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Merge branch 'main' into payload-add-uniform-ids@0.1.1.1
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‎.wfpm‎

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license: GNU Affero General Public License v3
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repo_type: git
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repo_server: github.com
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repo_account: icgc-argo
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repo_account: icgc-argo-workflows

‎README.md‎

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[![Build Status](https://travis-ci.org/icgc-argo/data-processing-utility-tools.svg?branch=master)](https://travis-ci.org/icgc-argo/data-processing-utility-tools)
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[![Build Status](https://travis-ci.org/icgc-argo-workflows/data-processing-utility-tools.svg?branch=master)](https://travis-ci.org/icgc-argo/data-processing-utility-tools)
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# Data processing utility tools
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This repository keeps a collect of data processing utility tools for ARGO analytic pipelines. All tools are defined using Nextflow workflow language.
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Every tool is self-sufficient, can be independently developed, tested, released and used. This clean isolation allows maximum flexibility, maintainability and portability.
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These tools are building blocks to create multi-step data analysis workflows as needed, like the
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workflows here: https://github.com/icgc-argo/dna-seq-processing-wfs and here: https://github.com/icgc-argo/variant-calling-wfs
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workflows here: https://github.com/icgc-argo-workflows/dna-seq-processing-wfs and here: https://github.com/icgc-argo-workflows/variant-calling-wfs
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## Development Process
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As tools are meant to be independent from each other, arguably a better choice is to

‎cleanup-workdir/Dockerfile‎

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FROM ubuntu:20.04
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LABEL org.opencontainers.image.source https://github.com/icgc-argo/data-processing-utility-tools
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LABEL org.opencontainers.image.source https://github.com/icgc-argo-workflows/data-processing-utility-tools
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RUN groupadd -g 1000 ubuntu && \
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useradd -l -u 1000 -g ubuntu ubuntu && \

‎cleanup-workdir/main.nf‎

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version = '1.0.0' // package version
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container = [
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'ghcr.io': 'ghcr.io/icgc-argo/data-processing-utility-tools.cleanup-workdir'
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'ghcr.io': 'ghcr.io/icgc-argo-workflows/data-processing-utility-tools.cleanup-workdir'
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]
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default_container_registry = 'ghcr.io'
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/********************************************************************/

‎cleanup-workdir/pkg.json‎

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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/data-processing-utility-tools.git"
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"url": "https://github.com/icgc-argo-workflows/data-processing-utility-tools.git"
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},
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"container": {
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"registries": [
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{
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"registry": "ghcr.io",
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"type": "docker",
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"org": "icgc-argo",
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"org": "icgc-argo-workflows",
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"default": true
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}
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]
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}
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],
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"license": "GNU Affero General Public License v3",
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"bugReport": "https://github.com/icgc-argo/data-processing-utility-tools/issues",
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"homepage": "https://github.com/icgc-argo/data-processing-utility-tools#readme"
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"bugReport": "https://github.com/icgc-argo-workflows/data-processing-utility-tools/issues",
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"homepage": "https://github.com/icgc-argo-workflows/data-processing-utility-tools#readme"
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}

‎cleanup-workdir/tests/files-exist.nf‎

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version = '1.0.0' // package version
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container = [
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'ghcr.io': 'ghcr.io/icgc-argo/data-processing-utility-tools.cleanup-workdir'
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'ghcr.io': 'ghcr.io/icgc-argo-workflows/data-processing-utility-tools.cleanup-workdir'
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]
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default_container_registry = 'ghcr.io'
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/********************************************************************/

‎cleanup-workdir/tests/generate-dummy-file.nf‎

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version = '1.0.0' // package version
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container = [
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'ghcr.io': 'ghcr.io/icgc-argo/data-processing-utility-tools.cleanup-workdir'
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'ghcr.io': 'ghcr.io/icgc-argo-workflows/data-processing-utility-tools.cleanup-workdir'
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]
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default_container_registry = 'ghcr.io'
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/********************************************************************/

‎helper-functions/Dockerfile‎

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FROM ubuntu:20.04
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LABEL org.opencontainers.image.source https://github.com/icgc-argo/data-processing-utility-tools
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LABEL org.opencontainers.image.source https://github.com/icgc-argo-workflows/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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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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USER ubuntu
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CMD ["/bin/bash"]

‎helper-functions/main.nf‎

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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 = '1.0.0' // package version
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version = '1.0.1'
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/********************************************************************/
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// this is kind of like CWL's secondary files
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def getSecondaryFiles(main_file, exts){
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if (!(main_file instanceof String)) {
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exit 1, "[getSecondaryFiles] param: main_file must be a string"
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}
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if (!(exts instanceof List)) {
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exit 1, "[getSecondaryFiles] param: exts must be a list of strings"
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}

‎helper-functions/pkg.json‎

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{
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"name": "helper-functions",
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"version": "1.0.0",
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"version": "1.0.1",
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"description": "A collection of helper functions",
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"main": "main.nf",
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"deprecated": false,
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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/data-processing-utility-tools.git"
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"url": "https://github.com/icgc-argo-workflows/data-processing-utility-tools.git"
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},
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"container": {
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"registries": [
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{
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"registry": "ghcr.io",
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"type": "docker",
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"org": "icgc-argo",
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"org": "icgc-argo-workflows",
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"default": true
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}
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]
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}
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],
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"license": "GNU Affero General Public License v3",
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"bugReport": "https://github.com/icgc-argo/data-processing-utility-tools/issues",
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"homepage": "https://github.com/icgc-argo/data-processing-utility-tools#readme"
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"bugReport": "https://github.com/icgc-argo-workflows/data-processing-utility-tools/issues",
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"homepage": "https://github.com/icgc-argo-workflows/data-processing-utility-tools#readme"
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}

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