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nf-core_modules/tests/modules/samtools/index/test.yml

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Add thread option to samtools modules (#1069) * add thread option to samtools modules * fix tests * fix tests * fix tests * Fix naming to fix tests * cpus-1 to account for mainthread * remove thread in ampliconclip, docu doesn't report this param * add -1 to all other applicable samtools modules * Update samtools version * Update checksums * retrigger GHA after update * Update modules/samtools/fastq/main.nf Co-authored-by: Patrick Hüther <patrick.huether@gmail.com> * Update modules/samtools/fixmate/main.nf Co-authored-by: Patrick Hüther <patrick.huether@gmail.com> * Update modules/samtools/flagstat/main.nf Co-authored-by: Patrick Hüther <patrick.huether@gmail.com> * Update modules/samtools/index/main.nf Co-authored-by: Patrick Hüther <patrick.huether@gmail.com> * Update modules/samtools/merge/main.nf Co-authored-by: Patrick Hüther <patrick.huether@gmail.com> * Update modules/samtools/stats/main.nf Co-authored-by: Patrick Hüther <patrick.huether@gmail.com> * Update modules/samtools/view/main.nf Co-authored-by: Patrick Hüther <patrick.huether@gmail.com> * Fix md5sum fixmate * Fix md5sums * sth funny with the fixmate checksums * more md5sums updates Co-authored-by: Patrick Hüther <patrick.huether@gmail.com>
2021-11-18 21:24:47 +00:00
- name: samtools index test_samtools_index_bai
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/samtools/index -entry test_samtools_index_bai -c tests/config/nextflow.config
Restructure tests to run individually for each module
2021-02-03 16:02:58 +00:00
tags:
- samtools
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
- samtools/index
Restructure tests to run individually for each module
2021-02-03 16:02:58 +00:00
files:
Update samtools from 1.10 to 1.12 (#530) * feat: remove social preview image to use GitHub OpenGraph * feat: update samtools from 1.10 to 1.12 * fix: CI tests * fix: add meta.yml file for samtools/merge * Update software/samtools/merge/meta.yml Co-authored-by: Jose Espinosa-Carrasco <kadomu@gmail.com> * Update software/samtools/merge/meta.yml Co-authored-by: Jose Espinosa-Carrasco <kadomu@gmail.com>
2021-06-07 11:07:32 +00:00
- path: output/samtools/test.paired_end.sorted.bam.bai
Update samtools modules with config logic (#381) * fixing paths for test * fixing paths for test * fixing pats to tests * fixing paths to tests * fixing paths to tests * fixing paths for tests * fixing paths for tests * fixing paths for tests * fixing paths fro tests * fixing paths for tests * indentation fixes * typo * renaming test results according to new file name * replacing the md5sums * fixing brackets * replacing md5sums * fixing md5sums * fixing md5sums' * Update test.yml * Update test.yml * Update test.yml * Update test.yml * Update test.yml * Update test.yml * Update test.yml * Update test.yml Co-authored-by: Ramon Rivera <ramon.rivera10@upr.edu> Co-authored-by: Ramon Rivera <riveravicens@gmail.com>
2021-03-24 18:15:30 +00:00
md5sum: 704c10dd1326482448ca3073fdebc2f4
Update modules required for rnaseq pipeline (#449) * Update HISAT2 build module * Bump preseq version * Fix tests * Add meta.yml for preseq to fix linting * Auto-detect --genomeSAindexNbases for smaller genomes * Add placeholder to use human data for the tests * Add CSI output option to samtools/index * Fix samtools/index tests
2021-04-16 07:56:47 +00:00
