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Merge pull request icgc-argo-workflows#28 from ICGC-ARGO-Structural-Variation-CN-WG/facets-wf@0.2.0
Facets wf@0.2.0 [release]
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‎facets-wf/main.nf‎

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#!/usr/bin/env nextflow
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/*
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Copyright (c) 2021, ICGC-ARGO-Structural-Variation-CN-WG
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Permission is hereby granted, free of charge, to any person obtaining a copy
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of this software and associated documentation files (the "Software"), to deal
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in the Software without restriction, including without limitation the rights
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to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
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copies of the Software, and to permit persons to whom the Software is
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furnished to do so, subject to the following conditions:
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The above copyright notice and this permission notice shall be included in all
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copies or substantial portions of the Software.
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THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
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IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
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FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
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AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
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LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
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OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
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SOFTWARE.
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Authors:
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Andrej Benjak
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*/
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nextflow.enable.dsl = 2
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version = '0.2.0'
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// universal params go here, change default value as needed
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params.container = ""
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params.container_registry = ""
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params.container_version = ""
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params.cpus = 1
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params.mem = 1 // GB
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params.publish_dir = "" // set to empty string will disable publishDir
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// tool specific parmas go here, add / change as needed
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params.tumor = ""
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params.normal = ""
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params.dbsnp = "${baseDir}/resources/dbsnp_151.common.hg38.vcf.gz"
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params.ref = ""
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params.cleanup = true
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include { getSecondaryFiles; snpPileup } from './wfpr_modules/github.com/icgc-argo-structural-variation-cn-wg/icgc-argo-sv-copy-number/snp-pileup@0.3.1/main.nf' params([*:params, 'cleanup': false])
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include { facets } from './wfpr_modules/github.com/icgc-argo-structural-variation-cn-wg/icgc-argo-sv-copy-number/facets@0.4.1/main.nf' params([*:params, 'cleanup': false])
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// please update workflow code as needed
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workflow FacetsWf {
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take:
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tumor
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normal
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dbsnp
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ref
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ref_idx
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main:
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snpPileup(
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tumor,
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normal,
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dbsnp,
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ref,
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ref_idx
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)
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facets(
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snpPileup.out.output_file
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)
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emit:
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results = facets.out.facets_results
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}
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// this provides an entry point for this main script, so it can be run directly without clone the repo
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// using this command: nextflow run <git_acc>/<repo>/<pkg_name>/<main_script>.nf -r <pkg_name>.v<pkg_version> --params-file xxx
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workflow {
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FacetsWf(
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file(params.tumor),
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file(params.normal),
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file(params.dbsnp),
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file(params.ref),
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Channel.fromPath(getSecondaryFiles(params.ref, ['fai','gzi']), checkIfExists: false).collect(),
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)
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}

‎facets-wf/nextflow.config‎

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docker {
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enabled = true
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runOptions = '-u \$(id -u):\$(id -g)'
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}

‎facets-wf/pkg.json‎

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{
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"name": "facets-wf",
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"version": "0.2.0",
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"description": "facets workflow",
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"main": "main.nf",
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"deprecated": false,
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"keywords": [
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"cna",
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"purity",
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"ploidy"
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],
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"repository": {
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"type": "git",
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"url": "https://github.com/icgc-argo-structural-variation-cn-wg/icgc-argo-sv-copy-number.git"
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},
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"dependencies": [
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"github.com/icgc-argo-structural-variation-cn-wg/icgc-argo-sv-copy-number/snp-pileup@0.3.1",
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"github.com/icgc-argo-structural-variation-cn-wg/icgc-argo-sv-copy-number/facets@0.4.1"
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],
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"devDependencies": [],
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"contributors": [
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{
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"name": "Andrej Benjak",
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"email": "abenjak@gmail.com"
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}
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],
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"license": "MIT",
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"bugReport": "https://github.com/icgc-argo-structural-variation-cn-wg/icgc-argo-sv-copy-number/issues",
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"homepage": "https://github.com/icgc-argo-structural-variation-cn-wg/icgc-argo-sv-copy-number#readme"
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}

