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nf-core_modules/tests/software/bismark/align/test.yml

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add bismark/report (#297) * add bismark/align module * bismark/align: add tests * bismark/align: update meta.yml * bismark/align: skip checksum for alignment logs they contain timestamps * bismark/align: restore correct checksum caused some mixup in the last commit * bismark/align: add genome_preparation to filters * Fix conda version pin * change options to be a global var * remove params from meta.yml * add bismark/report * fix test filepaths * remove mysterious index files
2021-03-22 12:38:08 +00:00
- name: Run bismark align single-end test workflow
command: nextflow run ./tests/software/bismark/align -entry test_bismark_align_single_end -c tests/config/nextflow.config
tags:
- bismark
Lint modules ci (#389) * ci: Add modules lint step Moved it ahead of the nextflow install so ideally it'll fail before we bother doing any more setup * ci: _ => / * Update tests/config/pytest_software.yml Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-04-08 08:10:52 +00:00
- bismark/align
add bismark/report (#297) * add bismark/align module * bismark/align: add tests * bismark/align: update meta.yml * bismark/align: skip checksum for alignment logs they contain timestamps * bismark/align: restore correct checksum caused some mixup in the last commit * bismark/align: add genome_preparation to filters * Fix conda version pin * change options to be a global var * remove params from meta.yml * add bismark/report * fix test filepaths * remove mysterious index files
2021-03-22 12:38:08 +00:00
files:
Fix 459 (#534) * Update test data names. Closes: #459 Thanks: @FriederikeHanssen (`samtools` tests are already fixed by another commit) * Fix file names in tests. The update of test data name required changes in the test yml files. I also updated the `bismark/summary/main.nf` file to get its data from the `params.test_data` map.
2021-06-14 11:24:59 +00:00
- path: output/test_single_end/test.methylated_1_bismark_bt2.bam
md5sum: dca4ba9ff705b70446f812e59bdb1a32
- path: output/test_single_end/test.methylated_1_bismark_bt2_SE_report.txt
add bismark/report (#297) * add bismark/align module * bismark/align: add tests * bismark/align: update meta.yml * bismark/align: skip checksum for alignment logs they contain timestamps * bismark/align: restore correct checksum caused some mixup in the last commit * bismark/align: add genome_preparation to filters * Fix conda version pin * change options to be a global var * remove params from meta.yml * add bismark/report * fix test filepaths * remove mysterious index files
2021-03-22 12:38:08 +00:00
- name: Run bismark align paired-end test workflow
command: nextflow run ./tests/software/bismark/align -entry test_bismark_align_paired_end -c tests/config/nextflow.config
tags:
- bismark
Lint modules ci (#389) * ci: Add modules lint step Moved it ahead of the nextflow install so ideally it'll fail before we bother doing any more setup * ci: _ => / * Update tests/config/pytest_software.yml Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-04-08 08:10:52 +00:00
- bismark/align
add bismark/report (#297) * add bismark/align module * bismark/align: add tests * bismark/align: update meta.yml * bismark/align: skip checksum for alignment logs they contain timestamps * bismark/align: restore correct checksum caused some mixup in the last commit * bismark/align: add genome_preparation to filters * Fix conda version pin * change options to be a global var * remove params from meta.yml * add bismark/report * fix test filepaths * remove mysterious index files
2021-03-22 12:38:08 +00:00
files:
Fix 459 (#534) * Update test data names. Closes: #459 Thanks: @FriederikeHanssen (`samtools` tests are already fixed by another commit) * Fix file names in tests. The update of test data name required changes in the test yml files. I also updated the `bismark/summary/main.nf` file to get its data from the `params.test_data` map.
2021-06-14 11:24:59 +00:00
- path: output/test_paired_end/test.methylated_1_bismark_bt2_pe.bam
md5sum: 43943b1f30d056fcbd9ed26061ea0583
- path: output/test_paired_end/test.methylated_1_bismark_bt2_PE_report.txt
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