11 commits

Author	SHA1	Message	Date
Harshil Patel	65a3422686	Add default publish_dir for index processes (#428)	2021-04-10 20:49:09 +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
Jose Espinosa-Carrasco	ee90e7af77	Add default output dir for modules that create indices, updated (#336) ... * Add default output dir for modules that create indices * Change path for index module test output * Fix bowtie2/align tests * Fixing bowtie/align tests * Fix genomegenerate test * Fixing README linting	2021-03-23 17:55:01 +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
drpatelh	f913a55d85	bowtie2 build - add build to conda definition	2021-02-03 09:16:10 +00:00
Harshil Patel	eab633776e	Update software/bowtie2/build/meta.yml	2021-01-30 13:21:56 +00:00
JoseEspinosa	29989035a5	Remove author entry from yml (copy-pasted :P)	2021-01-30 09:29:53 +01:00
JoseEspinosa	43f9815621	Adding module bowtie2 align	2021-01-29 19:29:32 +01:00
JoseEspinosa	2f9934c563	Adding bowtie2_build module	2021-01-29 18:57:27 +01:00