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Author	SHA1	Message	Date
sruthipsuresh	cb39fcb915	Added preseq module and workflow	2021-01-12 08:41:09 -06:00
sruthipsuresh	a812dceb23	Updated bam input in module	2021-01-12 08:32:29 -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	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
Harshil Patel	0305d873f4	Merge pull request #81 from nf-core/ec-ci ... Apply editorconfig and enable CI again	2020-12-18 00:46:44 +00:00
Edmund Miller	d76638d6f8	style(#77): Fix editorconfig errors	2020-12-17 17:50:24 -06:00
Edmund Miller	eb61638501	ci: Use verbose name for editorconfig-check ... I was getting confused myself with eclint	2020-12-17 17:48:19 -06:00
Edmund Miller	c6cf653f25	ci(#77): Ignore README for editorconfig ... Because of the nf-core examples it throws errors.	2020-12-17 17:48:02 -06:00
Edmund Miller	0b6f117d2a	ci(#77): eclint => editorconfig-checker	2020-12-17 17:48:02 -06:00
Harshil Patel	b236d0c834	Update main.nf	2020-12-17 10:24:01 +00:00
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
Harshil Patel	ceef4a6044	Merge pull request #109 from drpatelh/singularity ... Bump NF version and add direct download Singularity paths back in to modules	2020-12-14 12:20:03 +00:00
drpatelh	141ca290b7	Change md5sum for picard Markduplicates due to version bump	2020-12-14 00:44:49 +00:00
drpatelh	200c946693	Add --singularity_pull_docker_container to module yml	2020-12-14 00:34:24 +00:00
drpatelh	91726e4c55	Move old checksum file	2020-12-14 00:23:28 +00:00
drpatelh	992232b340	Bump NF version to 20.11.0-edge	2020-12-14 00:14:28 +00:00
drpatelh	e397c64c69	Add explicit Nextflow version to README	2020-12-14 00:08:38 +00:00
drpatelh	99a2364a26	Update all other modules	2020-12-14 00:05:48 +00:00
drpatelh	047dbde0af	Add singularity containers for rnaseq pipeline modules	2020-12-13 23:41:53 +00:00
Harshil Patel	5561fb58d8	Merge pull request #90 from nf-core/ci-nextflow-matrix ... Support multiple nextflow versions in CI	2020-12-10 12:39:00 +00:00
Harshil Patel	deb0a103db	Merge pull request #92 from drpatelh/salmon ... Update Salmon modules	2020-12-09 23:01:06 +00:00
drpatelh	115efec15c	Update Salmon quant to use BAM input	2020-12-09 21:20:52 +00:00
drpatelh	37b8b82c98	Fix tyop	2020-12-09 21:20:26 +00:00
drpatelh	42f318fe75	Update Salmon modules	2020-12-09 21:20:11 +00:00
Edmund Miller	8d27ff53c5	ci: Support multiple nextflow versions	2020-12-09 09:56:40 -06:00
Edmund Miller	f994d55c18	style: Fix indent on workflows	2020-12-09 09:56:11 -06:00
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