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

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add gatk4/fastqtosam #198 (#311) * Inital nf-core create * remove TODO comments, input and output files defined * add get version in script * added flow control for single/paired end data * added script main commands * removed completed TODO messages * removed completed TODO messages * added software info * added input reads description * added output description * added description and keywords * added single end test * added paired end test * fixed sample name flag * fixed reverse read variable * added test yaml * update for pytest_software * order in pytest_software was different * replaced functions.nf with copy from another module * simplify read command line Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> Co-authored-by: Nicholas TODA <nicholas.toda@mnhn.fr> Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-03-22 14:26:02 -04:00
- name: gatk4 fastqtosam test_gatk4_fastqtosam_single_end
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 05:10:18 -04:00
command: nextflow run tests/modules/gatk4/fastqtosam -entry test_gatk4_fastqtosam_single_end -c tests/config/nextflow.config
add gatk4/fastqtosam #198 (#311) * Inital nf-core create * remove TODO comments, input and output files defined * add get version in script * added flow control for single/paired end data * added script main commands * removed completed TODO messages * removed completed TODO messages * added software info * added input reads description * added output description * added description and keywords * added single end test * added paired end test * fixed sample name flag * fixed reverse read variable * added test yaml * update for pytest_software * order in pytest_software was different * replaced functions.nf with copy from another module * simplify read command line Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> Co-authored-by: Nicholas TODA <nicholas.toda@mnhn.fr> Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-03-22 14:26:02 -04:00
tags:
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 04:10:52 -04:00
- gatk4/fastqtosam
add gatk4/fastqtosam #198 (#311) * Inital nf-core create * remove TODO comments, input and output files defined * add get version in script * added flow control for single/paired end data * added script main commands * removed completed TODO messages * removed completed TODO messages * added software info * added input reads description * added output description * added description and keywords * added single end test * added paired end test * fixed sample name flag * fixed reverse read variable * added test yaml * update for pytest_software * order in pytest_software was different * replaced functions.nf with copy from another module * simplify read command line Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> Co-authored-by: Nicholas TODA <nicholas.toda@mnhn.fr> Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-03-22 14:26:02 -04:00
- gatk4
files:
- 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 02:58:59 -05:00
md5sum: 0a0d308b219837977b8df9daa26db7de
add gatk4/fastqtosam #198 (#311) * Inital nf-core create * remove TODO comments, input and output files defined * add get version in script * added flow control for single/paired end data * added script main commands * removed completed TODO messages * removed completed TODO messages * added software info * added input reads description * added output description * added description and keywords * added single end test * added paired end test * fixed sample name flag * fixed reverse read variable * added test yaml * update for pytest_software * order in pytest_software was different * replaced functions.nf with copy from another module * simplify read command line Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> Co-authored-by: Nicholas TODA <nicholas.toda@mnhn.fr> Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-03-22 14:26:02 -04:00
- name: gatk4 fastqtosam test_gatk4_fastqtosam_paired_end
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 05:10:18 -04:00
command: nextflow run tests/modules/gatk4/fastqtosam -entry test_gatk4_fastqtosam_paired_end -c tests/config/nextflow.config
add gatk4/fastqtosam #198 (#311) * Inital nf-core create * remove TODO comments, input and output files defined * add get version in script * added flow control for single/paired end data * added script main commands * removed completed TODO messages * removed completed TODO messages * added software info * added input reads description * added output description * added description and keywords * added single end test * added paired end test * fixed sample name flag * fixed reverse read variable * added test yaml * update for pytest_software * order in pytest_software was different * replaced functions.nf with copy from another module * simplify read command line Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> Co-authored-by: Nicholas TODA <nicholas.toda@mnhn.fr> Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-03-22 14:26:02 -04:00
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 04:10:52 -04:00
- gatk4/fastqtosam
add gatk4/fastqtosam #198 (#311) * Inital nf-core create * remove TODO comments, input and output files defined * add get version in script * added flow control for single/paired end data * added script main commands * removed completed TODO messages * removed completed TODO messages * added software info * added input reads description * added output description * added description and keywords * added single end test * added paired end test * fixed sample name flag * fixed reverse read variable * added test yaml * update for pytest_software * order in pytest_software was different * replaced functions.nf with copy from another module * simplify read command line Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> Co-authored-by: Nicholas TODA <nicholas.toda@mnhn.fr> Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-03-22 14:26:02 -04:00
files:
- 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 02:58:59 -05:00
md5sum: 0a0d308b219837977b8df9daa26db7de
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