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nf-core_modules/tests/modules/gatk4/mergebamalignment/test.yml

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modify test path - module gatk4 + added new module gatk4/haplotypecaller (#382) * new module: samtools/fastq * solve conflict: pytest_software.yml * solve linting conflicts * solved EditorConfig linting problem * Module samtools/fastq: * output compressed fastq.gz file(s) * add if conditionals for single/paired reads * samtools/fastq: modified test.yml * samtools/fastq: modified main.nf to avoid duplicated part of the script section * fix README.md * modify test path gatk4 * fix config * Add new module gatk4/haplotypecaller * solve check issues * fix test.yml file * fix test.yml gz.tbi * Update software/gatk4/haplotypecaller/main.nf Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> * Update software/gatk4/haplotypecaller/main.nf Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> * Update software/gatk4/haplotypecaller/main.nf Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> * Update software/gatk4/haplotypecaller/meta.yml Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> * Update software/gatk4/haplotypecaller/meta.yml Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> * Update tests/software/gatk4/haplotypecaller/main.nf Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> * Apply suggestions from code review Co-authored-by: suzannejin <suzanne.jin@crg.eu> Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-03-26 11:46:46 +00:00
- name: gatk4 mergebamalignment test_gatk4_mergebamalignment
Rename software/ directory to modules/ to re-organise module structure (#567) * Update README * Rename pytest_software.yml to pytest_modules.yml * Rename main software directory to modules * Remove deprecated modules * Rename tests software to modules * Replace paths for tests in pytest_modules.yml * Replace software with modules in Github Actions * Replace software with modules in main.nf tests * Rename software to modules in test.yml
2021-07-07 09:10:18 +00:00
command: nextflow run tests/modules/gatk4/mergebamalignment -entry test_gatk4_mergebamalignment -c tests/config/nextflow.config
add mergebamalignment (#259) * add mergebamalignment * fix test.yml * update to latest gatk4 version * Update software/gatk4/mergebamalignment/main.nf Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> * Update tests/data/README.md Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> * Update software/gatk4/mergebamalignment/main.nf Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> * Update software/gatk4/mergebamalignment/meta.yml * fixed unmapped/unaligned Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-03-17 14:56:56 +00:00
tags:
- gatk4
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
- gatk4/mergebamalignment
add mergebamalignment (#259) * add mergebamalignment * fix test.yml * update to latest gatk4 version * Update software/gatk4/mergebamalignment/main.nf Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> * Update tests/data/README.md Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> * Update software/gatk4/mergebamalignment/main.nf Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> * Update software/gatk4/mergebamalignment/meta.yml * fixed unmapped/unaligned Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-03-17 14:56:56 +00:00
files:
Modules TLC (#551) * Modules TLC * Fix all the tests
2021-07-01 15:13:01 +00:00
- path: output/gatk4/test.bam
feat: update gatk4 from 4.2.0.0 to 4.2.3.0 (#1059) * feat: update gatk4 from 4.2.0.0 to 4.2.3.0 * update md5checksum * commit all files * actually checksum was good, but I suspect something fishy with the tests
2021-11-11 07:58:59 +00:00
md5sum: e6f1b343700b7ccb94e81ae127433988
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