6 commits

Author	SHA1	Message	Date
Patrick Hüther	4a1571317d	update bwameth container build to match conda version (#402)	2021-04-06 10:45:14 +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
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
phue	c67e591caf	apply suggestions from review ... thanks @drpatelh	2021-02-20 12:51:01 +01:00
phue	a963c67481	bwameth: pass genome index as directory ... instead of single files	2021-02-18 11:51:36 +01:00
phue	180b1cf36b	add bwameth/index module + test	2021-02-17 18:03:48 +01:00