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Author	SHA1	Message	Date
kevinmenden	32f6191ff3	editorconfig	2020-12-18 11:11:19 +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	0be13edc52	next try at editorconfig	2020-12-18 09:52:38 +01:00
kevinmenden	07f0a2476a	fixed linting errors	2020-12-18 09:50:05 +01:00
kevinmenden	0eb20c14bf	fixed unaligned output	2020-12-18 09:20:35 +01:00
kevinmenden	1c89c9717b	Merge branch 'master' of https://github.com/KevinMenden/modules	2020-12-18 09:16:17 +01:00
kevinmenden	f840325ead	added unaligned output	2020-12-18 09:14:40 +01:00
Kevin Menden	7805d25cc5	Update software/bowtie/align/meta.yml ... Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>	2020-12-18 09:13:48 +01:00
Kevin Menden	a7f1ff29d7	Update software/bowtie/align/meta.yml ... Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>	2020-12-18 09:13:42 +01:00
Kevin Menden	dc4108fd9b	Update software/bowtie/align/meta.yml ... Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>	2020-12-18 09:13:35 +01:00
Kevin Menden	41329b8982	Apply suggestions from code review ... Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>	2020-12-18 08:16:18 +01:00
kevinmenden	57ab6dbcbf	groovy formatting	2020-12-17 10:24:48 +01:00
kevinmenden	8d3fc30eb3	fixed yml formatting	2020-12-17 07:39:34 +01:00
kevinmenden	d75cb75111	added singularity; edge NXF version	2020-12-17 07:33:44 +01:00
kevinmenden	f35850bf14	bowtie bam output	2020-12-16 11:02:58 +01:00
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
kevinmenden	cc72028d3d	output index as directory	2020-12-09 15:58:56 +01:00
Kevin Menden	560a6a578b	Apply suggestions from code review ... Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>	2020-12-09 15:45:05 +01:00
kevinmenden	fee0707af1	added bowtie_align workflow test	2020-12-08 14:19:34 +01:00
kevinmenden	73530e8df7	added bowtie index test github workflow	2020-12-08 14:13:30 +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
kevinmenden	508761e05c	Added bowtie index and align modules	2020-12-08 12:57:00 +01:00
Harshil Patel	cd2cf9cf2f	Merge pull request #85 from nf-core/pytest-workflow-refactor ... Refactor all tests to use pytest-workflow	2020-12-04 14:30:00 +00:00
Edmund Miller	6d8ba714d5	ci(fastqc): Use 20.10.0 => ''	2020-12-04 08:23:19 -06:00
Edmund Miller	65697532a1	ci: Get rid of software folder	2020-12-01 11:40:16 -06:00
Edmund Miller	6404c3390d	ci(fastqc): Remove md5sums ... These may not work across nextflow versions	2020-12-01 11:18:55 -06:00
Edmund Miller	8cd635f757	ci(fastqc): Fix test matrix	2020-12-01 11:13:43 -06:00
Edmund Miller	98c629583a	ci: Test whether subdirectories are breaking workflows	2020-11-30 19:03:56 -06:00
Edmund Miller	7d2b74a5f7	ci(fastqc): Use a test matrix for NXF versions	2020-11-30 18:57:56 -06:00
Harshil Patel	e02f0de514	Merge pull request #87 from drpatelh/rsem_index ... Use STAR to build initial index for RSEM	2020-11-30 14:45:32 +00:00
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