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junjun-zhangjunjun-zhang
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Merge pull request #14 from icgc-argo/sanger-wxs-variant-calling@3.1.6-3.4.0
[release]
2 parents edb52a6 + 1e7c75c commit ab7b010

12 files changed

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‎example-params.json‎

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{
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"study_id": "TEST-PR",
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"tumour_aln_analysis_id": "03905962-f1e1-41e8-9059-62f1e1c1e8fc",
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"normal_aln_analysis_id": "9940db0f-c100-496a-80db-0fc100d96ac1",
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"max_retries": 3,
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"first_retry_wait_time": 5,
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"cleanup": true,
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"song_url": "https://song.rdpc-qa.cancercollaboratory.org",
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"score_url": "https://score.rdpc-qa.cancercollaboratory.org",
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"download": {
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"song_url": "https://song.rdpc-qa.cancercollaboratory.org",
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"song_cpus": 2,
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"song_mem": 2,
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"score_url": "https://score.rdpc-qa.cancercollaboratory.org",
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"score_cpus": 3,
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"score_mem": 8
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},
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"sangerWxsVariantCaller": {
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"cpus": 4,
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"mem": 10,
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"exclude": "chr1,chr2,chr3,chr4,chr5,chr6,chr7,chr8,chr9,chr10,chr11,chr12,chr13,chr14,chr15,chr16,chr17,chr18,chr19,chr20,chr22,chrX,chrY,chrUn%,HLA%,%_alt,%_random,chrM,chrEBV",
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"vagrent_annot": "/nfs-dev-1-vol-qa-1/reference/sanger-variant-calling/VAGrENT_ref_GRCh38_hla_decoy_ebv_ensembl_91.tar.gz",
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"ref_genome_tar": "/nfs-dev-1-vol-qa-1/reference/sanger-variant-calling/core_ref_GRCh38_hla_decoy_ebv.tar.gz",
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"ref_snv_indel_tar": "/nfs-dev-1-vol-qa-1/reference/sanger-variant-calling/SNV_INDEL_ref_GRCh38_hla_decoy_ebv-fragment.tar.gz"
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},
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"generateBas": {
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"cpus":2,
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"mem":8,
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"ref_genome_fa": "/nfs-dev-1-vol-qa-1/reference/GRCh38_hla_decoy_ebv/GRCh38_hla_decoy_ebv.fa"
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},
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"repackSangerResults": {
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"cpus": 2,
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"mem": 4
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},
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"cavemanVcfFix": {
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"cpus": 2,
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"mem": 4
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},
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"prepSangerSupplement": {
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"cpus": 2,
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"mem": 4
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},
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"prepSangerQc": {
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"cpus": 2,
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"mem": 4
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},
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"extractSangerCall": {
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"cpus": 2,
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"mem": 4
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},
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"payloadGenVariantCall": {
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"cpus": 2,
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"mem": 4
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},
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"uploadVariant": {
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"cpus": 2,
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"mem": 4
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}
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}

modules/raw.githubusercontent.com/icgc-argo/variant-calling-tools/prep-sanger-qc.0.1.2.0/tools/prep-sanger-qc/prep-sanger-qc.nf renamed to modules/raw.githubusercontent.com/icgc-argo/variant-calling-tools/prep-sanger-qc.0.1.3.0/tools/prep-sanger-qc/prep-sanger-qc.nf

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*/
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nextflow.preview.dsl = 2
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version = '0.1.2.0'
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version = '0.1.3.0'
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params.qc_files = ""
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params.publish_dir = ""
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params.container_version = ""
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params.cpus = 1
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params.mem = 2 // in GB
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process prepSangerQc {
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container "quay.io/icgc-argo/prep-sanger-qc:prep-sanger-qc.${params.container_version ?: version}"
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publishDir "${params.publish_dir}/${task.process.replaceAll(':', '_')}", mode: "copy", enabled: params.publish_dir
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cpus params.cpus
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memory "${params.mem} GB"
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‎sanger-wxs-variant-calling/main.nf‎

