kevinmenden
73530e8df7
added bowtie index test github workflow
2020-12-08 14:13:30 +01:00
Abhinav Sharma
27b4b29976
Remove the extra data files
2020-12-04 20:20:59 +05:30
Edmund Miller
6d8ba714d5
ci(fastqc): Use 20.10.0 => ''
2020-12-04 08:23:19 -06:00
Abhinav Sharma
5fd3ba3ce6
Update the tests for MultiQC
2020-12-02 13:09:32 +05:30
Edmund Miller
65697532a1
ci: Get rid of software folder
2020-12-01 11:40:16 -06:00
Edmund Miller
8cd635f757
ci(fastqc): Fix test matrix
2020-12-01 11:13:43 -06:00
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
98c629583a
ci: Test whether subdirectories are breaking workflows
2020-11-30 19:03:56 -06:00
Edmund Miller
7d2b74a5f7
ci(fastqc): Use a test matrix for NXF versions
2020-11-30 18:57:56 -06:00
Edmund Miller
036427d73c
ci(pytest-workflow): Fix trigger paths
2020-11-24 21:24:55 -06:00
Edmund Miller
86219a586b
ci(trimgalore): Use pytest-workflow
2020-11-24 21:08:34 -06:00
Edmund Miller
445498d0c3
ci(samtools): Run tests with pytest-workflow
2020-11-24 21:08:34 -06:00
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
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
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