167 commits

Author	SHA1	Message	Date
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