295 commits

Author	SHA1	Message	Date
Phil Ewels	e71bb92534	Workflows - trigger on change to workflow and test data too	2020-07-16 17:14:57 +02:00
Phil Ewels	aa24c8d175	Fix a bunch of stuff in GitHub Actions test workflows	2020-07-16 17:11:34 +02:00
Stephen Kelly	4957eb98e5	update GitHub actions for Fastqc	2020-07-16 08:49:08 -04:00
Stephen Kelly	61d44c34d0	update GitHub actions for Fastqc	2020-07-16 08:31:19 -04:00
Gregor Sturm	8f3718795b	Fix markdownlint ... Move markdownlint.yml to root directory. Like that it is automatically discovered and applied by most IDEs	2020-07-14 12:21:33 +02:00
Phil Ewels	31c0f617b9	Fix up cutadapt tests	2020-07-11 17:14:14 +02:00
Phil Ewels	905e842f36	Update more paths	2020-07-11 14:36:12 +02:00
Phil Ewels	263f48d520	Fix markdownlint	2020-07-11 13:48:11 +02:00
Phil Ewels	45fb2ff4f4	Remove verbose job names	2020-07-11 13:45:08 +02:00
Phil Ewels	fc53a6f0b5	Added markdown lint config file	2020-07-11 13:44:28 +02:00
Phil Ewels	a547f27f21	New GitHub Action to lint code style	2020-07-11 13:41:31 +02:00
Phil Ewels	8b6065764e	Merge branch 'master' into tcoffee_dev	2020-07-11 13:12:17 +02:00
Phil Ewels	dce77ce3f1	Merge branch 'master' of github.com:nf-core/modules	2020-07-11 13:08:33 +02:00
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
Phil Ewels	198e9a85eb	FastQC: add dockerfile and environment.yml	2020-03-06 14:04:18 +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
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	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
Phil Ewels	93f7b26aa2	Use submodules for test data	2019-12-06 09:24:33 +01:00
Phil Ewels	51bd2c0277	Ansi log false for tests	2019-12-05 22:20:02 +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