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nextflow.enable.dsl = 2
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name = 'sanger-wxs-variant-calling'
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short_name = 'sanger-wxs'
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version = '3.1.6-3.3.0'
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version = '3.1.6-3.4.0'
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/*
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include { repackSangerResults as repack } from './modules/raw.githubusercontent.com/icgc-argo/variant-calling-tools/repack-sanger-results.0.2.0.0/tools/repack-sanger-results/repack-sanger-results' params(repackSangerResults_params)
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include { cavemanVcfFix as cavemanFix } from './modules/raw.githubusercontent.com/icgc-argo/variant-calling-tools/caveman-vcf-fix.0.1.0.0/tools/caveman-vcf-fix/caveman-vcf-fix' params(cavemanVcfFix_params)
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include { prepSangerSupplement as prepSupp } from './modules/raw.githubusercontent.com/icgc-argo/variant-calling-tools/prep-sanger-supplement.0.1.2.0/tools/prep-sanger-supplement/prep-sanger-supplement' params(prepSangerSupplement_params)
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include { prepSangerQc as prepQc } from './modules/raw.githubusercontent.com/icgc-argo/variant-calling-tools/prep-sanger-qc.0.1.2.0/tools/prep-sanger-qc/prep-sanger-qc' params(prepSangerQc_params)
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include { prepSangerQc as prepQc } from './modules/raw.githubusercontent.com/icgc-argo/variant-calling-tools/prep-sanger-qc.0.1.3.0/tools/prep-sanger-qc/prep-sanger-qc' params(prepSangerQc_params)
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include { extractFilesFromTarball as extractVarSnv; extractFilesFromTarball as extractVarIndel; extractFilesFromTarball as extractQC } from './modules/raw.githubusercontent.com/icgc-argo/data-processing-utility-tools/extract-files-from-tarball.0.2.0.0/tools/extract-files-from-tarball/extract-files-from-tarball' params(extractSangerCall_params)
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include { payloadGenVariantCalling as pGenVarSnv; payloadGenVariantCalling as pGenVarIndel; payloadGenVariantCalling as pGenVarSupp; payloadGenVariantCalling as pGenQc } from "./modules/raw.githubusercontent.com/icgc-argo/data-processing-utility-tools/payload-gen-variant-calling.0.3.6.0/tools/payload-gen-variant-calling/payload-gen-variant-calling" params(payloadGenVariantCall_params)
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include { payloadGenVariantCalling as pGenVarSnv; payloadGenVariantCalling as pGenVarIndel; payloadGenVariantCalling as pGenVarSupp; payloadGenVariantCalling as pGenQc } from "./wfpr_modules/github.com/icgc-argo/data-processing-utility-tools/payload-gen-variant-calling@0.4.0/main" params(payloadGenVariantCall_params)
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include { SongScoreUpload as upSnv; SongScoreUpload as upIndel; SongScoreUpload as upQc; SongScoreUpload as upSupp} from './wfpr_modules/github.com/icgc-argo/nextflow-data-processing-utility-tools/song-score-upload@2.6.1/main.nf' params(upload_params)
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include { cleanupWorkdir as cleanup } from './wfpr_modules/github.com/icgc-argo/data-processing-utility-tools/cleanup-workdir@1.0.0/main'
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include { getSecondaryFiles } from './wfpr_modules/github.com/icgc-argo/data-processing-utility-tools/helper-functions@1.0.0/main'

