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Merge remote-tracking branch 'nf-core/master'
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commit
52adaac196
5 changed files with 39 additions and 13 deletions
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@ -13,15 +13,16 @@ process SEACR_CALLPEAK {
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mode: params.publish_dir_mode,
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mode: params.publish_dir_mode,
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saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:meta, publish_by_meta:['id']) }
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saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:meta, publish_by_meta:['id']) }
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conda (params.enable_conda ? "bioconda::seacr=1.3 conda-forge::r-base=4.0.2 bioconda::bedtools=2.29.2" : null)
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conda (params.enable_conda ? "bioconda::seacr=1.3 conda-forge::r-base=4.0.2 bioconda::bedtools=2.30.0" : null)
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if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
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if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
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container "https://depot.galaxyproject.org/singularity/mulled-v2-03bfeb32fe80910c231f630d4262b83677c8c0f4:5bb5ed4307a8187a7f34730b00431de93688fa59-0"
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container "https://depot.galaxyproject.org/singularity/mulled-v2-03bfeb32fe80910c231f630d4262b83677c8c0f4:f4bb19b68e66de27e4c64306f951d5ff11919931-0"
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} else {
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} else {
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container 'quay.io/biocontainers/mulled-v2-03bfeb32fe80910c231f630d4262b83677c8c0f4:5bb5ed4307a8187a7f34730b00431de93688fa59-0'
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container 'quay.io/biocontainers/mulled-v2-03bfeb32fe80910c231f630d4262b83677c8c0f4:f4bb19b68e66de27e4c64306f951d5ff11919931-0'
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}
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}
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input:
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input:
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tuple val(meta), path(bedgraph), path(ctrlbedgraph)
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tuple val(meta), path(bedgraph), path(ctrlbedgraph)
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val (threshold)
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output:
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output:
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tuple val(meta), path("*.bed"), emit: bed
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tuple val(meta), path("*.bed"), emit: bed
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@ -29,13 +30,13 @@ process SEACR_CALLPEAK {
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script:
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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 function_switch = ctrlbedgraph ? "$ctrlbedgraph" : "$threshold"
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"""
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"""
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SEACR_1.3.sh \\
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SEACR_1.3.sh \\
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$bedgraph \\
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$bedgraph \\
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$ctrlbedgraph \\
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$function_switch \\
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$options.args \\
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$options.args \\
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$prefix
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$prefix
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cat <<-END_VERSIONS > versions.yml
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cat <<-END_VERSIONS > versions.yml
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${getProcessName(task.process)}:
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${getProcessName(task.process)}:
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${getSoftwareName(task.process)}: \$(echo $VERSION)
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${getSoftwareName(task.process)}: \$(echo $VERSION)
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@ -1,3 +1,4 @@
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name: seacr_callpeak
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name: seacr_callpeak
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description: Call peaks using SEACR on sequenced reads in bedgraph format
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description: Call peaks using SEACR on sequenced reads in bedgraph format
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keywords:
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keywords:
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@ -30,6 +31,10 @@ input:
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type: file
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type: file
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description: |
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description: |
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Control (IgG) data bedgraph file to generate an empirical threshold for peak calling.
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Control (IgG) data bedgraph file to generate an empirical threshold for peak calling.
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- threshold:
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type: value
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description: |
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Threshold value used to call peaks if the ctrlbedgraph input is set to []. Set to 1 if using a control bedgraph
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output:
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output:
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- meta:
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- meta:
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type: map
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type: map
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@ -200,6 +200,9 @@ params {
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test_yak = "${test_data_dir}/genomics/homo_sapiens/illumina/yak/test.yak"
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test_yak = "${test_data_dir}/genomics/homo_sapiens/illumina/yak/test.yak"
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test2_yak = "${test_data_dir}/genomics/homo_sapiens/illumina/yak/test2.yak"
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test2_yak = "${test_data_dir}/genomics/homo_sapiens/illumina/yak/test2.yak"
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cutandrun_bedgraph_test_1 = "${test_data_dir}/genomics/homo_sapiens/illumina/bedgraph/cutandtag_h3k27me3_test_1.bedGraph"
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cutandrun_bedgraph_test_2 = "${test_data_dir}/genomics/homo_sapiens/illumina/bedgraph/cutandtag_igg_test_1.bedGraph"
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}
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}
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'pacbio' {
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'pacbio' {
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primers = "${test_data_dir}/genomics/homo_sapiens/pacbio/fasta/primers.fasta"
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primers = "${test_data_dir}/genomics/homo_sapiens/pacbio/fasta/primers.fasta"
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@ -5,11 +5,19 @@ nextflow.enable.dsl = 2
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include { SEACR_CALLPEAK } from '../../../../modules/seacr/callpeak/main.nf' addParams( options: [ args:'norm stringent' ] )
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include { SEACR_CALLPEAK } from '../../../../modules/seacr/callpeak/main.nf' addParams( options: [ args:'norm stringent' ] )
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workflow test_seacr_callpeak {
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workflow test_seacr_callpeak {
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input = [
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input = [ [ id:'test_1'],
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[ id:'test_1'],
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file(params.test_data['homo_sapiens']['illumina']['cutandrun_bedgraph_test_1'], checkIfExists: true),
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file("https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/delete_me/bedgraph/K27me3_1_to_chr20.bedgraph", checkIfExists: true),
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file(params.test_data['homo_sapiens']['illumina']['cutandrun_bedgraph_test_2'], checkIfExists: true)
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file("https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/delete_me/bedgraph/IgG_1_to_chr20.bedgraph", checkIfExists: true)
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]
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]
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SEACR_CALLPEAK ( input )
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SEACR_CALLPEAK ( input, 0.05 )
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}
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workflow test_seacr_callpeak_threshold {
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input = [ [ id:'test_1'],
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file(params.test_data['homo_sapiens']['illumina']['cutandrun_bedgraph_test_1'], checkIfExists: true),
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[]
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]
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SEACR_CALLPEAK ( input, 0.05 )
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}
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}
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@ -5,4 +5,13 @@
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- seacr/callpeak
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- seacr/callpeak
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files:
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files:
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- path: output/seacr/test_1.stringent.bed
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- path: output/seacr/test_1.stringent.bed
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md5sum: 3ac70475669eb6a7b8ca89e19a08a28e
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md5sum: a3cb0c7c4ffa895788da3f0d6371b7df
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- name: seacr callpeak threshold
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command: nextflow run ./tests/modules/seacr/callpeak -entry test_seacr_callpeak_threshold -c tests/config/nextflow.config
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tags:
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- seacr
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- seacr/callpeak
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files:
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- path: output/seacr/test_1.stringent.bed
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md5sum: 1d23015c7087f7b48cc3139d53fd3463
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