Somalier relate (#2001)
* Working version of somalier relate * few changes * new changes * corrected test.yml * updated container paths and file paths * changed container and inputFile paths * changed left padding * requested changes * Update modules/somalier/relate/main.nf Co-authored-by: James A. Fellows Yates <jfy133@gmail.com> * Update modules/somalier/relate/main.nf Co-authored-by: James A. Fellows Yates <jfy133@gmail.com> * Update modules/somalier/relate/main.nf Co-authored-by: James A. Fellows Yates <jfy133@gmail.com> * Update modules/somalier/relate/main.nf Co-authored-by: James A. Fellows Yates <jfy133@gmail.com> * Update modules/somalier/relate/meta.yml Co-authored-by: James A. Fellows Yates <jfy133@gmail.com> * Update modules/somalier/relate/meta.yml Co-authored-by: James A. Fellows Yates <jfy133@gmail.com> * Update modules/somalier/relate/meta.yml Co-authored-by: James A. Fellows Yates <jfy133@gmail.com> * requested changes * requested changes Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>master
Ashot Margaryan
2 years ago
committed by
GitHub
parent
90aef30f43
commit
d8ba32c6b5
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process SOMALIER_RELATE {
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tag "$meta.id"
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label 'process_low'
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conda (params.enable_conda ? "bioconda::somalier=0.2.15" : null)
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container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
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'https://depot.galaxyproject.org/singularity/somalier:0.2.15--h37c5b7d_0':
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'quay.io/biocontainers/somalier:0.2.15--h37c5b7d_0' }"
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input:
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tuple val(meta), path(extract)
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path(sample_groups)
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path(ped)
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output:
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tuple val(meta), path("*.html"), emit: html
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tuple val(meta), path("*.pairs.tsv"), emit: pairs_tsv
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tuple val(meta), path("*.samples.tsv"), emit: samples_tsv
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path "versions.yml", emit: versions
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when:
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task.ext.when == null || task.ext.when
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script:
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def args = task.ext.args ?: ''
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def input_list = extract.collect{"$it"}.join(' ')
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def prefix = task.ext.prefix ?: "$meta.id"
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def sample_groups_command = sample_groups ? "-g $sample_groups" : ""
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def ped_command = ped ? "-p $ped" : ""
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"""
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somalier relate \\
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-o ${prefix} \\
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${input_list} \\
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${args} \\
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${sample_groups_command} \\
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${ped_command}
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cat <<-END_VERSIONS > versions.yml
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"${task.process}":
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somalier: \$(echo \$(somalier 2>&1) | sed 's/^.*somalier version: //; s/Commands:.*\$//')
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END_VERSIONS
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"""
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}
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name: "somalier_relate"
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description: Somalier can extract informative sites, evaluate relatedness, and perform quality-control on BAM/CRAM/BCF/VCF/GVCF or from jointly-called VCFs
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keywords:
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- relatedness
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- QC
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- bam
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- cram
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- vcf
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- gvcf
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- ancestry
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- identity
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- kinship
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- informative sites
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- family
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tools:
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- "somalier":
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description: "Somalier can extract informative sites, evaluate relatedness, and perform quality-control on BAM/CRAM/BCF/VCF/GVCF or from jointly-called VCFs"
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homepage: "https://github.com/brentp/somalier"
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documentation: "https://github.com/brentp/somalier/blob/master/README.md"
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tool_dev_url: "https://github.com/brentp/somalier"
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doi: "https://doi.org/10.1186/s13073-020-00761-2"
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licence: "MIT License"
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input:
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- meta:
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type: map
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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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- extract:
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type: file
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description: extract file from Somlaier extract
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pattern: "*.somalier"
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- sample_groups:
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type: file
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description: optional path to expected groups of samples such as tumor normal pairs specified as comma-separated groups per line
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pattern: "*.{txt,csv}"
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- ped:
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type: file
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description: optional path to a ped or fam file indicating the expected relationships among samples
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pattern: "*.{ped,fam}"
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output:
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- versions:
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type: file
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description: File containing software versions
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pattern: "versions.yml"
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- html:
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type: file
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description: html file
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pattern: "*.html"
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- pairs_tsv:
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type: file
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description: tsv file with output stats for pairs of samples
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pattern: "*.pairs.tsv"
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- samples_tsv:
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type: file
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description: tsv file with sample-level information
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pattern: "*.samples.tsv"
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authors:
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- "@ashotmarg"
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#!/usr/bin/env nextflow
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nextflow.enable.dsl = 2
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include { SOMALIER_RELATE } from '../../../../modules/somalier/relate/main.nf'
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workflow test_somalier_relate {
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input = [ [ id:'cohort', single_end:false ], // meta map
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[ file("https://github.com/nf-core/test-datasets/raw/modules/data/delete_me/somalier/normal.somalier", checkIfExists: true),
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file("https://github.com/nf-core/test-datasets/raw/modules/data/delete_me/somalier/tumour.somalier", checkIfExists: true) ]
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]
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SOMALIER_RELATE (input,[],[])
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}
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workflow test_somalier_relate_ped_groups {
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input = [ [ id:'cohort', single_end:false ], // meta map
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[ file("https://github.com/nf-core/test-datasets/raw/modules/data/delete_me/somalier/normal.somalier", checkIfExists: true),
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file("https://github.com/nf-core/test-datasets/raw/modules/data/delete_me/somalier/tumour.somalier", checkIfExists: true) ]
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]
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groups = file("https://github.com/nf-core/test-datasets/raw/modules/data/delete_me/somalier/groups.txt", checkIfExists: true)
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ped = file("https://github.com/nf-core/test-datasets/raw/modules/data/delete_me/somalier/family.ped", checkIfExists: true)
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SOMALIER_RELATE (input,groups,ped)
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}
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@ -0,0 +1,9 @@
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params.prefix = ""
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process {
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publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
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withName:SOMALIER_RELATE {
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ext.prefix = { params.prefix ? "${params.prefix}." : ""}
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}
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}
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@ -0,0 +1,25 @@
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- name: somalier relate test_somalier_relate
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command: nextflow run ./tests/modules/somalier/relate/main.nf -c ./tests/config/nextflow.config -c ./tests/modules/somalier/relate/nextflow.config -entry test_somalier_relate
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tags:
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- somalier/relate
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- somalier
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files:
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- path: output/somalier/cohort.html
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md5sum: 03cac9b2c67a8a06f63e07f83ee11e18
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- path: output/somalier/cohort.pairs.tsv
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md5sum: 54d1e9fca1bf9d747d4254c6fa98edcf
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- path: output/somalier/cohort.samples.tsv
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md5sum: 97257d88886db1325c4d7d10cefa7169
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- name: somalier relate test_somalier_relate_ped_groups
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command: nextflow run ./tests/modules/somalier/relate/main.nf -c ./tests/config/nextflow.config -c ./tests/modules/somalier/relate/nextflow.config -entry test_somalier_relate_ped_groups
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tags:
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- somalier/relate
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- somalier
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files:
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- path: output/somalier/cohort.html
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md5sum: 0d573016c9279ccdfdcfd4eb01d73b89
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- path: output/somalier/cohort.pairs.tsv
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md5sum: 8655714f1e5359329188e9f501168131
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- path: output/somalier/cohort.samples.tsv
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md5sum: 38ef93340e55fbeef47640abda9e48b0
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