97 commits

Author	SHA1	Message	Date
JoseEspinosa	22dcdc692d	Adding samtools_mpileup module	2021-01-29 17:58:42 +01:00
JoseEspinosa	3eedca9bb4	Add samtools_view	2021-01-29 17:18:45 +01:00
kevinmenden	5be1598b29	remove log.progress.out from test	2021-01-25 15:21:48 +01:00
kevinmenden	a1e1e27f67	updated test md5sums	2021-01-25 15:00:18 +01:00
kevinmenden	71e0de733c	adapdted star for mutliple output BAMs	2021-01-25 14:09:03 +01:00
kevinmenden	6444af7b36	star module tests	2021-01-25 09:02:03 +01:00
kevinmenden	f58c1c1e9e	added star genomegenerate test	2021-01-22 14:01:59 +01:00
Edmund Miller	daa25b9329	Merge branch 'preseq_test'	2021-01-15 17:41:13 -06:00
Edmund Miller	86850dc8a4	style: Remove old comment ... Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>	2021-01-15 10:32:20 -06:00
sruthipsuresh	7729fee5a9	Added gffread and gff3 file for testing	2021-01-15 10:32:20 -06:00
Edmund Miller	d7a78fa127	style: Fix indent ... Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>	2021-01-15 10:28:11 -06:00
sruthipsuresh	b95bd37780	Added ucsc module	2021-01-15 10:28:11 -06:00
Harshil Patel	27dbe8b52a	Merge pull request #115 from Functional-Genomics-Lab/stringtie_test ... Added testing for Stringtie	2021-01-15 16:09:39 +00:00
Edmund Miller	53830e05c7	test: Fix typo ... Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>	2021-01-15 10:07:44 -06:00
Edmund Miller	fe39c7822f	style: Fix indentation	2021-01-15 10:01:02 -06:00
Edmund Miller	b9e8f959b3	style: Standardize process names ... Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>	2021-01-15 10:00:40 -06:00
sruthipsuresh	ec91171152	Corrected naming to ensure test checks work	2021-01-15 09:38:13 -06:00
sruthipsuresh	5a1c1f90e5	removed md5sums for pdf, rdata	2021-01-15 09:38:13 -06:00
sruthipsuresh	3f814d1e2f	Workflow and md5sums added	2021-01-15 09:38:13 -06:00
sruthipsuresh	269d9888fe	Corrected bash error, tested process	2021-01-15 09:38:13 -06:00
Sruthi Suresh	b7435b0159	added test file for phantompeakqualtools for testing	2021-01-15 09:38:13 -06:00
sruthipsuresh	09d56efe12	Fixed with mr file for size issues	2021-01-14 02:12:57 -06:00
sruthipsuresh	00ef1d3863	Changed input to bed files	2021-01-15 16:52:17 -06:00
sruthipsuresh	a66618be98	Delete tests/software/phantompeakqualtools directory	2021-01-13 21:23:02 -06:00
sruthipsuresh	6f3cbfcd9a	Fixed test.yml	2021-01-12 18:14:28 -06:00
sruthipsuresh	b297f7aea1	Fixed test and removed phantompeak tests	2021-01-12 18:04:12 -06:00
sruthipsuresh	7c88cf4f67	Finished module with md5sums	2021-01-12 09:29:31 -06:00
sruthipsuresh	0a04c96357	Added module, TODO data	2021-01-12 09:13:37 -06:00
sruthipsuresh	3b581d1912	Updated test.yml	2021-01-12 08:56:11 -06:00
sruthipsuresh	a2faeb703f	Fixed md5sums	2021-01-12 08:50:20 -06:00
sruthipsuresh	cb39fcb915	Added preseq module and workflow	2021-01-12 08:41:09 -06:00
sruthipsuresh	e1a3d1b18a	Corrected naming to ensure test checks work	2020-12-21 19:53:03 -06:00
sruthipsuresh	5319eabbc5	removed md5sums for pdf, rdata	2020-12-19 06:09:04 -06:00
sruthipsuresh	522b896534	Workflow and md5sums added	2020-12-19 06:09:04 -06:00
sruthipsuresh	8c088d473b	Corrected bash error, tested process	2020-12-19 06:09:04 -06:00
Sruthi Suresh	10d0058a1a	added test file for phantompeakqualtools for testing	2020-12-19 06:09:04 -06:00
Harshil Patel	c98f9284a2	Merge pull request #89 from KevinMenden/master ... Add bowtie module	2020-12-18 14:56:29 +00:00
kevinmenden	8f75bac67e	update test.bam md5sums	2020-12-18 11:16:58 +01:00
kevinmenden	db0b631906	removed index from test output	2020-12-18 11:06:02 +01:00
kevinmenden	299a3fa07e	adding .index back	2020-12-18 10:58:37 +01:00
kevinmenden	07f0a2476a	fixed linting errors	2020-12-18 09:50:05 +01:00
kevinmenden	f35850bf14	bowtie bam output	2020-12-16 11:02:58 +01:00
drpatelh	141ca290b7	Change md5sum for picard Markduplicates due to version bump	2020-12-14 00:44:49 +00:00
kevinmenden	0d7c8276b7	added test yml and md5s	2020-12-09 16:54:11 +01:00
kevinmenden	42020ce5ac	added tests for bowtie paired-end alignment; resolved index bug	2020-12-09 16:39:05 +01:00
Harshil Patel	79a0ce79ab	Merge pull request #82 from abhi18av/master ... Add multiqc module	2020-12-09 11:31:07 +00:00
Abhinav Sharma	0c9f29e0a2	Give finishing touches after the review	2020-12-08 19:08:00 +05:30
Abhinav Sharma	b56a0322ab	Apply suggestions from code review by @drpatelh ... Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>	2020-12-08 18:57:14 +05:30
kevinmenden	fee0707af1	added bowtie_align workflow test	2020-12-08 14:19:34 +01:00
kevinmenden	6660a597a3	added tests for bowtie module	2020-12-08 13:59:14 +01:00