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Author SHA1 Message Date
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
Phil Ewels
9b4634a426 Use latest edge version of NXF for FastQC test 2020-07-17 10:35:17 +02:00
Phil Ewels
e71bb92534 Workflows - trigger on change to workflow and test data too 2020-07-16 17:14:57 +02:00
Phil Ewels
aa24c8d175 Fix a bunch of stuff in GitHub Actions test workflows 2020-07-16 17:11:34 +02:00
Gregor Sturm
2b6dc71338
Merge pull request #48 from grst/update-requirements 
Update module requirements with consensus from today's meeting
 2020-07-16 16:54:15 +02:00
Gregor Sturm
6634a37bfd
Update README.md 
Co-authored-by: Phil Ewels <phil.ewels@scilifelab.se>
 2020-07-16 16:48:47 +02:00
Gregor Sturm
f95f234562
Update README.md 
Co-authored-by: Phil Ewels <phil.ewels@scilifelab.se>
 2020-07-16 16:48:22 +02:00
JoseEspinosa
a09e3a633d I forgot to uncomment output 2020-07-16 16:38:37 +02:00
JoseEspinosa
d30089f12d Very preliminary implementation of passing optional params to bedtools/intersect modules 2020-07-16 16:37:33 +02:00
Gregor Sturm
9b83ad1fe2 Update README 2020-07-16 15:42:41 +02:00
Stephen Kelly
846a862513 move md5 function to lib dir and symlink to fastqc test dir, rename md5 function 2020-07-16 09:17:48 -04:00
Phil Ewels
9dfafb4a19
Merge pull request #46 from stevekm/fastqc-unit-test 
add FastQC output validation and md5 checksum hash checks
 2020-07-16 15:13:44 +02:00
Stephen Kelly
4957eb98e5 update GitHub actions for Fastqc 2020-07-16 08:49:08 -04:00
Stephen Kelly
61d44c34d0 update GitHub actions for Fastqc 2020-07-16 08:31:19 -04:00
Stephen Kelly
45fbbb538c add FastQC output validation and md5 checksum hash checks 2020-07-16 08:20:37 -04:00
Harshil Patel
4ee6da3a34
Merge pull request #45 from FelixKrueger/master 
Adding back in all input files we had before
 2020-07-16 09:32:06 +01:00
JoseEspinosa
759dd85c92 Removing biocontainer in favor of nf-core container 2020-07-16 10:22:09 +02:00
FelixKrueger
9402a2efbe Still fixing linting 2020-07-16 09:06:59 +01:00
FelixKrueger
c6f73f9d56 Trying to trigger CI tests 2020-07-16 09:01:29 +01:00
JoseEspinosa
6d8b616975 Bedtools sort adapted to the current module standard 2020-07-15 18:16:12 +02:00
JoseEspinosa
4d2e375a0d Bedtools merge adapted to the current module standard 2020-07-15 18:16:01 +02:00
JoseEspinosa
98c8f44130 Bedtools intersect adapted to the current module standard 2020-07-15 18:15:49 +02:00
JoseEspinosa
0b123f9e13 Bedtools genomecov adapted to the current module standard 2020-07-15 18:15:32 +02:00
JoseEspinosa
2cbc988d5f Bedtools complement adapted to the current module standard 2020-07-15 18:15:16 +02:00
JoseEspinosa
1273c31294 Adding files for bedtools testing 2020-07-15 18:13:51 +02:00
FelixKrueger
684005f2cb Fixing markdown lint 2 2020-07-15 16:00:21 +01:00
FelixKrueger
4f8b7a90aa Trying to fix markdown linting 2020-07-15 15:59:17 +01:00
FelixKrueger
02156d6b0d Removing old subsampled SRR files 2020-07-15 15:48:09 +01:00
FelixKrueger
e90164dd0b Adding back tool specific input output and index files 2020-07-15 15:46:45 +01:00
FelixKrueger
1c84a234ec Adding back in all input files we had before 2020-07-15 15:12:04 +01:00
Felix Krueger
45cc9ede3e
Merge pull request #44 from drpatelh/master 
Change test directory name to input for FastQC
 2020-07-15 15:17:52 +02:00
drpatelh
532859d437 Update path 2020-07-15 14:07:19 +01:00
JoseEspinosa
7f8b8189f8 Merge remote-tracking branch 'upstream/master' into bedtools_dev 2020-07-15 15:05:26 +02:00
Harshil Patel
6028bb080b
Merge pull request #40 from grst/update-fastqc 
Update fastqc to adhere to new module guidelines
 2020-07-15 12:59:28 +01:00
Harshil Patel
741b0786f9
Merge pull request #43 from grst/update-module-requirements 
Extend and formalize module requirements
 2020-07-15 12:58:12 +01:00
Gregor Sturm
5fe7b9eb66 Update README.md 2020-07-15 13:29:21 +02:00
Gregor Sturm
a2bcb5c36a Update module according to discussion on Slack 2020-07-15 13:04:49 +02:00