26 commits

Author	SHA1	Message	Date
Florian Wuennemann	592002aa23	add picard_collectwgsmetrics (#304) ... * Added new module picard/collectwgsmetrics. * Removed unused outputs from meta.yml * Added version.txt file back to meta.yml * Updated test.yml * Removed md5sum from test.yaml and added contain tests. * Update functions.nf Fixed missing newline formatting. * Update main.nf Fixed missing newline formatting. * style(picard): Remove trailing whitespace Co-authored-by: Kevin Menden <kevin.menden@t-online.de> Co-authored-by: Edmund Miller <edmund.a.miller@protonmail.com>	2021-03-22 17:05:59 +01:00
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	daab19a849	picard - add build to conda definition	2021-02-03 09:18:37 +00:00
Edmund Miller	d76638d6f8	style(#77): Fix editorconfig errors	2020-12-17 17:50:24 -06:00
drpatelh	200c946693	Add --singularity_pull_docker_container to module yml	2020-12-14 00:34:24 +00:00
drpatelh	99a2364a26	Update all other modules	2020-12-14 00:05:48 +00:00
drpatelh	047dbde0af	Add singularity containers for rnaseq pipeline modules	2020-12-13 23:41:53 +00:00
Edmund Miller	7848019cdb	test(picard): Refactor markduplicates to use pytest-workflow	2020-11-24 21:08:33 -06:00
Edmund Miller	939f5ca744	test(picard): Refactor collectmultiplemetrics to use pytest-workflow	2020-11-24 21:03:40 -06:00
Edmund Miller	234e85bdce	test(picard): Refactor mergesamfiles to use pytest-workflow	2020-11-24 19:01:12 -06:00
drpatelh	a3f46865ff	Remove Singularity image path	2020-11-12 14:55:16 +00:00
drpatelh	47d390772c	Update picard version command and default container	2020-10-19 15:17:19 +01:00
drpatelh	29f9b05433	Update docs	2020-10-15 11:13:54 +01:00
drpatelh	530789ba85	Get tests passing	2020-10-15 10:47:15 +01:00
drpatelh	1d30e2c21a	Update tools not in rnaseq pipeline too	2020-10-14 18:59:25 +01:00
drpatelh	d19a8c702d	Update picard version	2020-10-12 15:58:09 +01:00
drpatelh	e438d026bd	Unify syntax	2020-09-10 16:45:11 +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	08723c9d61	Add tests for mergesamfiles	2020-08-07 16:39:16 +01:00
drpatelh	3547b64eab	Add docs and tests for markduplicates	2020-08-07 16:30:28 +01:00
drpatelh	cb85acddf0	Add docs and tests for collectmultiplemetrics	2020-08-07 16:29:37 +01:00
drpatelh	f315a7b3c4	Hard copy files	2020-08-05 18:38:27 +01:00
drpatelh	993d0d5743	Add picard	2020-08-05 17:17:41 +01:00