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https://github.com/MillironX/nf-core_modules.git
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update tiddit/cov + more tests
This commit is contained in:
MaxUlysse
parent
36ffd4fbf7
commit
40996cdbe1
5 changed files with 66 additions and 25 deletions
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@ -2,17 +2,17 @@ process TIDDIT_COV {
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tag "$meta.id"
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label 'process_low'
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conda (params.enable_conda ? "bioconda::tiddit=2.12.1" : null)
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conda (params.enable_conda ? "bioconda::tiddit=3.0.0" : null)
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container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
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'https://depot.galaxyproject.org/singularity/tiddit:2.12.1--py38h1773678_0' :
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'quay.io/biocontainers/tiddit:2.12.1--py38h1773678_0' }"
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'https://depot.galaxyproject.org/singularity/tiddit:3.0.0--py39h59fae87_1' :
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'quay.io/biocontainers/tiddit:3.0.0--py39h59fae87_1' }"
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input:
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tuple val(meta), path(bam)
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tuple val(meta), path(input)
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path fasta
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output:
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tuple val(meta), path("*.tab"), optional: true, emit: cov
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tuple val(meta), path("*.bed"), optional: true, emit: cov
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tuple val(meta), path("*.wig"), optional: true, emit: wig
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path "versions.yml" , emit: versions
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@ -28,12 +28,12 @@ process TIDDIT_COV {
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--cov \\
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-o $prefix \\
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$args \\
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--bam $bam \\
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--bam $input \\
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$reference
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cat <<-END_VERSIONS > versions.yml
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"${task.process}":
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tiddit: \$(echo \$(tiddit 2>&1) | sed 's/^.*TIDDIT-//; s/ .*\$//')
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tiddit: \$(echo \$(tiddit 2>&1) | sed 's/^.*tiddit-//; s/ .*\$//')
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END_VERSIONS
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"""
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@ -45,7 +45,7 @@ process TIDDIT_COV {
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cat <<-END_VERSIONS > versions.yml
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"${task.process}":
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tiddit: \$(echo \$(tiddit 2>&1) | sed 's/^.*TIDDIT-//; s/ .*\$//')
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tiddit: \$(echo \$(tiddit 2>&1) | sed 's/^.*tiddit-//; s/ .*\$//')
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END_VERSIONS
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"""
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}
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@ -19,7 +19,7 @@ input:
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description: |
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Groovy Map containing sample information
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e.g. [ id:'test', single_end:false ]
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- bam:
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- input:
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type: file
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description: BAM/CRAM file
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pattern: "*.{bam,cram}"
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@ -2,22 +2,41 @@
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nextflow.enable.dsl = 2
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include { TIDDIT_COV } from '../../../../modules/tiddit/cov/main.nf'
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include { TIDDIT_COV as TIDDIT_COV_BED } from '../../../../modules/tiddit/cov/main.nf'
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include { TIDDIT_COV as TIDDIT_COV_WIG } from '../../../../modules/tiddit/cov/main.nf'
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workflow test_tiddit_cov {
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workflow test_tiddit_cov_cram_bed {
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input = [ [ id:'test', single_end:false ], // meta map
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file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_cram'], checkIfExists: true) ]
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fasta = file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true)
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TIDDIT_COV_BED ( input, fasta )
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}
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workflow test_tiddit_cov_bam_bed {
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input = [ [ id:'test', single_end:false ], // meta map
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file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true) ]
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fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
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TIDDIT_COV ( input, fasta )
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TIDDIT_COV_BED ( input, [] )
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}
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workflow test_tiddit_cov_no_ref {
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workflow test_tiddit_cov_cram_wig {
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input = [ [ id:'test', single_end:false ], // meta map
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file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_cram'], checkIfExists: true) ]
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fasta = file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true)
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TIDDIT_COV_WIG ( input, fasta )
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}
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workflow test_tiddit_cov_bam_wig {
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input = [ [ id:'test', single_end:false ], // meta map
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file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true) ]
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TIDDIT_COV ( input, [] )
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TIDDIT_COV_WIG ( input, [] )
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}
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@ -2,4 +2,8 @@ process {
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publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
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withName: TIDDIT_COV_WIG {
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ext.args = '-w'
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}
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}
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@ -1,17 +1,35 @@
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- name: tiddit cov test_tiddit_cov
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command: nextflow run ./tests/modules/tiddit/cov -entry test_tiddit_cov -c ./tests/config/nextflow.config -c ./tests/modules/tiddit/cov/nextflow.config
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- name: tiddit cov test_tiddit_cov_cram_bed
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command: nextflow run ./tests/modules/tiddit/cov -entry test_tiddit_cov_cram_bed -c ./tests/config/nextflow.config -c ./tests/modules/tiddit/cov/nextflow.config
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tags:
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- tiddit
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- tiddit/cov
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files:
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- path: output/tiddit/test.tab
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md5sum: f7974948f809f94879d8a60b726194f5
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- path: output/tiddit/test.bed
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md5sum: 3b1a28c62a5f25bbba77c1042e9abdf7
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- name: tiddit cov test_tiddit_cov_no_ref
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command: nextflow run ./tests/modules/tiddit/cov -entry test_tiddit_cov_no_ref -c ./tests/config/nextflow.config -c ./tests/modules/tiddit/cov/nextflow.config
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- name: tiddit cov test_tiddit_cov_bam_bed
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command: nextflow run ./tests/modules/tiddit/cov -entry test_tiddit_cov_bam_bed -c ./tests/config/nextflow.config -c ./tests/modules/tiddit/cov/nextflow.config
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tags:
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- tiddit
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- tiddit/cov
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files:
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- path: output/tiddit/test.tab
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md5sum: f7974948f809f94879d8a60b726194f5
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- path: output/tiddit/test.bed
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md5sum: 9d1474f1c7c6516205254077087bb026
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- name: tiddit cov test_tiddit_cov_cram_wig
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command: nextflow run ./tests/modules/tiddit/cov -entry test_tiddit_cov_cram_wig -c ./tests/config/nextflow.config -c ./tests/modules/tiddit/cov/nextflow.config
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tags:
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- tiddit
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- tiddit/cov
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files:
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- path: output/tiddit/test.wig
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md5sum: ca3645fd0c3491c86c075c91d16d57c4
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- name: tiddit cov test_tiddit_cov_bam_wig
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command: nextflow run ./tests/modules/tiddit/cov -entry test_tiddit_cov_bam_wig -c ./tests/config/nextflow.config -c ./tests/modules/tiddit/cov/nextflow.config
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tags:
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- tiddit
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- tiddit/cov
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files:
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- path: output/tiddit/test.wig
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md5sum: 44bea2ac6a56774738e65773065da670
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