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Author SHA1 Message Date
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
Gregor Sturm
01a926866e
Update software/fastqc/test/main.nf 
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
 2020-07-15 12:48:21 +02:00
Gregor Sturm
9d7cece077
Update software/fastqc/meta.yml 
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
 2020-07-15 12:48:11 +02:00
Gregor Sturm
5a8803ee2f
Update software/fastqc/meta.yml 
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
 2020-07-15 12:48:03 +02:00
Gregor Sturm
a3db769a93
Update software/fastqc/meta.yml 
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
 2020-07-15 12:47:52 +02:00
Gregor Sturm
180310bf0a
Update software/fastqc/meta.yml 
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
 2020-07-15 12:47:42 +02:00
Gregor Sturm
6ad2b570c2
Update software/fastqc/meta.yml 
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
 2020-07-15 12:47:30 +02:00
Gregor Sturm
53897f4d97
Update software/fastqc/meta.yml 
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
 2020-07-15 12:47:19 +02:00
Gregor Sturm
450e2839d5 Extend and formalize module requirements 2020-07-15 12:44:52 +02:00
Gregor Sturm
b00bb83532 Document params 2020-07-15 11:01:15 +02:00
Gregor Sturm
86d6daf9de Implement publish_results parameter 2020-07-15 10:55:52 +02:00
Gregor Sturm
1dc47e7cd3 Make publishDir more flexible 2020-07-15 10:16:48 +02:00
Gregor Sturm
dd34fa5853 Use moduleDir for conda env 2020-07-15 09:48:17 +02:00
Gregor Sturm
f7c42ac4fd Add tests for fastqc module 2020-07-15 09:48:14 +02:00
Gregor Sturm
167067a92e Clean up module file 2020-07-15 09:47:41 +02:00
Harshil Patel
a5306b33da
Merge pull request #39 from grst/document-module-standards 
Document preliminary module structure
 2020-07-14 18:53:24 +01:00
JoseEspinosa
c485d56972 Indentation error in yml 2020-07-14 18:00:23 +02:00
JoseEspinosa
562fc74550 Indentation error in yml 2020-07-14 17:57:42 +02:00
JoseEspinosa
39b9ca205c Correcting path to test data 2020-07-14 17:42:03 +02:00
JoseEspinosa
b38135ff6b Moving bedtools/intersectbed to bedtools/intersect 2020-07-14 17:40:17 +02:00
JoseEspinosa
c059a485b9 Using bedtools{_,-}genomecov instead of genomecov alone 2020-07-14 17:31:40 +02:00
JoseEspinosa
71eaa83bf6 bedtoools/complementBed changed to bedtools/complement 2020-07-14 17:26:45 +02:00
JoseEspinosa
8c3d7aa2d8 Standardizing process names to BEDTOOLS_FOO and same with some variables 2020-07-14 17:25:32 +02:00
JoseEspinosa
99a8196776 Module bedtools-sort added 2020-07-14 17:20:12 +02:00
MaxUlysse
56ee2cc8e2 fix lint 2020-07-14 17:19:12 +02:00
MaxUlysse
1223614e15 add modules for bwa-mem2 2020-07-14 17:10:23 +02:00