12 commits

Author	SHA1	Message	Date
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
Edmund Miller	a3684d9594	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 09:10:52 +01:00
Jose Espinosa-Carrasco	572abb00b3	Remove def from module options definition in main (#270) ... * Remove def from module options definition in main * Fix bismark_deduplicate tests * Fix bwameth_align tests * Fixing gatk4 conda tests ("=" instead of ':' in build id) * Same as previous commit (Fix gatk4 test) * Fix qualimap bamqc test (no md5 check for pngs) * Fix seqkit split2 tests. Changed to new test data * Fix samtools tests. Some were missing initOptions include * Removing TOOL SUBTOOL template module since now it is included on tools repo	2021-03-15 12:16:43 +00:00
FriederikeHanssen	7627e656ee	Add all tests back in	2021-02-24 09:57:23 +01:00
FriederikeHanssen	7f6e5d9ab5	try to make a single test pass on GHA, passes locally	2021-02-24 09:48:55 +01:00
FriederikeHanssen	e67515809a	try to only make paired-end test work, pass locally with conda & docker	2021-02-23 15:47:16 +01:00
FriederikeHanssen	13733b2581	Add beautiful md5sums	2021-02-23 14:57:07 +01:00
FriederikeHanssen	5e365d5eff	Make all these tests pass	2021-02-23 14:09:46 +01:00
FriederikeHanssen	25a2a16f2d	Try to make a single test pass	2021-02-23 13:34:50 +01:00
FriederikeHanssen	9c51e05125	remove wrong md5 sums	2021-02-23 11:25:45 +01:00
FriederikeHanssen	c7d2bc8d43	Add tests for different options	2021-02-23 11:14:51 +01:00
FriederikeHanssen	5f9aa7264e	Add tests	2021-02-17 17:25:41 +01:00