Add thread option to samtools modules (#1069) * add thread option to samtools modules * fix tests * fix tests * fix tests * Fix naming to fix tests * cpus-1 to account for mainthread * remove thread in ampliconclip, docu doesn't report this param * add -1 to all other applicable samtools modules * Update samtools version * Update checksums * retrigger GHA after update * Update modules/samtools/fastq/main.nf Co-authored-by: Patrick Hüther <patrick.huether@gmail.com> * Update modules/samtools/fixmate/main.nf Co-authored-by: Patrick Hüther <patrick.huether@gmail.com> * Update modules/samtools/flagstat/main.nf Co-authored-by: Patrick Hüther <patrick.huether@gmail.com> * Update modules/samtools/index/main.nf Co-authored-by: Patrick Hüther <patrick.huether@gmail.com> * Update modules/samtools/merge/main.nf Co-authored-by: Patrick Hüther <patrick.huether@gmail.com> * Update modules/samtools/stats/main.nf Co-authored-by: Patrick Hüther <patrick.huether@gmail.com> * Update modules/samtools/view/main.nf Co-authored-by: Patrick Hüther <patrick.huether@gmail.com> * Fix md5sum fixmate * Fix md5sums * sth funny with the fixmate checksums * more md5sums updates Co-authored-by: Patrick Hüther <patrick.huether@gmail.com>
2021-11-18 21:24:47 +00:00
- name: samtools index test_samtools_index_crai
Add CRAM to samtools/index (#1049) * feat: update samtools/index * feat: add test * fix: lint * fix: output file + md5
2021-11-10 09:30:48 +00:00
command: nextflow run tests/modules/samtools/index -entry test_samtools_index_crai -c tests/config/nextflow.config
tags:
- samtools
- samtools/index
files:
- path: output/samtools/test.paired_end.recalibrated.sorted.cram.crai
md5sum: 537e3d8c937bcc4e34e1cf47cd71d484
Add thread option to samtools modules (#1069) * add thread option to samtools modules * fix tests * fix tests * fix tests * Fix naming to fix tests * cpus-1 to account for mainthread * remove thread in ampliconclip, docu doesn't report this param * add -1 to all other applicable samtools modules * Update samtools version * Update checksums * retrigger GHA after update * Update modules/samtools/fastq/main.nf Co-authored-by: Patrick Hüther <patrick.huether@gmail.com> * Update modules/samtools/fixmate/main.nf Co-authored-by: Patrick Hüther <patrick.huether@gmail.com> * Update modules/samtools/flagstat/main.nf Co-authored-by: Patrick Hüther <patrick.huether@gmail.com> * Update modules/samtools/index/main.nf Co-authored-by: Patrick Hüther <patrick.huether@gmail.com> * Update modules/samtools/merge/main.nf Co-authored-by: Patrick Hüther <patrick.huether@gmail.com> * Update modules/samtools/stats/main.nf Co-authored-by: Patrick Hüther <patrick.huether@gmail.com> * Update modules/samtools/view/main.nf Co-authored-by: Patrick Hüther <patrick.huether@gmail.com> * Fix md5sum fixmate * Fix md5sums * sth funny with the fixmate checksums * more md5sums updates Co-authored-by: Patrick Hüther <patrick.huether@gmail.com>
2021-11-18 21:24:47 +00:00
- name: samtools index test_samtools_index_csi
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/samtools/index -entry test_samtools_index_csi -c tests/config/nextflow.config
Update modules required for rnaseq pipeline (#449) * Update HISAT2 build module * Bump preseq version * Fix tests * Add meta.yml for preseq to fix linting * Auto-detect --genomeSAindexNbases for smaller genomes * Add placeholder to use human data for the tests * Add CSI output option to samtools/index * Fix samtools/index tests
2021-04-16 07:56:47 +00:00
tags:
- samtools
- samtools/index
files:
Update samtools from 1.10 to 1.12 (#530) * feat: remove social preview image to use GitHub OpenGraph * feat: update samtools from 1.10 to 1.12 * fix: CI tests * fix: add meta.yml file for samtools/merge * Update software/samtools/merge/meta.yml Co-authored-by: Jose Espinosa-Carrasco <kadomu@gmail.com> * Update software/samtools/merge/meta.yml Co-authored-by: Jose Espinosa-Carrasco <kadomu@gmail.com>
2021-06-07 11:07:32 +00:00
- path: output/samtools/test.paired_end.sorted.bam.csi
Update modules required for rnaseq pipeline (#449) * Update HISAT2 build module * Bump preseq version * Fix tests * Add meta.yml for preseq to fix linting * Auto-detect --genomeSAindexNbases for smaller genomes * Add placeholder to use human data for the tests * Add CSI output option to samtools/index * Fix samtools/index tests
2021-04-16 07:56:47 +00:00
md5sum: 3dd9e3ed959fca075b88bb8dc3cf7dbd
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