millironx/nf-core_modules
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445 commits 30 branches 0 tags 142 MiB
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66 commits

Author SHA1 Message Date
Abhinav Sharma
27b4b29976 Remove the extra data files 2020-12-04 20:20:59 +05:30
Abhinav Sharma
5fd3ba3ce6 Update the tests for MultiQC 2020-12-02 13:09:32 +05:30
Paolo Cozzi
835ac48565 Fixing MULTIQC module and adding tests (#1) 
* fix multiqc process

* fix multiqc tests

* move multiqc test input data into tests/data/fastqc/ folder

Move input tests data into tests/data/fastqc/ and linking those files into software/multiqc/test/input/ as stated from the project documentation

* add multiqc github workflow

* remove unused file

* generalize multiqc input data

User must collect all desidered files in a channel (as described in https://seqera.io/training/#_multiqc_report

* update meta information
 2020-12-01 12:03:37 +05:30
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
45fb2ff4f4 Remove verbose job names 2020-07-11 13:45:08 +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