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Author	SHA1	Message	Date
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
drpatelh	d5b16db27d	Add samtools sort	2020-08-07 15:21:28 +01:00
drpatelh	0287cad1f8	Add samtools index tests	2020-08-07 15:17:46 +01:00
drpatelh	17b5f5ef3b	Get samtools idxstats tests passing	2020-08-07 15:14:45 +01:00
drpatelh	46e4d35ec3	Get samtools flagstat passing	2020-08-07 15:12:03 +01:00
drpatelh	cf5cb8945c	Get samtools flagstat passing	2020-08-07 15:11:31 +01:00
drpatelh	736a0aa43c	Update indents and syntax	2020-08-07 15:05:25 +01:00
drpatelh	29f1585068	Remove test functions folder	2020-08-07 14:05:55 +01:00
drpatelh	6333786d62	Add test BAM files	2020-08-07 14:04:39 +01:00
drpatelh	953256f967	Reformat paired-end fastqs	2020-08-07 13:46:23 +01:00
Harshil Patel	347bbcc609	Merge pull request #62 from drpatelh/master ... Add docs and test data for BWA mem	2020-08-07 13:29:56 +01:00
drpatelh	0ad26e3b19	Add output files	2020-08-07 13:28:18 +01:00
drpatelh	d10878f19d	Change to SE	2020-08-07 13:27:06 +01:00