290 commits

Author	SHA1	Message	Date
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
Chris Cheshire	a57169a5da	seacr | updated test script	2020-12-17 14:23:20 +00:00
Chris Cheshire	b24834dfce	seacr | local testing implimented	2020-12-17 14:20:24 +00:00
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
kevinmenden	9d67da2b2c	added module yml files	2020-12-08 13:40:32 +01:00
Abhinav Sharma	5949bfc15b	Edit the location of multiqc_config file	2020-12-04 22:55:15 +05:30
Abhinav Sharma	27b4b29976	Remove the extra data files	2020-12-04 20:20:59 +05:30
Abhinav Sharma	3da7aec183	Update the signatures	2020-12-04 12:25:16 +05:30
Abhinav Sharma	a30df8a59b	Iterate again on MultiQC	2020-12-04 12:11:17 +05:30
Abhinav Sharma	84c0bda00e	Apply suggestions from code review by @Emiller88	2020-12-03 12:57:24 +05:30
Abhinav Sharma	5fd3ba3ce6	Update the tests for MultiQC	2020-12-02 13:09:32 +05:30
Edmund Miller	6404c3390d	ci(fastqc): Remove md5sums ... These may not work across nextflow versions	2020-12-01 11:18:55 -06:00
Abhinav Sharma	b43c1f3937	Refactor the multiqc test code	2020-12-01 12:19:52 +05:30
Edmund Miller	2fc39e02e2	test(trimgalore): Refactor se and pe to use pytest-workflow	2020-11-24 21:08:34 -06:00
Edmund Miller	b2cd464ad3	test(samtools): Refactor stats to use pytest-workflow	2020-11-24 21:08:34 -06:00
Edmund Miller	36bbf6baa3	test(samtools): Refactor sort to use pytest-workflow ... Pretty sure this is passing it a sorted bam though?	2020-11-24 21:08:34 -06:00
Edmund Miller	6448638b55	test(samtools): Refactor index to use pytest-workflow	2020-11-24 21:08:34 -06:00
Edmund Miller	16cb794892	test(samtools): Refactor idxstats to use pytest-workflow	2020-11-24 21:08:34 -06:00
Edmund Miller	34d86427a6	test(samtools): Refactor flagstat to use pytest-workflow	2020-11-24 21:08:33 -06:00
Edmund Miller	d1a77b2fb2	test(picard): Add failing test for markduplicates	2020-11-24 21:08:33 -06:00
Edmund Miller	7848019cdb	test(picard): Refactor markduplicates to use pytest-workflow	2020-11-24 21:08:33 -06:00
Edmund Miller	d009420a0c	test(fastqc): Fix md5sums ... These must have gotten messed up at some point 83539fcdf2 is my guess	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
Edmund Miller	016d8684f3	test(bwa): Refactor to use pytest-workflow	2020-11-24 19:00:11 -06:00
Edmund Miller	83539fcdf2	test(fastqc): restructure under software/fastqc ... Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>	2020-11-24 15:30:51 -06:00