‎facets-wf/scripts/fetch_resources.sh‎

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mkdir -p $(dirname $0)/../resources
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# No "chr" prefix in contig names
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# wget -O $(dirname $0)/../resources/dbsnp_151.common.hg38.vcf.gz https://ftp.ncbi.nih.gov/snp/organisms/human_9606/VCF/00-common_all.vcf.gz
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# With "chr" prefix in contig names
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wget -O $(dirname $0)/../resources/dbsnp_151.common.hg38.vcf.gz "https://campuscloud.unibe.ch/rest/files/public/links/02dc8054785e096c0179d79a20382c09?passKey=-5889296840140272093&shareId=45112"
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echo -e "Checking file integrity.\n"
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if [ $(md5sum $(dirname $0)/../resources/dbsnp_151.common.hg38.vcf.gz | cut -f1 -d " ") = "e1050e1014c6726127c4d8d4278e2a6a" ]
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then
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echo "Checksum OK."
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else
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rm -f $(dirname $0)/resources/dbsnp_151.common.hg38.vcf.gz
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echo "Checksum failed. Try downloading again."
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fi

‎facets-wf/tests/checker.nf‎

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#!/usr/bin/env nextflow
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/*
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Copyright (c) 2021, ICGC-ARGO-Structural-Variation-CN-WG
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Permission is hereby granted, free of charge, to any person obtaining a copy
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of this software and associated documentation files (the "Software"), to deal
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in the Software without restriction, including without limitation the rights
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to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
10+
copies of the Software, and to permit persons to whom the Software is
11+
furnished to do so, subject to the following conditions:
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The above copyright notice and this permission notice shall be included in all
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copies or substantial portions of the Software.
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THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
17+
IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
18+
FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
19+
AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
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LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
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OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
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SOFTWARE.
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Authors:
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Andrej Benjak
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*/
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/*
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This is an auto-generated checker workflow to test the generated main template workflow, it's
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meant to illustrate how testing works. Please update to suit your own needs.
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*/
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nextflow.enable.dsl = 2
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version = '0.2.0'
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// universal params
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params.publish_dir = ""
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params.container = ""
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params.container_registry = ""
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params.container_version = ""
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// tool specific parmas go here, add / change as needed
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params.tumor = ""
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params.normal = ""
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params.dbsnp = ""
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params.ref = ""
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params.genome = ""
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params.out_prefix = ""
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params.expected_output = ""
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params.cleanup = false
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include { FacetsWf } from '../main'
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include { getSecondaryFiles } from '../wfpr_modules/github.com/icgc-argo/data-processing-utility-tools/helper-functions@1.0.1/main.nf'
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process file_smart_diff {
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input:
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path output_file
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path expected_file
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output:
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stdout()
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shell:
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'''
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tar -zxvf !{output_file} test.out
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diff $(basename -s .tgz !{output_file}).out !{expected_file} \
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&& ( echo "Test PASSED" && exit 0 ) || ( echo "Test FAILED, output file mismatch." && exit 1 )
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'''
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}
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workflow checker {
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take:
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tumor
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normal
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dbsnp
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ref
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ref_idx
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expected_output
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main:
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FacetsWf(
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tumor,
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normal,
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dbsnp,
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ref,
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ref_idx
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)
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file_smart_diff(
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FacetsWf.out.results,
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expected_output
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)
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}
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workflow {
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checker(
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file(params.tumor),
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file(params.normal),
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file(params.dbsnp),
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file(params.ref),
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Channel.fromPath(getSecondaryFiles(params.ref, ['fai','gzi']), checkIfExists: false).collect(),
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file(params.expected_output)
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)
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}

‎facets-wf/tests/expected/expected.out‎

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# Version = 0.6.1
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# Input = test_T.cram.bc.gz
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# tumor = test
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# snp.nbhd = 500
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# cval = 200
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# min.nhet = 25
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# genome = hg19
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# Purity = NA
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# Ploidy = 2
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# dipLogR = 0.001613941
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# dipt =
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# loglik =

‎facets-wf/tests/input/README.md‎

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This folder contains tiny data files for testing.

‎facets-wf/tests/input/test.chr17_1-100k.fasta.gz‎

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‎facets-wf/tests/input/test.chr17_1-100k.fasta.gz.fai‎

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17 100000 13 60 61

‎facets-wf/tests/input/test.chr17_1-100k.fasta.gz.gzi‎

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