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

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Getpileupsummaries (#689) * first commit, added template files for new module * created getpileupsummaries script, tests and both yml files * fixed typo in meta.yml * Update modules/gatk4/getpileupsummaries/meta.yml changed gz_tbi to gz.tbi as suggested Co-authored-by: Maxime U. Garcia <maxime.garcia@scilifelab.se> Co-authored-by: GCJMackenzie <gavin.mackenzie@nibsc.org> Co-authored-by: Maxime U. Garcia <max.u.garcia@gmail.com> Co-authored-by: Maxime U. Garcia <maxime.garcia@scilifelab.se>
2021-09-13 15:04:14 +00:00
- name: gatk4 getpileupsummaries test_gatk4_getpileupsummaries_separate_sites
Update intervals (#1278) * Match target bed to input files * Intervals in getpileupsumamries * more interval updates * change targets in strelka * remove leftover channel * fix checksums * add new test vcfs * add new test vcfs * Update modules/freebayes/main.nf Co-authored-by: Maxime U. Garcia <maxime.garcia@scilifelab.se>
2022-02-10 09:34:22 +00:00
command: nextflow run tests/modules/gatk4/getpileupsummaries -entry test_gatk4_getpileupsummaries_separate_sites -c tests/config/nextflow.config
Getpileupsummaries (#689) * first commit, added template files for new module * created getpileupsummaries script, tests and both yml files * fixed typo in meta.yml * Update modules/gatk4/getpileupsummaries/meta.yml changed gz_tbi to gz.tbi as suggested Co-authored-by: Maxime U. Garcia <maxime.garcia@scilifelab.se> Co-authored-by: GCJMackenzie <gavin.mackenzie@nibsc.org> Co-authored-by: Maxime U. Garcia <max.u.garcia@gmail.com> Co-authored-by: Maxime U. Garcia <maxime.garcia@scilifelab.se>
2021-09-13 15:04:14 +00:00
tags:
Update intervals (#1278) * Match target bed to input files * Intervals in getpileupsumamries * more interval updates * change targets in strelka * remove leftover channel * fix checksums * add new test vcfs * add new test vcfs * Update modules/freebayes/main.nf Co-authored-by: Maxime U. Garcia <maxime.garcia@scilifelab.se>
2022-02-10 09:34:22 +00:00
- gatk4/getpileupsummaries
Getpileupsummaries (#689) * first commit, added template files for new module * created getpileupsummaries script, tests and both yml files * fixed typo in meta.yml * Update modules/gatk4/getpileupsummaries/meta.yml changed gz_tbi to gz.tbi as suggested Co-authored-by: Maxime U. Garcia <maxime.garcia@scilifelab.se> Co-authored-by: GCJMackenzie <gavin.mackenzie@nibsc.org> Co-authored-by: Maxime U. Garcia <max.u.garcia@gmail.com> Co-authored-by: Maxime U. Garcia <maxime.garcia@scilifelab.se>
2021-09-13 15:04:14 +00:00
- gatk4
Update intervals (#1278) * Match target bed to input files * Intervals in getpileupsumamries * more interval updates * change targets in strelka * remove leftover channel * fix checksums * add new test vcfs * add new test vcfs * Update modules/freebayes/main.nf Co-authored-by: Maxime U. Garcia <maxime.garcia@scilifelab.se>
2022-02-10 09:34:22 +00:00
files:
Fix formatting in yaml files, add yamllint config (#1279) * fix yml formatting * allow fastq.gz and fq.gz as file input, add meta.yml and test * fix yaml files * Revert "allow fastq.gz and fq.gz as file input, add meta.yml and test" This reverts commit 34002d7a7a8c7f7bb4600c3377f35c87849f71a4. * prettier magic! * fix comments for yamllint * remove node version number * fix linting errors Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2022-02-15 11:15:27 +00:00
- path: output/gatk4/test.pileups.table
Update intervals (#1278) * Match target bed to input files * Intervals in getpileupsumamries * more interval updates * change targets in strelka * remove leftover channel * fix checksums * add new test vcfs * add new test vcfs * Update modules/freebayes/main.nf Co-authored-by: Maxime U. Garcia <maxime.garcia@scilifelab.se>
2022-02-10 09:34:22 +00:00
md5sum: 8e0ca6f66e112bd2f7ec1d31a2d62469
