668 commits

This branch

This branch

All branches

Author	SHA1	Message	Date
Edmund Miller	0b6f117d2a	ci(#77): eclint => editorconfig-checker	2020-12-17 17:48:02 -06:00
Chris Cheshire	6f1c66f22f	Merge remote-tracking branch 'nf-core/master'	2020-12-17 14:29:20 +00:00
Chris Cheshire	4436f59a1c	seacr | Syntax error	2020-12-17 14:27:37 +00:00
Chris Cheshire	15e1b860f9	seacr | added github action workflow	2020-12-17 14:25:42 +00:00
Chris Cheshire	a57169a5da	seacr | updated test script	2020-12-17 14:23:20 +00:00
Chris Cheshire	1aa7ed187a	seacr | Updated gitignore to ignore output folder	2020-12-17 14:23:07 +00:00
Chris Cheshire	b24834dfce	seacr | local testing implimented	2020-12-17 14:20:24 +00:00
Chris Cheshire	4e55bdcf84	seacr | removed test files	2020-12-17 14:20:02 +00:00
Chris Cheshire	a964d98d7f	seacr | Added test data	2020-12-17 13:55:58 +00:00
Chris Cheshire	74e7b5385f	seacr | Added main process structure	2020-12-17 13:54:48 +00:00
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
Chris Cheshire	05f7933afa	Merge remote-tracking branch 'origin/master'	2020-12-16 11:05:15 +00:00
Chris Cheshire	3ff2b558e0	seacr | Added callpeak skeleton	2020-12-16 11:05:06 +00:00
Chris Cheshire	89eee34df9	seacr | Added callpeak skeletonmain.nf	2020-12-16 11:04:46 +00:00
Chris Cheshire	174652c77b	Merge remote-tracking branch 'nf-core/master'	2020-12-16 10:19:20 +00:00
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
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	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
Chris Cheshire	4d2b1dd68f	Merge remote-tracking branch 'nf-core/master'	2020-12-07 13:51:23 +00:00
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
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