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Author SHA1 Message Date
Phil Ewels
c8ceddfe77 Tidying, add samtools and trim_galore 2020-03-06 14:33:48 +00:00
Piotr Faba
f33dd2d2e9 add ci test 2020-03-06 14:31:44 +00:00
Piotr Faba
c90474202c update meta 2020-03-06 14:23:32 +00:00
Phil Ewels
198e9a85eb FastQC: add dockerfile and environment.yml 2020-03-06 14:04:18 +00:00
Piotr Faba
1c941ef8d6 Update test-data commit and references 2020-03-06 13:59:14 +00:00
Piotr Faba
490eca706c single and paired end supported 2020-03-06 13:23:12 +00:00
FelixKrueger
a6f7296e22 Initial commit 2020-03-06 13:21:17 +00:00
Phil Ewels
b3cc751e78 Build tool docker images: first attempt 2020-03-06 11:54:09 +00:00
JoseEspinosa
bcc89c27ca Fixing command to run nxf 2020-03-06 12:47:55 +01:00
JoseEspinosa
7fe0a936f6 Fixing another typo on the yml for CI github actions 2020-03-06 12:41:07 +01:00
JoseEspinosa
36c0c56fdd Fixing typo on the yml for CI github actions 2020-03-06 12:38:21 +01:00
JoseEspinosa
5f9cf40f5a Changing publishDir to take params.outdir and modifying yml for github actions 2020-03-06 12:23:23 +01:00
JoseEspinosa
5de4c86bac symlink working? (github actions error) 2020-03-06 12:02:40 +01:00
Piotr Faba
88bc7dcdd8 the module is working in test 2020-03-06 10:51:46 +00:00
JoseEspinosa
4312ddc1fe Is the file in the submodule? (github actions error) 2020-03-06 11:46:37 +01:00
JoseEspinosa
c8c2d0e659 Trying to fix git actions 2020-03-05 17:48:10 +01:00
JoseEspinosa
5bb7d9c497 Updating submodule with tcoffee dataset 2020-03-05 17:39:00 +01:00
Jeremy1805
60f1d3b7a1 Updated tools/bwa/mem/meta.yml 2020-03-05 16:35:56 +00:00
Jeremy1805
356e23823c Updated tools/bwa/mem/meta.yml 2020-03-05 16:31:46 +00:00
JoseEspinosa
707d2855d6 Adding tcoffee module 2020-03-05 17:18:35 +01:00
JoseEspinosa
17ccbce67b Update test-datasets with msa data 2020-03-05 17:17:14 +01:00
Jeremy1805
a4836ae3c3 Added tools/bwa/mem 2020-03-05 16:06:25 +00:00
Piotr Faba
97d9ae76f0 add cutadapt module 2020-03-05 15:56:11 +00:00
annacprice
e623dca3b7 initial commit of shovill 2020-03-05 09:29:23 +00:00
MaxUlysse
3e8475baf0 add social preview image 2020-02-12 15:27:56 +01:00
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