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Author SHA1 Message Date
drpatelh
9142ad7016 Move terminology to bottom 2020-08-06 12:17:24 +01:00
drpatelh
c2f797d820 Update existing pipeline usage 2020-08-06 12:12:40 +01:00
drpatelh
2c9cd2d89b Update main script 2020-08-06 12:00:38 +01:00
drpatelh
83b61fcccd Update README 2020-08-06 12:00:24 +01:00
drpatelh
530b4c1bd9 Add test directory 2020-08-06 11:32:38 +01:00
drpatelh
b7d0ee043e Initial commit 2020-08-06 11:32:18 +01:00
drpatelh
f021ab119b Initial commit 2020-08-06 11:32:11 +01:00
drpatelh
ab512be9aa Initial commit 2020-08-06 11:31:52 +01:00
Harshil Patel
d286fdf995
Merge pull request #54 from drpatelh/master 
Hard copy functions.nf
 2020-08-05 18:39:53 +01:00
drpatelh
f315a7b3c4 Hard copy files 2020-08-05 18:38:27 +01:00
Harshil Patel
1073ea47fa
Merge pull request #53 from drpatelh/master 
Add in chipseq modules
 2020-08-05 17:46:59 +01:00
drpatelh
71a6a9decc Fix markdownlint 2020-08-05 17:46:23 +01:00
drpatelh
9988dacfc6 Fix yaml lint 2020-08-05 17:32:47 +01:00
drpatelh
ab8a9025a0 Copy across test data and docs for trimgalore 2020-08-05 17:28:25 +01:00
drpatelh
50fce8b3cf Copy across test data and docs for samtools sort 2020-08-05 17:28:09 +01:00
drpatelh
de9d33da12 Copy across test data and docs for samtools index 2020-08-05 17:27:58 +01:00
drpatelh
fb697eca2f Copy across test data and docs for bwa mem 2020-08-05 17:27:42 +01:00
drpatelh
da4dcee934 Copy across test data and docs for bwa index 2020-08-05 17:27:28 +01:00
drpatelh
4f590ff239 Remove some more modules 2020-08-05 17:25:34 +01:00
drpatelh
1edc58a36b Pinch docs and delete redundant modules 2020-08-05 17:24:40 +01:00
drpatelh
5d224740cd Change path 2020-08-05 17:17:58 +01:00
drpatelh
137db462a7 Add samtools 2020-08-05 17:17:47 +01:00
drpatelh
993d0d5743 Add picard 2020-08-05 17:17:41 +01:00
drpatelh
9d168cf29e Add deeptools 2020-08-05 17:17:34 +01:00
drpatelh
f481899049 Add subread 2020-08-05 17:17:19 +01:00
drpatelh
20e6d847a3 Add trimgalore 2020-08-05 17:17:12 +01:00
drpatelh
c5bb9c2fde Add macs2 2020-08-05 17:17:05 +01:00
drpatelh
f61ad7506a Add homer 2020-08-05 17:16:56 +01:00
drpatelh
71d7aecf74 Add preseq 2020-08-05 17:16:45 +01:00
drpatelh
e94676a2b2 Add phantompeakqualtools 2020-08-05 17:16:34 +01:00
drpatelh
6fe4ec16df Add ucsc 2020-08-05 17:16:23 +01:00
drpatelh
3b1669c317 Add bwa mem 2020-08-05 17:16:08 +01:00
drpatelh
7938a60a02 Add bwa index 2020-08-05 17:15:56 +01:00
drpatelh
7f5ca56413 Soft-link functions to top-level module dir 2020-08-05 17:03:04 +01:00
Harshil Patel
7f13463d0b
Merge pull request #52 from drpatelh/master 
Why isn't GitHub API refreshing with these changes?!
 2020-08-05 16:36:25 +01:00
drpatelh
4a65c77e58 deprecated/trim_galore/Dockerfile 2020-08-05 16:34:07 +01:00
drpatelh
3ec4f63fd8 Use correct link to fastqc 2020-08-05 16:28:42 +01:00
Harshil Patel
2b6a68260b
Merge pull request #51 from drpatelh/master 
Test latest FastQC implementation
 2020-08-05 16:10:41 +01:00
drpatelh
c08e6959a5 Reorganise everything 2020-08-05 16:09:25 +01:00
Harshil Patel
88eac382be
Merge pull request #41 from MaxUlysse/bwa-mem2 
add module for bwa-mem2 index
 2020-08-05 15:45:43 +01:00
Harshil Patel
95a91032ce
Merge pull request #42 from JoseEspinosa/bedtools_dev 
Add modules complement, genomecov, intersect, merge, sort for bedtools
 2020-08-05 15:45:17 +01:00
Harshil Patel
b3145e3f19
Merge pull request #50 from nf-core/minor-style-improvements 
Minor style improvements
 2020-07-27 12:04:04 +01:00
Paolo Di Tommaso
70daf8be30
Minor style improvents 
This commit provides a minor refactoring with som
Nextflow code style improvments:
- Replaces `.toGiga()` with `.giga`
- Replaces `tag { foo }` with `tag "$foo"`
- Move publishDir before input declarations. Directives should be
  before the first input. Tho this is not enforced, it may be in
  future versions.
- Replaces input `file` with `path`
- Remove unnecessary parentheses
 2020-07-27 12:11:42 +02:00
Phil Ewels
6dfb9f02c9
Merge pull request #47 from stevekm/fastqc-unit-test 
move md5 function to lib dir and symlink to fastqc test dir, rename m…
 2020-07-23 11:46:10 +02:00
Phil Ewels
dbf5b267b1
Fix code format linting 2020-07-23 11:43:48 +02:00
Phil Ewels
3406ed4da0 Merge branch 'master' into fastqc-unit-test 2020-07-17 16:00:59 +02:00
Phil Ewels
c2aef67408
Merge pull request #49 from ewels/fix-actions 
Fix a bunch of stuff in GitHub Actions test workflows
 2020-07-17 16:00:23 +02:00
Phil Ewels
f01b3f13a6 Remove debugging statement 2020-07-17 16:00:08 +02:00
Phil Ewels
2d1252c804 FastQC tests - disable hash check 2020-07-17 11:30:28 +02:00
Phil Ewels
dcc4beacb1 Fix FastQC test 2020-07-17 11:26:50 +02:00