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Author SHA1 Message Date
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
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