mirror of
https://github.com/MillironX/nf-core_modules.git
synced 2024-09-21 15:52:05 +00:00
e526eae472
* initial commit hisat2/build * initial commit hisat2/build * changed names for hisat2 * fixed directory structure and args * added splice site test data * added splice site inputs * replaced list with individual args * fixed removed commas * added test yml file * updated hisat2 conda version * added meta.yml * added meta.yml description * added meta.yml inputs * added meta.yml outputs * update conda version for hisat2 * removed trailing whitespace meta.yml * fixed version number for containers * added test data to test config * updated for new test logic * fix pytest issue? * fix pytest issue * fixed wrong tool in meta.yaml * updated tets.yaml name * handle build bug for testing * handle build bug for testing in yaml * moved test folder to fix build bug * use old hisat2 version to avoid conda giving inconsistent md5sum * initial commit * removed temp file * added meta yaml * add to pytest * added tests * added test yml * add align meta yaml * add hisat2 align to pytest * remove need for splice data by calling process * add hisat2 align se test * add hisat2 align pe test * update names hisat2 align * update software pytest for using mutiple modules * remove splice site test data since using module instead * remove splice site from config since using module instead * fixed extra brace * added hisat2 align test.yml * removed md5sum for bam files * updated build md5sums * Apply suggestions from code review Co-authored-by: Nicholas TODA <nicholas.toda@mnhn.fr> Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
57 lines
2.4 KiB
YAML
57 lines
2.4 KiB
YAML
- name: hisat2 align test_hisat2_align_single_end
|
|
command: nextflow run tests/software/hisat2/align -entry test_hisat2_align_single_end -c tests/config/nextflow.config
|
|
tags:
|
|
- hisat2_align_single_end
|
|
- hisat2_align
|
|
- hisat2
|
|
files:
|
|
- path: output/hisat2/test.hisat2.summary.log
|
|
md5sum: 7b8a9e61b7646da1089b041333c41a87
|
|
- path: output/hisat2/genome.splice_sites.txt
|
|
md5sum: d41d8cd98f00b204e9800998ecf8427e
|
|
- path: output/hisat2/test.bam
|
|
- path: output/index/hisat2/genome.5.ht2
|
|
md5sum: 91198831aaba993acac1734138c5f173
|
|
- path: output/index/hisat2/genome.7.ht2
|
|
md5sum: 9013eccd91ad614d7893c739275a394f
|
|
- path: output/index/hisat2/genome.1.ht2
|
|
md5sum: 3ea3dc41304941ad8d047e4d71b4899e
|
|
- path: output/index/hisat2/genome.2.ht2
|
|
md5sum: 47b153cd1319abc88dda532462651fcf
|
|
- path: output/index/hisat2/genome.6.ht2
|
|
md5sum: 265e1284ce85686516fae5d35540994a
|
|
- path: output/index/hisat2/genome.3.ht2
|
|
md5sum: 4ed93abba181d8dfab2e303e33114777
|
|
- path: output/index/hisat2/genome.8.ht2
|
|
md5sum: 33cdeccccebe80329f1fdbee7f5874cb
|
|
- path: output/index/hisat2/genome.4.ht2
|
|
md5sum: c25be5f8b0378abf7a58c8a880b87626
|
|
|
|
- name: hisat2 align test_hisat2_align_paired_end
|
|
command: nextflow run tests/software/hisat2/align -entry test_hisat2_align_paired_end -c tests/config/nextflow.config
|
|
tags:
|
|
- hisat2_align_paired_end
|
|
- hisat2_align
|
|
- hisat2
|
|
files:
|
|
- path: output/hisat2/test.hisat2.summary.log
|
|
md5sum: 9839b31db795958cc4b70711a3414e9c
|
|
- path: output/hisat2/genome.splice_sites.txt
|
|
md5sum: d41d8cd98f00b204e9800998ecf8427e
|
|
- path: output/hisat2/test.bam
|
|
- path: output/index/hisat2/genome.5.ht2
|
|
md5sum: 91198831aaba993acac1734138c5f173
|
|
- path: output/index/hisat2/genome.7.ht2
|
|
md5sum: 9013eccd91ad614d7893c739275a394f
|
|
- path: output/index/hisat2/genome.1.ht2
|
|
md5sum: 3ea3dc41304941ad8d047e4d71b4899e
|
|
- path: output/index/hisat2/genome.2.ht2
|
|
md5sum: 47b153cd1319abc88dda532462651fcf
|
|
- path: output/index/hisat2/genome.6.ht2
|
|
md5sum: 265e1284ce85686516fae5d35540994a
|
|
- path: output/index/hisat2/genome.3.ht2
|
|
md5sum: 4ed93abba181d8dfab2e303e33114777
|
|
- path: output/index/hisat2/genome.8.ht2
|
|
md5sum: 33cdeccccebe80329f1fdbee7f5874cb
|
|
- path: output/index/hisat2/genome.4.ht2
|
|
md5sum: c25be5f8b0378abf7a58c8a880b87626
|