14 commits

Author	SHA1	Message	Date
Nicholas Toda	f126d980d7	Add tests for subread #106 (#393) ... * inital commit * added meta.yaml info * add initial logic for featurecounts test * add args and change SE/PE to strandedness for featurecounts test * added tests to pytest * added test.yml * removed GTF flag in options * corrected test meta params * meta yaml corrected tool info * update test.yml * fix lint errors meta.yml Co-authored-by: Nicholas TODA <nicholas.toda@mnhn.fr>	2021-04-01 20:02:36 +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
drpatelh	dcc580e4fb	Remove Conda build ids for all modules	2021-02-16 23:58:23 +00:00
drpatelh	3ae4c51f42	various - add build to conda definition	2021-02-03 09:20:34 +00:00
Edmund Miller	d76638d6f8	style(#77): Fix editorconfig errors	2020-12-17 17:50:24 -06:00
drpatelh	047dbde0af	Add singularity containers for rnaseq pipeline modules	2020-12-13 23:41:53 +00:00
drpatelh	a3f46865ff	Remove Singularity image path	2020-11-12 14:55:16 +00:00
drpatelh	14525ed50d	Remove functions file	2020-10-14 18:29:50 +01:00
drpatelh	e438d026bd	Unify syntax	2020-09-10 16:45:11 +01:00
drpatelh	46edf8ae4c	Update featurecounts module	2020-09-10 16:07:21 +01:00
drpatelh	473f1b192f	Update functions script	2020-09-10 15:59:26 +01:00
Jeremy1805	789dc4f09a	Changed options.publish_files definition in functions.nf/initOptions	2020-08-20 11:57:10 +01:00
drpatelh	f315a7b3c4	Hard copy files	2020-08-05 18:38:27 +01:00
drpatelh	f481899049	Add subread	2020-08-05 17:17:19 +01:00