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Merge pull request #3 from ICGC-TCGA-PanCancer/my-wf-2@0.1.1
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*.py[cod] | ||
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# C extensions | ||
*.so | ||
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# Packages | ||
*.egg | ||
*.egg-info | ||
dist | ||
build | ||
eggs | ||
.eggs | ||
parts | ||
bin | ||
var | ||
sdist | ||
develop-eggs | ||
.installed.cfg | ||
lib | ||
lib64 | ||
venv*/ | ||
pyvenv*/ | ||
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# Installer logs | ||
pip-log.txt | ||
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||
# Unit test / coverage reports | ||
.coverage | ||
.tox | ||
.coverage.* | ||
nosetests.xml | ||
coverage.xml | ||
htmlcov | ||
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||
# Translations | ||
*.mo | ||
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||
# Mr Developer | ||
.mr.developer.cfg | ||
.project | ||
.pydevproject | ||
.idea | ||
*.iml | ||
*.komodoproject | ||
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||
# Complexity | ||
output/*.html | ||
output/*/index.html | ||
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# Sphinx | ||
docs/_build | ||
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||
.DS_Store | ||
*~ | ||
.*.sw[po] | ||
.build | ||
.ve | ||
.env | ||
.cache | ||
.pytest | ||
.bootstrap | ||
.appveyor.token | ||
*.bak | ||
*.log | ||
.vscode | ||
.python-version | ||
.nextflow* | ||
work | ||
outdir |
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#!/usr/bin/env nextflow | ||
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nextflow.enable.dsl = 2 | ||
version = '0.1.1' // tool version | ||
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// universal params go here, change default value as needed | ||
params.container_version = "" | ||
params.cpus = 1 | ||
params.mem = 1 // GB | ||
params.publish_dir = "" // set to empty string will disable publishDir | ||
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// tool specific parmas go here, add / change as needed | ||
params.input_file = "" | ||
params.output_pattern = "*.html" // fastqc output html report | ||
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include { fastqc } from "./wfpr_modules/github.com/icgc-tcga-pancancer/awesome-wfpkgs1/fastqc@0.1.0/fastqc" | ||
include { cleanupWorkdir as cleanup } from "./wfpr_modules/github.com/icgc-argo/demo-wfpkgs/demo-utils@1.1.0/main" | ||
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workflow MyWf2 { | ||
take: // input, make update as needed | ||
input_file | ||
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main: | ||
fastqc(input_file) | ||
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cleanup(fastqc.out, true) | ||
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emit: | ||
output_file = fastqc.out.output | ||
} |
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docker { | ||
enabled = true | ||
runOptions = '-u \$(id -u):\$(id -g)' | ||
} |
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{ | ||
"name": "my-wf-2", | ||
"version": "0.1.1", | ||
"description": "FastQC workflow", | ||
"main": "my-wf-2", | ||
"scripts": { | ||
"test": "wfpm test" | ||
}, | ||
"deprecated": false, | ||
"keywords": [ | ||
"bioinformatics", | ||
"seq", | ||
"qc metrics" | ||
], | ||
"repository": { | ||
"type": "git", | ||
"url": "https://github.com/icgc-tcga-pancancer/demo-wfs.git" | ||
}, | ||
"dependencies": [ | ||
"github.com/icgc-tcga-pancancer/demo-wfs/my-wf-1@0.1.0" | ||
], | ||
"devDependencies": [], | ||
"contributors": [ | ||
{ | ||
"name": "Junjun Zhang", | ||
"email": "junjun.zhang@oicr.on.ca" | ||
} | ||
], | ||
"license": "MIT", | ||
"bugReport": "https://github.com/icgc-tcga-pancancer/demo-wfs/issues", | ||
"homepage": "https://github.com/icgc-tcga-pancancer/demo-wfs#readme" | ||
} |
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#!/usr/bin/env nextflow | ||
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/* | ||
This is an auto-generated checker workflow, please update as needed | ||
*/ | ||
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nextflow.enable.dsl = 2 | ||
version = '0.1.1' // tool version | ||
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// universal params | ||
params.publish_dir = "" | ||
params.container_version = "" | ||
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// tool specific parmas go here, add / change as needed | ||
params.input_file = "" | ||
params.expected_output = "" | ||
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include { MyWf2 } from '../my-wf-2' | ||
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Channel | ||
.fromPath(params.input_file, checkIfExists: true) | ||
.set { input_file } | ||
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process file_diff { | ||
input: | ||
path output_file | ||
path expected_gzip | ||
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output: | ||
stdout() | ||
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script: | ||
""" | ||
# remove date field before comparison eg, <div id="header_filename">Tue 19 Jan 2021<br/>test_rg_3.bam</div> | ||
# sed -e 's#"header_filename">.*<br/>test_rg_3.bam#"header_filename"><br/>test_rg_3.bam</div>#' | ||
diff <( cat ${output_file} | sed -e 's#"header_filename">.*<br/>test_rg_3.bam#"header_filename"><br/>test_rg_3.bam</div>#' ) \ | ||
