Merge branch 'master' into new-module-gatk4/CalibrateDragstrModel

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nvnieuwk 2022-06-02 13:18:36 +02:00 committed by GitHub
commit eadab8e002
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4 changed files with 82 additions and 24 deletions

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@ -2,13 +2,15 @@ process DEEPTOOLS_BAMCOVERAGE {
tag "$meta.id" tag "$meta.id"
label 'process_low' label 'process_low'
conda (params.enable_conda ? "bioconda::deeptools=3.5.1" : null) conda (params.enable_conda ? "bioconda::deeptools=3.5.1 bioconda::samtools=1.15.1" : null)
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/deeptools:3.5.1--py_0': 'https://depot.galaxyproject.org/singularity/mulled-v2-eb9e7907c7a753917c1e4d7a64384c047429618a:2c687053c0252667cca265c9f4118f2c205a604c-0':
'quay.io/biocontainers/deeptools:3.5.1--py_0' }" 'quay.io/biocontainers/mulled-v2-eb9e7907c7a753917c1e4d7a64384c047429618a:2c687053c0252667cca265c9f4118f2c205a604c-0' }"
input: input:
tuple val(meta), path(input), path(input_index) tuple val(meta), path(input), path(input_index)
path(fasta)
path(fasta_fai)
output: output:
tuple val(meta), path("*.bigWig") , emit: bigwig, optional: true tuple val(meta), path("*.bigWig") , emit: bigwig, optional: true
@ -22,16 +24,44 @@ process DEEPTOOLS_BAMCOVERAGE {
def args = task.ext.args ?: '' def args = task.ext.args ?: ''
def prefix = task.ext.prefix ?: "${meta.id}.bigWig" def prefix = task.ext.prefix ?: "${meta.id}.bigWig"
""" // cram_input is currently not working with deeptools
bamCoverage \\ // therefore it's required to convert cram to bam first
--bam $input \\ def is_cram = input.Extension == "cram" ? true : false
$args \\ def input_out = is_cram ? input.BaseName + ".bam" : "${input}"
--numberOfProcessors ${task.cpus} \\ def fai_reference = fasta_fai ? "--fai-reference ${fasta_fai}" : ""
--outFileName ${prefix}
if (is_cram){
"""
samtools view -T $fasta $input $fai_reference -@ $task.cpus -o $input_out
samtools index -b $input_out -@ $task.cpus
bamCoverage \\
--bam $input_out \\
$args \\
--numberOfProcessors ${task.cpus} \\
--outFileName ${prefix}
cat <<-END_VERSIONS > versions.yml
"${task.process}":
samtools: \$(echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//')
deeptools: \$(bamCoverage --version | sed -e "s/bamCoverage //g")
END_VERSIONS
"""
}
else {
"""
bamCoverage \\
--bam $input_out \\
$args \\
--numberOfProcessors ${task.cpus} \\
--outFileName ${prefix}
cat <<-END_VERSIONS > versions.yml
"${task.process}":
deeptools: \$(bamCoverage --version | sed -e "s/bamCoverage //g")
END_VERSIONS
"""
}
cat <<-END_VERSIONS > versions.yml
"${task.process}":
deeptools: \$(bamCoverage --version | sed -e "s/bamCoverage //g")
END_VERSIONS
"""
} }

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@ -25,6 +25,14 @@ input:
type: file type: file
description: BAM/CRAM index file description: BAM/CRAM index file
pattern: "*.{bai,crai}" pattern: "*.{bai,crai}"
- fasta:
type: file
description: Reference file the CRAM file was created with (required with CRAM input)
pattern: "*.{fasta,fa}"
- fasta_fai:
type: file
description: Index of the reference file (optional, but recommended)
pattern: "*.{fai}"
output: output:
- meta: - meta:
@ -47,3 +55,4 @@ output:
authors: authors:
- "@FriederikeHanssen" - "@FriederikeHanssen"
- "@SusiJo"

