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

- name: samtools index bai
  command: nextflow run tests/modules/samtools/index -entry test_samtools_index_bai -c tests/config/nextflow.config
  tags:
    - samtools
    - samtools/index
  files:
    - path: output/samtools/test.paired_end.sorted.bam.bai
      md5sum: 704c10dd1326482448ca3073fdebc2f4

- name: samtools index csi
  command: nextflow run tests/modules/samtools/index -entry test_samtools_index_csi -c tests/config/nextflow.config
  tags:
    - samtools
    - samtools/index
  files:
    - path: output/samtools/test.paired_end.sorted.bam.csi
      md5sum: 3dd9e3ed959fca075b88bb8dc3cf7dbd
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			`- name: 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
			`- name: 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`