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Author	SHA1	Message	Date
Edmund Miller	c264c66a49	test(fastqc): Use -entry to speed up tests ... `--wt, --workflow-threads` is now an option and can be used to run tests simultaneously.	2020-11-16 13:41:59 -06:00
Edmund Miller	a4544a11ad	chore(fastqc): Remove test output	2020-11-16 10:22:19 -06:00
Edmund Miller	29937fe198	test(fastqc): Add expected files and md5sums ... The md5 sums change for the zip files every run so it's difficult to hit a moving target.	2020-11-16 10:20:29 -06:00
Edmund Miller	6d857a2584	ci(fastqc): Run pytest-workflow instead of workflow ... This will check for the actual output files and their contents not just whether the module runs or not.	2020-11-16 09:37:45 -06:00
Edmund Miller	07017f401e	test(fastqc): Add initial pytest-workflow	2020-11-16 09:35:01 -06:00
Harshil Patel	751204ef33	Merge pull request #76 from drpatelh/versions ... Remove Singularity image path	2020-11-12 15:27:06 +00:00
drpatelh	082c582258	Remove EClint for now	2020-11-12 15:22:15 +00:00
drpatelh	a3f46865ff	Remove Singularity image path	2020-11-12 14:55:16 +00:00
Harshil Patel	65ba3128ee	Merge pull request #72 from drpatelh/versions ... Update badges in README	2020-10-20 11:09:50 +01:00
drpatelh	99f5d49d37	Update README	2020-10-20 11:04:12 +01:00
drpatelh	5eb735f561	Update README	2020-10-20 11:02:46 +01:00
Harshil Patel	86dca6bfc2	Merge pull request #71 from drpatelh/versions ... Update picard version command and default container	2020-10-20 10:24:02 +01:00
drpatelh	47d390772c	Update picard version command and default container	2020-10-19 15:17:19 +01:00
Harshil Patel	ff0fe1a910	Merge pull request #70 from drpatelh/versions ... Update existing modules with new options and container syntax	2020-10-15 11:28:13 +01:00
drpatelh	29f9b05433	Update docs	2020-10-15 11:13:54 +01:00
drpatelh	7e2c7b1b41	Update README	2020-10-15 11:02:04 +01:00
drpatelh	530789ba85	Get tests passing	2020-10-15 10:47:15 +01:00
drpatelh	c32fcb39fc	Remove git update script	2020-10-15 10:22:40 +01:00
drpatelh	1d30e2c21a	Update tools not in rnaseq pipeline too	2020-10-14 18:59:25 +01:00
drpatelh	14525ed50d	Remove functions file	2020-10-14 18:29:50 +01:00
Harshil Patel	a6aab020df	Merge pull request #69 from drpatelh/versions ... Revert RSeQC version	2020-10-12 18:03:21 +01:00
drpatelh	e9e81e8691	Revert RSeQC version	2020-10-12 17:47:13 +01:00
Harshil Patel	d8f202c563	Merge pull request #68 from drpatelh/versions ... Update tool versions	2020-10-12 16:22:31 +01:00
drpatelh	6bb3d5caea	Update container	2020-10-12 16:20:35 +01:00
drpatelh	64377d4035	Bug fixes	2020-10-12 16:20:22 +01:00
drpatelh	a1b705d412	Update RSeQC version	2020-10-12 16:04:04 +01:00
drpatelh	436a1f983c	Update trimgalore version	2020-10-12 15:59:46 +01:00
drpatelh	d19a8c702d	Update picard version	2020-10-12 15:58:09 +01:00
drpatelh	74f27803b4	Update stringtie version	2020-10-12 15:55:07 +01:00
drpatelh	f4f96ff792	Update gffread version	2020-10-12 15:52:05 +01:00
Harshil Patel	0e11679748	Update main.nf	2020-09-18 10:39:41 +01:00
Harshil Patel	fb44f36f66	Update main.nf	2020-09-16 19:08:24 +01:00
Harshil Patel	436e37bcd0	Merge pull request #67 from drpatelh/master ... Add rnaseq DSL2 modules	2020-09-10 16:49:26 +01:00
drpatelh	e438d026bd	Unify syntax	2020-09-10 16:45:11 +01:00
drpatelh	cbf8329ffd	Add new modules	2020-09-10 16:09:54 +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
Harshil Patel	b1b0a6e3b1	Merge pull request #66 from Jeremy1805/master ... Changed options.publish_files definition in functions.nf/initOptions	2020-08-20 13:20:04 +01:00
Jeremy1805	789dc4f09a	Changed options.publish_files definition in functions.nf/initOptions	2020-08-20 11:57:10 +01:00
Harshil Patel	47b6dd70e4	Merge pull request #64 from drpatelh/master ... Add tests and docs for picard tools	2020-08-07 16:46:59 +01:00
drpatelh	b22ec332e9	Add GitHub Actions	2020-08-07 16:42:56 +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	50a628ad0a	Remove deprecated tests	2020-08-07 15:55:23 +01:00
Harshil Patel	bd98988f23	Merge pull request #63 from drpatelh/master ... Add docs and tests for all samtools commands	2020-08-07 15:40:03 +01:00
drpatelh	238f43789e	Add tests for all samtools commands	2020-08-07 15:35:19 +01:00
drpatelh	14480affba	Add flagstat test	2020-08-07 15:32:09 +01:00
drpatelh	d6f7bb055b	Fix indents	2020-08-07 15:27:35 +01:00
drpatelh	e648dc335c	Add samtools stats commands	2020-08-07 15:23:39 +01:00