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@ -12,7 +12,7 @@ workflow test_deeptools_bamcoverage_bam {
file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_bam_bai'], checkIfExists: true) file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_bam_bai'], checkIfExists: true)
] ]
DEEPTOOLS_BAMCOVERAGE ( input ) DEEPTOOLS_BAMCOVERAGE ( input, [], [] )
} }
workflow test_deeptools_bamcoverage_cram { workflow test_deeptools_bamcoverage_cram {
@ -22,6 +22,20 @@ workflow test_deeptools_bamcoverage_cram {
file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_cram'], checkIfExists: true), file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_cram'], checkIfExists: true),
file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_cram_crai'], checkIfExists: true) file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_cram_crai'], checkIfExists: true)
] ]
fasta = file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true)
fasta_fai = file(params.test_data['homo_sapiens']['genome']['genome_fasta_fai'], checkIfExists: true)
DEEPTOOLS_BAMCOVERAGE ( input ) DEEPTOOLS_BAMCOVERAGE ( input, fasta, fasta_fai)
}
workflow test_deeptools_bamcoverage_cram_no_fasta_fai {
input = [
[ id:'test', single_end:false ], // meta map
file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_cram'], checkIfExists: true),
file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_cram_crai'], checkIfExists: true)
]
fasta = file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true)
DEEPTOOLS_BAMCOVERAGE ( input, fasta, [])
} }

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@ -1,21 +1,26 @@
- name: deeptools bamcoverage test_deeptools_bamcoverage_bam - name: deeptools bamcoverage test_deeptools_bamcoverage_bam
command: nextflow run tests/modules/deeptools/bamcoverage -entry test_deeptools_bamcoverage_bam -c tests/config/nextflow.config command: nextflow run ./tests/modules/deeptools/bamcoverage -entry test_deeptools_bamcoverage_bam -c ./tests/config/nextflow.config -c ./tests/modules/deeptools/bamcoverage/nextflow.config
tags: tags:
- deeptools
- deeptools/bamcoverage - deeptools/bamcoverage
- deeptools
files: files:
- path: output/deeptools/test.bigWig - path: output/deeptools/test.bigWig
md5sum: 95fe9383a9e6c02aea6b785cf074274f md5sum: 95fe9383a9e6c02aea6b785cf074274f
- path: output/deeptools/versions.yml
md5sum: 68c94e73b7a8c0935578bad61fea54c1
- name: deeptools bamcoverage test_deeptools_bamcoverage_cram - name: deeptools bamcoverage test_deeptools_bamcoverage_cram
command: nextflow run tests/modules/deeptools/bamcoverage -entry test_deeptools_bamcoverage_cram -c tests/config/nextflow.config command: nextflow run ./tests/modules/deeptools/bamcoverage -entry test_deeptools_bamcoverage_cram -c ./tests/config/nextflow.config -c ./tests/modules/deeptools/bamcoverage/nextflow.config
tags: tags:
- deeptools
- deeptools/bamcoverage - deeptools/bamcoverage
- deeptools
files:
- path: output/deeptools/test.bigWig
md5sum: 95fe9383a9e6c02aea6b785cf074274f
- name: deeptools bamcoverage test_deeptools_bamcoverage_cram_no_fasta_fai
command: nextflow run ./tests/modules/deeptools/bamcoverage -entry test_deeptools_bamcoverage_cram_no_fasta_fai -c ./tests/config/nextflow.config -c ./tests/modules/deeptools/bamcoverage/nextflow.config
tags:
- deeptools/bamcoverage
- deeptools
files: files:
- path: output/deeptools/test.bigWig - path: output/deeptools/test.bigWig
md5sum: 95fe9383a9e6c02aea6b785cf074274f md5sum: 95fe9383a9e6c02aea6b785cf074274f
- path: output/deeptools/versions.yml
md5sum: 665bbd2979c49bf3974a24bd44a88e94