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Author	SHA1	Message	Date
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
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