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Author	SHA1	Message	Date
drpatelh	e5c7ecc89c	Use STAR to build initial index for RSEM	2020-11-30 11:29:24 +00:00
Edmund Miller	036427d73c	ci(pytest-workflow): Fix trigger paths	2020-11-24 21:24:55 -06:00
Edmund Miller	6eeb930bdb	chore: Remove test directory from dummy tool	2020-11-24 21:09:55 -06:00
Edmund Miller	86219a586b	ci(trimgalore): Use pytest-workflow	2020-11-24 21:08:34 -06:00
Edmund Miller	2fc39e02e2	test(trimgalore): Refactor se and pe to use pytest-workflow	2020-11-24 21:08:34 -06:00
Edmund Miller	445498d0c3	ci(samtools): Run tests with 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	ebf3a4529f	ci(picard): Update markduplicates	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	dfc8528df9	ci: Remove docker workflow ... This only applies to deprecated software	2020-11-24 18:58:02 -06:00
Edmund Miller	691df9d469	style(actions): Create seperate software dir ... For future subworkflows	2020-11-24 18:57:53 -06:00
Harshil Patel	794a5cbd0c	Merge pull request #80 from nf-core/pytest-workflow ... Pytest-workflow	2020-11-24 22:55:07 +00:00
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
Edmund Miller	b96f2d6a5e	test(config): One config to rule them all ... Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>	2020-11-24 20:26:04 +00:00
Edmund Miller	2e56022e31	test(fastqc): Remove input symlinks ... Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>	2020-11-24 20:26:04 +00:00
Edmund Miller	1fd97e8804	test(fastqc): Fix md5sums	2020-11-24 20:26:04 +00:00
Edmund Miller	ba681c6f27	refactor(pytest-workflow): Move fastqc tests to tests/	2020-11-24 20:26:04 +00:00
Edmund Miller	f235732a58	ci(fastqc): Use both threads in GitHub runner	2020-11-16 13:45:00 -06:00
Edmund Miller	c264c66a49	test(fastqc): Use -entry to speed up tests ... `--wt, --workflow-threads` is now an option and can be used to run tests simultaneously.	2020-11-16 13:41:59 -06:00
Edmund Miller	a4544a11ad	chore(fastqc): Remove test output	2020-11-16 10:22:19 -06:00
Edmund Miller	29937fe198	test(fastqc): Add expected files and md5sums ... The md5 sums change for the zip files every run so it's difficult to hit a moving target.	2020-11-16 10:20:29 -06:00
Edmund Miller	6d857a2584	ci(fastqc): Run pytest-workflow instead of workflow ... This will check for the actual output files and their contents not just whether the module runs or not.	2020-11-16 09:37:45 -06:00
Edmund Miller	07017f401e	test(fastqc): Add initial pytest-workflow	2020-11-16 09:35:01 -06:00
Harshil Patel	751204ef33	Merge pull request #76 from drpatelh/versions ... Remove Singularity image path	2020-11-12 15:27:06 +00:00
drpatelh	082c582258	Remove EClint for now	2020-11-12 15:22:15 +00:00
drpatelh	a3f46865ff	Remove Singularity image path	2020-11-12 14:55:16 +00:00
Harshil Patel	65ba3128ee	Merge pull request #72 from drpatelh/versions ... Update badges in README	2020-10-20 11:09:50 +01:00
drpatelh	99f5d49d37	Update README	2020-10-20 11:04:12 +01:00
drpatelh	5eb735f561	Update README	2020-10-20 11:02:46 +01:00
Harshil Patel	86dca6bfc2	Merge pull request #71 from drpatelh/versions ... Update picard version command and default container	2020-10-20 10:24:02 +01:00
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