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https://github.com/MillironX/nf-core_modules.git
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Merge branch 'master' into haplocheck
This commit is contained in:
Taniguti
GitHub
commit
d037f0ec97
8 changed files with 58 additions and 15 deletions
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@ -9,7 +9,7 @@ process BCFTOOLS_ROH {
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input:
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tuple val(meta), path(vcf), path(tbi)
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path af_file
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tuple path(af_file), path(af_file_tbi)
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path genetic_map
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path regions_file
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path samples_file
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@ -23,6 +23,9 @@ input:
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- af_file:
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type: file
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description: "Read allele frequencies from a tab-delimited file containing the columns: CHROM\tPOS\tREF,ALT\tAF."
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- af_file_tbi:
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type: file
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description: "tbi index of af_file."
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- genetic_map:
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type: file
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description: "Genetic map in the format required also by IMPUTE2."
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@ -7,7 +7,8 @@ process MULTIQC {
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'quay.io/biocontainers/multiqc:1.12--pyhdfd78af_0' }"
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input:
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path multiqc_files
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path multiqc_files, stageAs: "?/*"
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tuple path(multiqc_config), path(multiqc_logo)
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output:
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path "*multiqc_report.html", emit: report
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@ -20,8 +21,13 @@ process MULTIQC {
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script:
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def args = task.ext.args ?: ''
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def config = multiqc_config ? "--config $multiqc_config" : ''
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"""
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multiqc -f $args .
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multiqc \\
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--force \\
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$config \\
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$args \\
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.
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cat <<-END_VERSIONS > versions.yml
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"${task.process}":
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@ -17,6 +17,14 @@ input:
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type: file
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description: |
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List of reports / files recognised by MultiQC, for example the html and zip output of FastQC
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- multiqc_config:
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type: file
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description: Config yml for MultiQC
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pattern: "*.{yml,yaml}"
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- multiqc_logo:
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type: file
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description: Logo file for MultiQC
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pattern: "*.{png}"
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output:
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- report:
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type: file
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@ -10,7 +10,7 @@ workflow test_bcftools_roh {
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file(params.test_data['sarscov2']['illumina']['test_vcf_gz'], checkIfExists: true),
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file(params.test_data['sarscov2']['illumina']['test_vcf_gz_tbi'], checkIfExists: true)]
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af_file = []
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af_file = [[],[]]
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gen_map = []
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regions = []
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targets = []
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@ -25,7 +25,7 @@ workflow test_bcftools_roh_stub {
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file(params.test_data['sarscov2']['illumina']['test_vcf_gz'], checkIfExists: true),
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file(params.test_data['sarscov2']['illumina']['test_vcf_gz_tbi'], checkIfExists: true)]
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af_file = []
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af_file = [[],[]]
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gen_map = []
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regions = []
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targets = []
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@ -2,15 +2,32 @@
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nextflow.enable.dsl = 2
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include { FASTQC } from '../../../modules/fastqc/main.nf'
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include { MULTIQC } from '../../../modules/multiqc/main.nf'
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include { FASTQC } from '../../../modules/fastqc/main.nf'
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include { FASTQC as FASTQC2 } from '../../../modules/fastqc/main.nf'
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include { MULTIQC } from '../../../modules/multiqc/main.nf'
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workflow test_multiqc {
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input = [ [ id: 'test', single_end: false ],
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[ file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true),
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file(params.test_data['sarscov2']['illumina']['test_2_fastq_gz'], checkIfExists: true) ]
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]
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input = [
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[ id: 'test', single_end: false ],
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[ file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true)]
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]
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FASTQC ( input )
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MULTIQC ( FASTQC.out.zip.collect { it[1] } )
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MULTIQC ( FASTQC.out.zip.collect { it[1] }, [[],[]] )
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}
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workflow test_multiqc_fn_collision {
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fqc_input = [
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[ id: 'test', single_end: false ],
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[ file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true)]
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]
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mqc_input = Channel.empty()
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FASTQC ( fqc_input )
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mqc_input = mqc_input.mix(FASTQC.out.zip.collect { it[1] })
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FASTQC2 ( fqc_input )
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mqc_input = mqc_input.mix(FASTQC2.out.zip.collect { it[1] })
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MULTIQC ( mqc_input, [[],[]] )
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}
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@ -1,5 +1,7 @@
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process {
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publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
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withName: "FASTQC*" {
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publishDir = [ enabled: false ]
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}
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}
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@ -1,5 +1,12 @@
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- name: multiqc
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command: nextflow run ./tests/modules/multiqc -entry test_multiqc -c ./tests/config/nextflow.config -c ./tests/modules/multiqc/nextflow.config
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- name: multiqc test_multiqc
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command: nextflow run ./tests/modules/multiqc -entry test_multiqc -c ./tests/config/nextflow.config -c ./tests/modules/multiqc/nextflow.config
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tags:
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- multiqc
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files:
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- path: output/multiqc/multiqc_report.html
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- name: multiqc test_multiqc_fn_collision
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command: nextflow run ./tests/modules/multiqc -entry test_multiqc_fn_collision -c ./tests/config/nextflow.config -c ./tests/modules/multiqc/nextflow.config
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tags:
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- multiqc
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files:
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