‎sanger-wxs-variant-calling/pkg.json‎

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{
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"name": "sanger-wxs-variant-calling",
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"version": "3.1.6-3.3.0",
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"version": "3.1.6-3.4.0",
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"description": "ICGC ARGO Sanger WXS Variant Calling Workflow",
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"main": "main.nf",
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"deprecated": false,
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"url": "https://github.com/icgc-argo/sanger-wxs-variant-calling.git"
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},
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"dependencies": [
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"github.com/icgc-argo/data-processing-utility-tools/payload-gen-variant-calling@0.4.0",
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"github.com/icgc-argo/data-processing-utility-tools/payload-add-uniform-ids@0.1.1",
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"github.com/icgc-argo/data-processing-utility-tools/helper-functions@1.0.0",
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"github.com/icgc-argo/data-processing-utility-tools/cleanup-workdir@1.0.0",

‎sanger-wxs-variant-calling/tests/local-test-qa.nf.json‎

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../../example-params.json

‎wfpr_modules/github.com/icgc-argo/data-processing-utility-tools/payload-gen-variant-calling@0.4.0/.dockerignore‎

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.gitignore
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.nextflow*
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tests
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work
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outdir

‎wfpr_modules/github.com/icgc-argo/data-processing-utility-tools/payload-gen-variant-calling@0.4.0/Dockerfile‎

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FROM python:3.7.9
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LABEL org.opencontainers.image.source https://github.com/icgc-argo/data-processing-utility-tools
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RUN groupadd -g 1000 ubuntu && \
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useradd -l -u 1000 -g ubuntu ubuntu && \
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install -d -m 0755 -o ubuntu -g ubuntu /home/ubuntu
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ENV PATH="/tools:${PATH}"
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COPY *.py /tools/
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WORKDIR /tools
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USER ubuntu
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ENTRYPOINT ["/usr/bin/env"]
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CMD ["/bin/bash"]

modules/raw.githubusercontent.com/icgc-argo/data-processing-utility-tools/payload-gen-variant-calling.0.3.6.0/tools/payload-gen-variant-calling/payload-gen-variant-calling.nf renamed to wfpr_modules/github.com/icgc-argo/data-processing-utility-tools/payload-gen-variant-calling@0.4.0/main.nf

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* Author Junjun Zhang <junjun.zhang@oicr.on.ca>
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*/
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/********************************************************************/
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/* this block is auto-generated based on info from pkg.json where */
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/* changes can be made if needed, do NOT modify this block manually */
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nextflow.enable.dsl = 2
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version = '0.3.6.0'
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version = '0.4.0' // package version
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container = [
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'ghcr.io': 'ghcr.io/icgc-argo/data-processing-utility-tools.payload-gen-variant-calling'
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]
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default_container_registry = 'ghcr.io'
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/********************************************************************/
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// universal params go here
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params.container_registry = ""
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params.container_version = ""
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params.container = ""
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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.normal_analysis = ""
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params.tumour_analysis = ""
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params.files_to_upload = []
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params.wf_name = ""
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params.wf_short_name = ""
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params.wf_version = ""
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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 = ""
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process payloadGenVariantCalling {
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container "quay.io/icgc-argo/payload-gen-variant-calling:payload-gen-variant-calling.${params.container_version ?: version}"
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container "${params.container ?: container[params.container_registry ?: default_container_registry]}:${params.container_version ?: version}"
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cpus params.cpus
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memory "${params.mem} GB"
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publishDir "${params.publish_dir}/${task.process.replaceAll(':', '_')}", mode: "copy", enabled: "${params.publish_dir ? true : ''}"
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script:
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args_tumour_analysis = !tumour_analysis.empty() ? "-t ${tumour_analysis}" : ""
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"""
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payload-gen-variant-calling.py \
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main.py \
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-f ${files_to_upload} \
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-n ${normal_analysis} \
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-r ${workflow.runName} \
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-v ${wf_version} ${args_tumour_analysis}
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"""
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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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payloadGenVariantCalling(
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file(params.normal_analysis),
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file(params.tumour_analysis),
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Channel.fromPath(params.files_to_upload).collect(),
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params.wf_name,
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params.wf_short_name,
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params.wf_version
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)
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}

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