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nf-core_modules/tests/modules/controlfreec/freec/test.yml

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controlfreec significance (#1451) * controlfreec significance * move freec files to own subfolder * Fix meta.yml naming * Fix meta.yml naming * Fix linting * Forgot to refactor * forgot more refactoring * Too much refactoring on output paths * Too little refactoring here * update checksum
2022-03-25 13:22:17 -04:00
- name: controlfreec test_controlfreec_freec
command: nextflow run tests/modules/controlfreec/freec -entry test_controlfreec_freec -c tests/config/nextflow.config
add controlfreec (#1333) * add drafty controlfreec * get sofatware version * use maps in map * update paths to new and soon-to-be merged test files, add more input docu * Stab at documenting args map * Update syntax * Bit more description * Make the linter happy * tests pass locally * Add outputs & docu * tests are failing locally now :/ but cpn file can also be added * All tests passing, need to update test data again to add folder * Clean up files * Clean up files * Clean up files * Don't know how to get the test to run with the direcotry for now. they pass locally though * Make linter happy * Name process back * Update to use tar folder * fix the checksum
2022-02-28 13:08:58 -05:00
tags:
- controlfreec
controlfreec significance (#1451) * controlfreec significance * move freec files to own subfolder * Fix meta.yml naming * Fix meta.yml naming * Fix linting * Forgot to refactor * forgot more refactoring * Too much refactoring on output paths * Too little refactoring here * update checksum
2022-03-25 13:22:17 -04:00
- controlfreec/freec
add controlfreec (#1333) * add drafty controlfreec * get sofatware version * use maps in map * update paths to new and soon-to-be merged test files, add more input docu * Stab at documenting args map * Update syntax * Bit more description * Make the linter happy * tests pass locally * Add outputs & docu * tests are failing locally now :/ but cpn file can also be added * All tests passing, need to update test data again to add folder * Clean up files * Clean up files * Clean up files * Don't know how to get the test to run with the direcotry for now. they pass locally though * Make linter happy * Name process back * Update to use tar folder * fix the checksum
2022-02-28 13:08:58 -05:00
files:
- path: output/controlfreec/config.txt
- path: output/controlfreec/test.mpileup.gz_control.cpn
md5sum: 1768b571677c418560e5a8fe203bdc79
- path: output/controlfreec/test2.mpileup.gz_BAF.txt
md5sum: 3bb7437001cf061a77eaf87b8558c48d
- path: output/controlfreec/test2.mpileup.gz_CNVs
md5sum: 1f4f5834dbd1490afdb22f6d3091c4c9
- path: output/controlfreec/test2.mpileup.gz_info.txt
md5sum: 1a3055d35028525ccc9e693cc9f335e0
- path: output/controlfreec/test2.mpileup.gz_ratio.BedGraph
md5sum: 8ba455b232be20cdcc5bf1e4035e8032
- path: output/controlfreec/test2.mpileup.gz_ratio.txt
md5sum: b76b2434de710325069e37fb1e132760
- path: output/controlfreec/test2.mpileup.gz_sample.cpn
md5sum: c80dad58a77b1d7ba6d273999f4b4b4b
- path: output/controlfreec/versions.yml
Fix Controlfreec: Add stub runs to test single sample input & make conda work with R scripts (#1504) * Fix typo * Add stub runs for testing input without matched normals * Add missing -stub-run * remove empty file checksum tests and change workflow names * test controlfreec naming * fix output file names * fix output file names * fix output file names * fix conda and container path difference for R scripts * update tar version to work with conda * fix version number in docker * try to fix path to script, pretty sure it won't work * try new ways to set path with wildcard * try which * add which but with escape * remove comment
2022-04-08 05:43:40 -04:00
- name: controlfreec test_controlfreec_freec_single
command: nextflow run tests/modules/controlfreec/freec -entry test_controlfreec_freec_single -c tests/config/nextflow.config -stub-run
tags:
- controlfreec
- controlfreec/freec
files:
- path: output/controlfreec/config.txt
- path: output/controlfreec/test2_BAF.txt
- path: output/controlfreec/test2_CNVs
- path: output/controlfreec/test2_info.txt
- path: output/controlfreec/test2_ratio.BedGraph
- path: output/controlfreec/test2_ratio.txt
- path: output/controlfreec/test2_sample.cpn
- path: output/controlfreec/versions.yml
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