1392 commits

This branch

This branch

All branches

Author	SHA1	Message	Date
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
drpatelh	0cbefde4b0	Add index test data for BWA	2020-08-07 13:25:02 +01:00
drpatelh	7ab1245eb5	Add test data	2020-08-07 13:24:39 +01:00
drpatelh	b5338efb7d	Add tests for BWA mem	2020-08-07 13:24:24 +01:00
Harshil Patel	efce3024de	Merge pull request #61 from drpatelh/master ... Add docs and tests for BWA index	2020-08-07 13:01:10 +01:00
drpatelh	cff81ef875	Add test data	2020-08-07 12:57:32 +01:00
drpatelh	7604bd27fc	Add test nextflow.config	2020-08-07 12:56:52 +01:00
drpatelh	f367f9ef69	Add main test script	2020-08-07 12:56:39 +01:00
drpatelh	375af1428e	Minor change	2020-08-07 12:38:10 +01:00
drpatelh	a6fc702c8b	Update bwa index docs	2020-08-07 12:38:01 +01:00
Harshil Patel	ad4151703f	Merge pull request #60 from drpatelh/master ... Add docs and tests for TrimGalore!	2020-08-07 12:27:43 +01:00
drpatelh	9f4192d433	Add TrimGalore GitHub Actions test	2020-08-07 12:21:47 +01:00
drpatelh	36f2544c36	Add single_end input file for testing	2020-08-07 12:19:47 +01:00
drpatelh	6522b04ee3	Remove old code	2020-08-07 12:19:28 +01:00
drpatelh	30256d8e81	Update tests	2020-08-07 12:18:53 +01:00
drpatelh	2c0f552908	Add output files	2020-08-07 12:18:43 +01:00
drpatelh	4df72f0396	Update nextflow.config	2020-08-07 12:14:12 +01:00
drpatelh	f32950d0f2	Update docs for trimgalore	2020-08-07 12:10:42 +01:00
Harshil Patel	7c900e2d17	Merge pull request #59 from drpatelh/master ... Refine module TEMPLATE	2020-08-07 11:41:56 +01:00
drpatelh	a63897ee9c	Add input output test folders	2020-08-07 11:40:51 +01:00
drpatelh	d63982b41e	Update README	2020-08-07 11:38:48 +01:00
drpatelh	3a4fbf36ae	Add test	2020-08-07 11:31:07 +01:00