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Author SHA1 Message Date
Gregor Sturm
bc1f77f0f9
Create .editorconfig 2020-06-15 15:57:51 +02:00
Alexander Peltzer
9dee710b04
Merge pull request #25 from piotr-faba-ardigen/add_cutadapt_tool 
Add cutadapt tool
 2020-03-16 18:46:00 +01:00
Harshil Patel
7738dbe4df
Merge pull request #26 from nf-core/readme-update-modules 
Propose module organization
 2020-03-16 14:49:24 +00:00
Harshil Patel
5e71d61f27
Update README.md 2020-03-16 14:47:20 +00:00
Harshil Patel
d553406fa5
Update README.md 2020-03-16 14:47:11 +00:00
Harshil Patel
300e89c4dc
Update README.md 2020-03-16 14:47:03 +00:00
Alexander Peltzer
95d57bcef2
Apply suggestions from code review 
Co-Authored-By: Harshil Patel <drpatelh@users.noreply.github.com>
 2020-03-16 15:42:52 +01:00
Alexander Peltzer
771e53625b
Update README.md 2020-03-16 14:42:22 +01:00
Alexander Peltzer
05b4bbe8a1
Update README.md 2020-03-16 14:39:27 +01:00
Alexander Peltzer
f091e174c0
Update README.md 2020-03-16 14:37:07 +01:00
Alexander Peltzer
9753e803e0
Update README.md 2020-03-16 14:27:08 +01:00
Alexander Peltzer
4303ec700c
Propose module organization 
See above changes to readme :_)
 2020-03-16 14:06:03 +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
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
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
Piotr Faba
88bc7dcdd8 the module is working in test 2020-03-06 10:51:46 +00:00
Piotr Faba
97d9ae76f0 add cutadapt module 2020-03-05 15:56:11 +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