" : ""
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if (!args_token.contains('-bg') && (scale > 0 && scale != 1)) {
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args += " -bg"
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}
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if (intervals.name =~ /\.bam/) {
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"""
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bedtools \\
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genomecov \\
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-ibam $intervals \\
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$options.args \\
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$args \\
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> ${prefix}.${extension}
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cat <<-END_VERSIONS > versions.yml
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@ -48,7 +56,7 @@ process BEDTOOLS_GENOMECOV {
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genomecov \\
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-i $intervals \\
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-g $sizes \\
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$options.args \\
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$args \\
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> ${prefix}.${extension}
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cat <<-END_VERSIONS > versions.yml
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@ -20,6 +20,9 @@ input:
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type: file
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description: BAM/BED/GFF/VCF
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pattern: "*.{bam|bed|gff|vcf}"
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- scale:
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type: value
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description: Number containing the scale factor for the output. Set to 1 to disable. Setting to a value other than 1 will also get the -bg bedgraph output format as this is required for this command switch
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- sizes:
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type: file
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description: Tab-delimited table of chromosome names in the first column and chromosome sizes in the second column
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@ -45,3 +48,4 @@ authors:
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- "@sruthipsuresh"
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- "@drpatelh"
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- "@sidorov-si"
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- "@chris-cheshire"
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@ -4,10 +4,37 @@ nextflow.enable.dsl = 2
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include { BEDTOOLS_GENOMECOV } from '../../../../modules/bedtools/genomecov/main.nf' addParams( options: [suffix: '_out'] )
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workflow test_bedtools_genomecov {
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workflow test_bedtools_genomecov_noscale {
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input = [
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[ id:'test'],
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file(params.test_data['sarscov2']['illumina']['test_paired_end_bam'], checkIfExists: true)
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file(params.test_data['sarscov2']['illumina']['test_paired_end_bam'], checkIfExists: true),
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1
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]
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sizes = []
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extension = 'txt'
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BEDTOOLS_GENOMECOV ( input, sizes, extension )
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}
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workflow test_bedtools_genomecov_nonbam_noscale {
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input = [
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[ id:'test'],
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file(params.test_data['sarscov2']['genome']['baits_bed'], checkIfExists: true),
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1
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]
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sizes = file(params.test_data['sarscov2']['genome']['genome_sizes'], checkIfExists: true)
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extension = 'txt'
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BEDTOOLS_GENOMECOV ( input, sizes, extension )
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}
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workflow test_bedtools_genomecov_scale {
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input = [
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[ id:'test'],
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file(params.test_data['sarscov2']['illumina']['test_paired_end_bam'], checkIfExists: true),
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0.5
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]
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sizes = file('dummy_chromosome_sizes')
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@ -16,10 +43,11 @@ workflow test_bedtools_genomecov {
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BEDTOOLS_GENOMECOV ( input, sizes, extension )
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}
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workflow test_bedtools_genomecov_nonbam {
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workflow test_bedtools_genomecov_nonbam_scale {
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input = [
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[ id:'test'],
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file(params.test_data['sarscov2']['genome']['baits_bed'], checkIfExists: true)
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file(params.test_data['sarscov2']['genome']['baits_bed'], checkIfExists: true),
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0.5
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]
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sizes = file(params.test_data['sarscov2']['genome']['genome_sizes'], checkIfExists: true)
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@ -1,5 +1,5 @@
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- name: bedtools genomecov test_bedtools_genomecov
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command: nextflow run ./tests/modules/bedtools/genomecov -entry test_bedtools_genomecov -c tests/config/nextflow.config
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- name: bedtools genomecov test_bedtools_genomecov_noscale
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command: nextflow run ./tests/modules/bedtools/genomecov -entry test_bedtools_genomecov_noscale -c tests/config/nextflow.config
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tags:
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- bedtools
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- bedtools/genomecov
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@ -7,11 +7,29 @@
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- path: output/bedtools/test_out.txt
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md5sum: 66083198daca6c001d328ba9616e9b53
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- name: bedtools genomecov test_bedtools_genomecov_nonbam
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command: nextflow run tests/modules/bedtools/genomecov -entry test_bedtools_genomecov_nonbam -c tests/config/nextflow.config
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- name: bedtools genomecov test_bedtools_genomecov_nonbam_noscale
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command: nextflow run tests/modules/bedtools/genomecov -entry test_bedtools_genomecov_nonbam_noscale -c tests/config/nextflow.config
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tags:
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- bedtools
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- bedtools/genomecov
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files:
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- path: output/bedtools/test_out.txt
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md5sum: f47b58840087426e5b643d8dfd155c1f
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- name: bedtools genomecov test_bedtools_genomecov_scale
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command: nextflow run ./tests/modules/bedtools/genomecov -entry test_bedtools_genomecov_scale -c tests/config/nextflow.config
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tags:
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- bedtools
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- bedtools/genomecov
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files:
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- path: output/bedtools/test_out.txt
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md5sum: 01291b6e1beab72e046653e709eb0e10
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- name: bedtools genomecov test_bedtools_genomecov_nonbam_scale
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command: nextflow run tests/modules/bedtools/genomecov -entry test_bedtools_genomecov_nonbam_scale -c tests/config/nextflow.config
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tags:
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- bedtools
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- bedtools/genomecov
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files:
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- path: output/bedtools/test_out.txt
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md5sum: de3c59c0ea123bcdbbad27bc0a0a601e
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