<( gunzip -c ${expected_gzip} | sed -e 's#"header_filename">.*<br/>test_rg_3.bam#"header_filename"><br/>test_rg_3.bam</div>#' ) \ | ||
&& ( echo "Test PASSED" && exit 0 ) || ( echo "Test FAILED, output file mismatch." && exit 1 ) | ||
""" | ||
} | ||
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workflow checker { | ||
take: | ||
input_file | ||
expected_output | ||
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main: | ||
MyWf2( | ||
input_file | ||
) | ||
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file_diff( | ||
MyWf2.out.output_file, | ||
expected_output | ||
) | ||
} | ||
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workflow { | ||
checker( | ||
file(params.input_file), | ||
file(params.expected_output) | ||
) | ||
} |
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The input file name is README.md |
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This folder contains tiny data files for testing. |
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includeConfig '../nextflow.config' |
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{ | ||
"input_file": "input/test_rg_3.bam", | ||
"expected_output": "expected/expected.test_rg_3_fastqc.out.gz", | ||
"publish_dir": "outdir", | ||
"cpus": 1, | ||
"mem": 0.5 | ||
} |
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../wfpr_modules |
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../wfpr_modules |
69 changes: 69 additions & 0 deletions
69
wfpr_modules/github.com/icgc-tcga-pancancer/demo-wfs/my-wf-1@0.1.0/.gitignore
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*.py[cod] | ||
|
||
# C extensions | ||
*.so | ||
|
||
# Packages | ||
*.egg | ||
*.egg-info | ||
dist | ||
build | ||
eggs | ||
.eggs | ||
parts | ||
bin | ||
var | ||
sdist | ||
develop-eggs | ||
.installed.cfg | ||
lib | ||
lib64 | ||
venv*/ | ||
pyvenv*/ | ||
|
||
# Installer logs | ||
pip-log.txt | ||
|
||
# Unit test / coverage reports | ||
.coverage | ||
.tox | ||
.coverage.* | ||
nosetests.xml | ||
coverage.xml | ||
htmlcov | ||
|
||
# Translations | ||
*.mo | ||
|
||
# Mr Developer | ||
.mr.developer.cfg | ||
.project | ||
.pydevproject | ||
.idea | ||
*.iml | ||
*.komodoproject | ||
|
||
# Complexity | ||
output/*.html | ||
output/*/index.html | ||
|
||
# Sphinx | ||
docs/_build | ||
|
||
.DS_Store | ||
*~ | ||
.*.sw[po] | ||
.build | ||
.ve | ||
.env | ||
.cache | ||
.pytest | ||
.bootstrap | ||
.appveyor.token | ||
*.bak | ||
*.log | ||
.vscode | ||
.python-version | ||
.nextflow* | ||
work | ||
outdir |
31 changes: 31 additions & 0 deletions
31
wfpr_modules/github.com/icgc-tcga-pancancer/demo-wfs/my-wf-1@0.1.0/my-wf-1.nf
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Original file line number | Diff line number | Diff line change |
---|---|---|
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#!/usr/bin/env nextflow | ||
|
||
nextflow.enable.dsl = 2 | ||
version = '0.1.0' // tool version | ||
|
||
// universal params go here, change default value as needed | ||
params.container_version = "" | ||
params.cpus = 1 | ||
params.mem = 1 // GB | ||
params.publish_dir = "" // set to empty string will disable publishDir | ||
|
||
// tool specific parmas go here, add / change as needed | ||
params.input_file = "" | ||
params.output_pattern = "*.html" // fastqc output html report | ||
|
||
include { fastqc } from "./wfpr_modules/github.com/icgc-tcga-pancancer/awesome-wfpkgs1/fastqc@0.1.0/fastqc" | ||
include { cleanupWorkdir as cleanup } from "./wfpr_modules/github.com/icgc-argo/demo-wfpkgs/demo-utils@1.1.0/main" | ||
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||
|
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workflow MyWf1 { | ||
take: // input, make update as needed | ||
input_file | ||
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||
main: | ||
fastqc(input_file) | ||
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cleanup(fastqc.out, true) | ||
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emit: | ||
output_file = fastqc.out.output | ||
} |
4 changes: 4 additions & 0 deletions
4
wfpr_modules/github.com/icgc-tcga-pancancer/demo-wfs/my-wf-1@0.1.0/nextflow.config
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docker { | ||
enabled = true | ||
runOptions = '-u \$(id -u):\$(id -g)' | ||
} |
33 changes: 33 additions & 0 deletions
33
wfpr_modules/github.com/icgc-tcga-pancancer/demo-wfs/my-wf-1@0.1.0/pkg.json
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{ | ||
"name": "my-wf-1", | ||
"version": "0.1.0", | ||
"description": "FastQC workflow", | ||
"main": "my-wf-1", | ||
"scripts": { | ||
"test": "wfpm test" | ||
}, | ||
"deprecated": false, | ||
"keywords": [ | ||
"bioinformatics", | ||
"seq", | ||
"qc metrics" | ||
], | ||
"repository": { | ||
"type": "git", | ||
"url": "https://github.com/icgc-tcga-pancancer/demo-wfs.git" | ||
}, | ||
"dependencies": [ | ||
"github.com/icgc-tcga-pancancer/awesome-wfpkgs1/fastqc@0.1.0", | ||
"github.com/icgc-argo/demo-wfpkgs/demo-utils@1.1.0" | ||
], | ||
"devDependencies": [], | ||
"contributors": [ | ||
{ | ||
"name": "Junjun Zhang", | ||
"email": "junjun.zhang@oicr.on.ca" | ||
} | ||
], | ||
"license": "MIT", | ||
"bugReport": "https://github.com/icgc-tcga-pancancer/demo-wfs/issues", | ||
"homepage": "https://github.com/icgc-tcga-pancancer/demo-wfs#readme" | ||
} |
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1
wfpr_modules/github.com/icgc-tcga-pancancer/demo-wfs/my-wf-1@0.1.0/wfpr_modules
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../../../../../wfpr_modules |