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Author SHA1 Message Date
Alexander Peltzer
4303ec700c
Propose module organization 
See above changes to readme :_)
 2020-03-16 14:06:03 +01:00
FelixKrueger
0ceb45068e FastQ Screen works with E coli paired-end test file 2020-03-10 22:14:25 +00:00
FelixKrueger
d9a3b02b00 Updated yaml description 2020-03-10 14:13:36 +00:00
JoseEspinosa
787bf44c62 Name was fixed to tcoffee instead of FastQC (used as template) 2020-03-06 16:35:02 +01:00
Piotr Faba
6fd86ad9e5 2 tests 2020-03-06 14:56:33 +00:00
Piotr Faba
fa134a1196 fix path error 2020-03-06 14:54:26 +00:00
Piotr Faba
2646e55e2b get test working 2020-03-06 14:50:29 +00:00
Piotr Faba
660be04708 fix test 2020-03-06 14:41:37 +00:00
Piotr Faba
36cad50593 test submodules checkout 2020-03-06 14:38:49 +00:00
Piotr Faba
977a9b3ee8 test fix 2020-03-06 14:34:34 +00:00
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