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Author SHA1 Message Date
FelixKrueger
f8916eb9b5 FastQC module is working and now accepting arguments 2020-03-16 14:17:38 +00:00
Maxime Garcia
f62fad63ca
Merge pull request #12 from MaxUlysse/dev 
Add some modules
 2020-02-10 17:10:35 +01:00
Maxime Garcia
48be154434
Update tools/bwa/index/meta.yml 
Co-Authored-By: Olga Botvinnik <olga.botvinnik@gmail.com>
 2020-01-24 10:39:52 +01:00
MaxUlysse
7fbfd2d6cb add samtools faidx to index fasta file 2020-01-23 11:36:21 +01:00
MaxUlysse
b8dda67338 add htslib tabix to index bgzipped vcf files 2020-01-23 11:35:49 +01:00
MaxUlysse
9db873c3bc add gatk dict to create dictionnary from fasta file 2020-01-23 11:35:19 +01:00
MaxUlysse
a69aebd01b fix index process 2020-01-23 10:19:00 +01:00
MaxUlysse
ad3c14a964 fix typo 2020-01-21 11:25:13 +01:00
MaxUlysse
1f46499e3b add bwa index 2020-01-21 11:24:32 +01:00
Phil Ewels
a88b867498
Merge pull request #10 from ewels/master 
Fix trim galore process name
 2019-12-06 11:24:45 +01:00
Phil Ewels
5fbde1c69d Fix trim galore process name 2019-12-06 11:24:07 +01:00
Phil Ewels
4eb1428931 Added empty test_import.nf file 2019-12-06 10:38:57 +01:00
Maxime Garcia
9fd356468d
Merge pull request #9 from ewels/master 
Added samtools, restructured directory structures
 2019-12-06 10:37:42 +01:00
Phil Ewels
c77ea13d35 Fixed FastQC tests with submodule 2019-12-06 10:15:49 +01:00
Phil Ewels
93f7b26aa2 Use submodules for test data 2019-12-06 09:24:33 +01:00
Phil Ewels
36df850298 Added test-datasets as a git submodule 2019-12-06 09:19:00 +01:00
Phil Ewels
51bd2c0277 Ansi log false for tests 2019-12-05 22:20:02 +01:00
Phil Ewels
e2a205c8df Added nextflow.config files for all 2019-12-05 22:18:33 +01:00
Phil Ewels
eb41e5ebba FastQC: actually run a test 2019-12-05 22:11:12 +01:00
Phil Ewels
ef486a908b Use empty dict instead for workflow 2019-12-05 16:09:28 +01:00
Phil Ewels
d682c6f7a8 Workflows: test everything on paths 2019-12-05 16:08:12 +01:00
Phil Ewels
a065ac3532 Actions: install nextflow 2019-12-05 16:03:00 +01:00
Phil Ewels
acc4eb0054 GitHub actions - run nextflow in a docker image 2019-12-05 15:57:32 +01:00
Phil Ewels
af766a9cc7 Added TrimGalore 2019-12-05 15:53:38 +01:00
Phil Ewels
497573fc5d Refactor GitHub actions workflows 2019-12-05 15:44:10 +01:00
Phil Ewels
8837c2b81d GitHub actions: paths, not path 2019-12-05 15:39:01 +01:00
Phil Ewels
97fbd32644 Added samtools sort + index 
Added container to FastQC
 2019-12-05 15:36:35 +01:00
Phil Ewels
5e4c023edd Start work on FastQC module files 2019-12-05 15:18:09 +01:00
Phil Ewels
4582ab344c Add GitHub Actions, put FastQC in to a directory 2019-12-05 14:52:43 +01:00
Harshil Patel
ada7b5f9a3
Merge pull request #5 from ewels/master 
Replace Slack join URL
 2019-07-30 15:33:41 +01:00
Phil Ewels
44b6e1250d Replace Slack join URL 2019-07-30 16:31:44 +02:00
drpatelh
adb9074f55 Typo 2019-07-26 16:06:49 +01:00
drpatelh
56608c0ad4 FastQC prototype with docs 2019-07-26 16:05:13 +01:00
drpatelh
c4456ad334 Fix links 2019-07-26 13:38:08 +01:00
drpatelh
eb9aeea775 Refine README 2019-07-26 13:30:26 +01:00
drpatelh
ef8c13a7d8 Fill out repo 2019-07-26 10:19:07 +01:00
drpatelh
8f5a297705 first commit 2019-07-26 09:54:25 +01:00