10 commits

Author	SHA1	Message	Date
Jose Espinosa-Carrasco	95e02f913f	Update comments with new style (#497) ... * Update comment style on functions.nf files * Update test main.nf comments * Add meta for ggread	2021-05-12 14:56:46 +01:00
Harshil Patel	dce27b8102	Update functions.nf to be more flexible for publishing by meta keys (#423) ... * Update functions.nf * Replace saveAs line in module main script * Add spacing for ECLint	2021-04-09 17:23:56 +01:00
FriederikeHanssen	555f1710e0	Update test paths in bwa mappers (#387) ... * Update test paths in bwa mappers * Fix indentation * indices pass lcoally now * no idea how they could ever pass before, Tests pass locally no * Update samtools and bwamem2 versions * Correct mulled containers + md5	2021-03-25 09:24:21 +00:00
Patrick Hüther	8a44258548	remove params section from meta.yml (#282)	2021-03-19 13:16:50 +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
MaxUlysse	9c98194d3c	chores: remove fasta file from bwamem2 mem process	2021-02-12 16:00:59 +01:00
MaxUlysse	0afddf6ca4	fix: CI is working	2021-02-12 15:24:09 +01:00
Maxime Garcia	c1ff201518	Apply suggestions from code review ... Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>	2021-02-12 13:24:10 +01:00
MaxUlysse	6b34ddf239	chores: bwa-mem2 -> bwamem2	2021-02-12 13:08:44 +01:00