mirror of
https://github.com/MillironX/nf-core_modules.git
synced 2024-12-22 02:58:17 +00:00
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
|
|
@ -19,7 +19,7 @@ process BEDTOOLS_GENOMECOV {
|
|||
}
|
||||
|
||||
input:
|
||||
tuple val(meta), path(intervals)
|
||||
tuple val(meta), path(intervals), val(scale)
|
||||
path sizes
|
||||
val extension
|
||||
|
||||
|
|
@ -28,13 +28,21 @@ process BEDTOOLS_GENOMECOV {
|
|||
path "versions.yml" , emit: versions
|
||||
|
||||
script:
|
||||
def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
|
||||
def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
|
||||
def args_token = options.args.tokenize()
|
||||
def args = options.args
|
||||
args += (scale > 0 && scale != 1) ? " -scale $scale" : ""
|
||||
|
||||
if (!args_token.contains('-bg') && (scale > 0 && scale != 1)) {
|
||||
args += " -bg"
|
||||
}
|
||||
|
||||
if (intervals.name =~ /\.bam/) {
|
||||
"""
|
||||
bedtools \\
|
||||
genomecov \\
|
||||
-ibam $intervals \\
|
||||
$options.args \\
|
||||
$args \\
|
||||
> ${prefix}.${extension}
|
||||
|
||||
cat <<-END_VERSIONS > versions.yml
|
||||
|
|
@ -48,7 +56,7 @@ process BEDTOOLS_GENOMECOV {
|
|||
genomecov \\
|
||||
-i $intervals \\
|
||||
-g $sizes \\
|
||||
$options.args \\
|
||||
$args \\
|
||||
> ${prefix}.${extension}
|
||||
|
||||
cat <<-END_VERSIONS > versions.yml
|
||||
|
|
|
|||
|
|
@ -20,6 +20,9 @@ input:
|
|||
type: file
|
||||
description: BAM/BED/GFF/VCF
|
||||
pattern: "*.{bam|bed|gff|vcf}"
|
||||
- scale:
|
||||
type: value
|
||||
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
|
||||
- sizes:
|
||||
type: file
|
||||
description: Tab-delimited table of chromosome names in the first column and chromosome sizes in the second column
|
||||
|
|
@ -45,3 +48,4 @@ authors:
|
|||
- "@sruthipsuresh"
|
||||
- "@drpatelh"
|
||||
- "@sidorov-si"
|
||||
- "@chris-cheshire"
|
||||
|
|
|
|||
|
|
@ -4,10 +4,37 @@ nextflow.enable.dsl = 2
|
|||
|
||||
include { BEDTOOLS_GENOMECOV } from '../../../../modules/bedtools/genomecov/main.nf' addParams( options: [suffix: '_out'] )
|
||||
|
||||
workflow test_bedtools_genomecov {
|
||||
workflow test_bedtools_genomecov_noscale {
|
||||
input = [
|
||||
[ id:'test'],
|
||||
file(params.test_data['sarscov2']['illumina']['test_paired_end_bam'], checkIfExists: true)
|
||||
file(params.test_data['sarscov2']['illumina']['test_paired_end_bam'], checkIfExists: true),
|
||||
1
|
||||
]
|
||||
|
||||
sizes = []
|
||||
extension = 'txt'
|
||||
|
||||
BEDTOOLS_GENOMECOV ( input, sizes, extension )
|
||||
}
|
||||
|
||||
workflow test_bedtools_genomecov_nonbam_noscale {
|
||||
input = [
|
||||
[ id:'test'],
|
||||
file(params.test_data['sarscov2']['genome']['baits_bed'], checkIfExists: true),
|
||||
1
|
||||
]
|
||||
|
||||
sizes = file(params.test_data['sarscov2']['genome']['genome_sizes'], checkIfExists: true)
|
||||
extension = 'txt'
|
||||
|
||||
BEDTOOLS_GENOMECOV ( input, sizes, extension )
|
||||
}
|
||||
|
||||
workflow test_bedtools_genomecov_scale {
|
||||
input = [
|
||||
[ id:'test'],
|
||||
file(params.test_data['sarscov2']['illumina']['test_paired_end_bam'], checkIfExists: true),
|
||||
0.5
|
||||
]
|
||||
|
||||
sizes = file('dummy_chromosome_sizes')
|
||||
|
|
@ -16,10 +43,11 @@ workflow test_bedtools_genomecov {
|
|||
BEDTOOLS_GENOMECOV ( input, sizes, extension )
|
||||
}
|
||||
|
||||
workflow test_bedtools_genomecov_nonbam {
|
||||
workflow test_bedtools_genomecov_nonbam_scale {
|
||||
input = [
|
||||
[ id:'test'],
|
||||
file(params.test_data['sarscov2']['genome']['baits_bed'], checkIfExists: true)
|
||||
file(params.test_data['sarscov2']['genome']['baits_bed'], checkIfExists: true),
|
||||
0.5
|
||||
]
|
||||
|
||||
sizes = file(params.test_data['sarscov2']['genome']['genome_sizes'], checkIfExists: true)
|
||||
|
|
|
|||
|
|
@ -1,5 +1,5 @@
|
|||
- name: bedtools genomecov test_bedtools_genomecov
|
||||
command: nextflow run ./tests/modules/bedtools/genomecov -entry test_bedtools_genomecov -c tests/config/nextflow.config
|
||||
- name: bedtools genomecov test_bedtools_genomecov_noscale
|
||||
command: nextflow run ./tests/modules/bedtools/genomecov -entry test_bedtools_genomecov_noscale -c tests/config/nextflow.config
|
||||
tags:
|
||||
- bedtools
|
||||
- bedtools/genomecov
|
||||
|
|
@ -7,11 +7,29 @@
|
|||
- path: output/bedtools/test_out.txt
|
||||
md5sum: 66083198daca6c001d328ba9616e9b53
|
||||
|
||||
- name: bedtools genomecov test_bedtools_genomecov_nonbam
|
||||
command: nextflow run tests/modules/bedtools/genomecov -entry test_bedtools_genomecov_nonbam -c tests/config/nextflow.config
|
||||
- name: bedtools genomecov test_bedtools_genomecov_nonbam_noscale
|
||||
command: nextflow run tests/modules/bedtools/genomecov -entry test_bedtools_genomecov_nonbam_noscale -c tests/config/nextflow.config
|
||||
tags:
|
||||
- bedtools
|
||||
- bedtools/genomecov
|
||||
files:
|
||||
- path: output/bedtools/test_out.txt
|
||||
md5sum: f47b58840087426e5b643d8dfd155c1f
|
||||
|
||||
- name: bedtools genomecov test_bedtools_genomecov_scale
|
||||
command: nextflow run ./tests/modules/bedtools/genomecov -entry test_bedtools_genomecov_scale -c tests/config/nextflow.config
|
||||
tags:
|
||||
- bedtools
|
||||
- bedtools/genomecov
|
||||
files:
|
||||
- path: output/bedtools/test_out.txt
|
||||
md5sum: 01291b6e1beab72e046653e709eb0e10
|
||||
|
||||
- name: bedtools genomecov test_bedtools_genomecov_nonbam_scale
|
||||
command: nextflow run tests/modules/bedtools/genomecov -entry test_bedtools_genomecov_nonbam_scale -c tests/config/nextflow.config
|
||||
tags:
|
||||
- bedtools
|
||||
- bedtools/genomecov
|
||||
files:
|
||||
- path: output/bedtools/test_out.txt
|
||||
md5sum: de3c59c0ea123bcdbbad27bc0a0a601e
|
||||
|
|
|
|||
Loading…
Reference in a new issue