4 commits

Author	SHA1	Message	Date
Harshil Patel	e937c7950a	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 10:10:18 +01:00
Kevin Menden	043a7d1e3c	remove deprecated test tags (#440) ... * remove deprecated test tags * fix bowtie, gatk4/applybsqr * fix gatk4 baserecalibrator * fixed shovill * fixed yara/mapper * fixed kallistobustools/ref paths	2021-04-13 18:03:09 +01:00
Harshil Patel	5e18e36895	Update and check tests are running for all modules (#420) ... * Fixes for PR 371 * Fix tags * Add md5sum * Add md5sums for stringtie * Fix tests for modules where subtool = build * Fix pytest_software name conflicts * Change _ to / in test.yml tags * Nope...that didnt work * Fix sequenzautils/bam2seqz tests	2021-04-09 13:47:05 +01:00
Nicholas Toda	e526eae472	Add tests for hisat2 (#366) ... * initial commit hisat2/build * initial commit hisat2/build * changed names for hisat2 * fixed directory structure and args * added splice site test data * added splice site inputs * replaced list with individual args * fixed removed commas * added test yml file * updated hisat2 conda version * added meta.yml * added meta.yml description * added meta.yml inputs * added meta.yml outputs * update conda version for hisat2 * removed trailing whitespace meta.yml * fixed version number for containers * added test data to test config * updated for new test logic * fix pytest issue? * fix pytest issue * fixed wrong tool in meta.yaml * updated tets.yaml name * handle build bug for testing * handle build bug for testing in yaml * moved test folder to fix build bug * use old hisat2 version to avoid conda giving inconsistent md5sum * initial commit * removed temp file * added meta yaml * add to pytest * added tests * added test yml * add align meta yaml * add hisat2 align to pytest * remove need for splice data by calling process * add hisat2 align se test * add hisat2 align pe test * update names hisat2 align * update software pytest for using mutiple modules * remove splice site test data since using module instead * remove splice site from config since using module instead * fixed extra brace * added hisat2 align test.yml * removed md5sum for bam files * updated build md5sums * Apply suggestions from code review Co-authored-by: Nicholas TODA <nicholas.toda@mnhn.fr> Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>	2021-03-25 21:08:46 +00:00