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

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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
command: nextflow run tests/software/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 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
- path: output/samtools/test_paired_end.sorted.bam.bai
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
command: nextflow run tests/software/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
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