72 commits

Author	SHA1	Message	Date
Edmund Miller	34d86427a6	test(samtools): Refactor flagstat to use pytest-workflow	2020-11-24 21:08:33 -06:00
Edmund Miller	ebf3a4529f	ci(picard): Update markduplicates	2020-11-24 21:08:33 -06:00
Edmund Miller	939f5ca744	test(picard): Refactor collectmultiplemetrics to use pytest-workflow	2020-11-24 21:03:40 -06:00
Edmund Miller	234e85bdce	test(picard): Refactor mergesamfiles to use pytest-workflow	2020-11-24 19:01:12 -06:00
Edmund Miller	016d8684f3	test(bwa): Refactor to use pytest-workflow	2020-11-24 19:00:11 -06:00
Edmund Miller	dfc8528df9	ci: Remove docker workflow ... This only applies to deprecated software	2020-11-24 18:58:02 -06:00
Edmund Miller	691df9d469	style(actions): Create seperate software dir ... For future subworkflows	2020-11-24 18:57:53 -06:00
Edmund Miller	f235732a58	ci(fastqc): Use both threads in GitHub runner	2020-11-16 13:45:00 -06:00
Edmund Miller	6d857a2584	ci(fastqc): Run pytest-workflow instead of workflow ... This will check for the actual output files and their contents not just whether the module runs or not.	2020-11-16 09:37:45 -06:00
drpatelh	082c582258	Remove EClint for now	2020-11-12 15:22:15 +00:00
drpatelh	b22ec332e9	Add GitHub Actions	2020-08-07 16:42:56 +01:00
drpatelh	50a628ad0a	Remove deprecated tests	2020-08-07 15:55:23 +01:00
drpatelh	238f43789e	Add tests for all samtools commands	2020-08-07 15:35:19 +01:00
drpatelh	14480affba	Add flagstat test	2020-08-07 15:32:09 +01:00
drpatelh	b5338efb7d	Add tests for BWA mem	2020-08-07 13:24:24 +01:00
drpatelh	cff81ef875	Add test data	2020-08-07 12:57:32 +01:00
drpatelh	9f4192d433	Add TrimGalore GitHub Actions test	2020-08-07 12:21:47 +01:00
drpatelh	49e37cb22c	Add profile docker	2020-08-07 10:07:20 +01:00
drpatelh	7efd46b489	Add nextflow.config	2020-08-07 09:59:19 +01:00
drpatelh	fab020461b	Add -with-docker	2020-08-07 09:44:16 +01:00
drpatelh	b0abd14135	Update tests	2020-08-07 09:31:27 +01:00
drpatelh	cb08a7326a	Change NF version	2020-08-07 00:38:56 +01:00
drpatelh	3e0c63a0a0	Update badge	2020-08-06 12:42:45 +01:00
drpatelh	3428157910	Add badges	2020-08-06 12:39:33 +01:00
drpatelh	3ec4f63fd8	Use correct link to fastqc	2020-08-05 16:28:42 +01:00
Phil Ewels	dcc4beacb1	Fix FastQC test	2020-07-17 11:26:50 +02:00
Phil Ewels	9b4634a426	Use latest edge version of NXF for FastQC test	2020-07-17 10:35:17 +02:00
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