Fix formatting in yaml files, add yamllint config (#1279) * fix yml formatting * allow fastq.gz and fq.gz as file input, add meta.yml and test * fix yaml files * Revert "allow fastq.gz and fq.gz as file input, add meta.yml and test" This reverts commit 34002d7a7a8c7f7bb4600c3377f35c87849f71a4. * prettier magic! * fix comments for yamllint * remove node version number * fix linting errors Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2022-02-15 11:15:27 +00:00
- path: output/gatk4/versions.yml
Update intervals (#1278) * Match target bed to input files * Intervals in getpileupsumamries * more interval updates * change targets in strelka * remove leftover channel * fix checksums * add new test vcfs * add new test vcfs * Update modules/freebayes/main.nf Co-authored-by: Maxime U. Garcia <maxime.garcia@scilifelab.se>
2022-02-10 09:34:22 +00:00
- name: gatk4 getpileupsummaries test_gatk4_getpileupsummaries_separate_sites_cram
command: nextflow run tests/modules/gatk4/getpileupsummaries -entry test_gatk4_getpileupsummaries_separate_sites_cram -c tests/config/nextflow.config
tags:
Getpileupsummaries (#689) * first commit, added template files for new module * created getpileupsummaries script, tests and both yml files * fixed typo in meta.yml * Update modules/gatk4/getpileupsummaries/meta.yml changed gz_tbi to gz.tbi as suggested Co-authored-by: Maxime U. Garcia <maxime.garcia@scilifelab.se> Co-authored-by: GCJMackenzie <gavin.mackenzie@nibsc.org> Co-authored-by: Maxime U. Garcia <max.u.garcia@gmail.com> Co-authored-by: Maxime U. Garcia <maxime.garcia@scilifelab.se>
2021-09-13 15:04:14 +00:00
- gatk4/getpileupsummaries
Update intervals (#1278) * Match target bed to input files * Intervals in getpileupsumamries * more interval updates * change targets in strelka * remove leftover channel * fix checksums * add new test vcfs * add new test vcfs * Update modules/freebayes/main.nf Co-authored-by: Maxime U. Garcia <maxime.garcia@scilifelab.se>
2022-02-10 09:34:22 +00:00
- gatk4
Getpileupsummaries (#689) * first commit, added template files for new module * created getpileupsummaries script, tests and both yml files * fixed typo in meta.yml * Update modules/gatk4/getpileupsummaries/meta.yml changed gz_tbi to gz.tbi as suggested Co-authored-by: Maxime U. Garcia <maxime.garcia@scilifelab.se> Co-authored-by: GCJMackenzie <gavin.mackenzie@nibsc.org> Co-authored-by: Maxime U. Garcia <max.u.garcia@gmail.com> Co-authored-by: Maxime U. Garcia <maxime.garcia@scilifelab.se>
2021-09-13 15:04:14 +00:00
files:
Fix formatting in yaml files, add yamllint config (#1279) * fix yml formatting * allow fastq.gz and fq.gz as file input, add meta.yml and test * fix yaml files * Revert "allow fastq.gz and fq.gz as file input, add meta.yml and test" This reverts commit 34002d7a7a8c7f7bb4600c3377f35c87849f71a4. * prettier magic! * fix comments for yamllint * remove node version number * fix linting errors Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2022-02-15 11:15:27 +00:00
- path: output/gatk4/test.pileups.table
Update version for log4j vulnerability (#1176) * Update version for log4j vulnerability * update checksums * update checksums * update checksums * Remove todo string * remove werid output paths * remove werid output paths * remove werid output paths * Update various checksums * Update various checksums * Remove unstable md5sums * Update md5sums * Fix pileupsummary * Fix genotypegvcfs * Update test files mutect2 * hm genotypevcf updated again * Update some mutect checksums and whatnot * Fix last mutect checksum * Apply suggestion to use mtochondria data instead
2021-12-20 16:10:49 +00:00
md5sum: 8e0ca6f66e112bd2f7ec1d31a2d62469
Fix formatting in yaml files, add yamllint config (#1279) * fix yml formatting * allow fastq.gz and fq.gz as file input, add meta.yml and test * fix yaml files * Revert "allow fastq.gz and fq.gz as file input, add meta.yml and test" This reverts commit 34002d7a7a8c7f7bb4600c3377f35c87849f71a4. * prettier magic! * fix comments for yamllint * remove node version number * fix linting errors Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2022-02-15 11:15:27 +00:00
- path: output/gatk4/versions.yml
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