Edmund Miller
bdee7804ca
build: Bump version to 21.04.0 ( #481 )
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* build: Bump version to 21.04.0
Recent stable release https://github.com/nextflow-io/nextflow/releases/tag/v21.04.0
* Update README.md
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-05-04 00:38:29 +01:00
Harshil Patel
f34892c1af
Test PR for nf-core modules lint ( #414 )
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* Update functions.nf for publish_by_id
* Pass a list of publish_by_id instead of a string
* Remove NF version
* Rename code linting file
* Run separate workflow for nf-core modules lint
* Adjust nf-core update comment
* Comment out linting from pytest-workflow.yml
* Remove commented out linting code from pytest-workflow.yml
* Adjust spacing
* Adjust spacing again
* Move NF version to job level for linting
* Add CAPSULE_LOG none env when installing NF
* Remove NXF_ANSI_LOG env for linting
* Revert changes
2021-04-09 07:58:43 +01:00
Edmund Miller
a3684d9594
Lint modules ci ( #389 )
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* ci: Add modules lint step
Moved it ahead of the nextflow install so ideally it'll fail before we
bother doing any more setup
* ci: _ => /
* Update tests/config/pytest_software.yml
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-04-08 09:10:52 +01:00
Edmund Miller
6e4b23a1ca
ci: Upload work directory on failure ( #388 )
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Closes #374
2021-03-25 09:34:19 +00:00
Edmund Miller
1fc4aa260d
ci: Add 21.03.0 version to matrix ( #317 )
2021-03-22 22:57:59 +00:00
Harshil Patel
9b99b33401
Rename .github/filters.yml -> tests/config/pytest_software.yml ( #271 )
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* Rename pytest filters.yml
* Change filters.yml name
* Update resoures for ivar trim
2021-03-15 12:51:30 +00:00
Gregor Sturm
38349417ad
Update .github/workflows/pytest-workflow.yml
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Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-02-23 14:14:29 +01:00
Gregor Sturm
94bdc62123
Only use one thread for pytest-workflow
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This avoids a race condition on the conda cache.
2021-02-23 14:06:52 +01:00
drpatelh
418bd64e80
Test module with Conda
2021-02-07 21:33:42 +00:00
Edmund Miller
05c09429a3
ci: Fix artifact path
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Had to change it for singularity
2021-02-04 08:45:34 -06:00
Edmund Miller
6fe7b48b5b
Revert "Run alllll the testsgit add .github/workflows/pytest-workflow.yml"
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This reverts commit ffc218e51b
2021-02-03 20:08:11 -06:00
drpatelh
ffc218e51b
Run alllll the testsgit add .github/workflows/pytest-workflow.yml
2021-02-03 20:03:45 -06:00
drpatelh
0c88ff7458
Upgrade Singularity and change TMPDIR for pytest output
2021-02-03 20:03:43 -06:00
drpatelh
3968c18fd7
Only run Docker tests
2021-02-03 14:04:58 +00:00
drpatelh
9e44b0f4f2
Add conda clean step to action
2021-02-03 12:57:55 +00:00
drpatelh
49fecaa4f0
Switch channel order
2021-02-03 12:07:39 +00:00
drpatelh
d783e2d535
Only test Docker and Conda
2021-02-03 09:02:12 +00:00
Edmund Miller
54bb0ae7a1
ci: Name logs
2021-02-02 17:51:20 -06:00
Edmund Miller
42b8962320
ci: Add bioconda channels
2021-02-02 17:13:35 -06:00
Edmund Miller
0813e61c01
ci: Kick off all container types
2021-02-02 17:08:10 -06:00
Edmund Miller
725de25ce4
Revert "ci: Only test docker for now"
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This reverts commit c63ba06777
2021-02-02 17:03:29 -06:00
Edmund Miller
c63ba06777
ci: Only test docker for now
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I can't access the artifacts.
2021-02-02 16:49:03 -06:00
Edmund Miller
bb3196ddeb
ci: Update name to use matrix
2021-02-02 16:49:03 -06:00
Edmund Miller
dcfd1089e5
ci: Add --keep-workflow-wd-on-fail
2021-02-02 16:49:03 -06:00
Edmund Miller
983b024010
ci: Use ubuntu-20.04 for singularity
2021-02-02 16:49:02 -06:00
Edmund Miller
8cd6e41df9
ci: Change singularity version 3.6.4 => 3.5.3
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Per @grst having issues after 3.6
2021-02-02 16:49:02 -06:00
Edmund Miller
bf2e027fdf
ci: Remove conda to kickoff CI
2021-02-02 16:48:58 -06:00
Edmund Miller
1e9aad430d
ci: Remove ${{}} for style points
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It's not necessary in if statements
2021-02-02 15:40:30 -06:00
Edmund Miller
654c6225f0
ci: Setup multiple profiles for testing
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Added conda and singularity
2021-02-02 15:38:51 -06:00
Edmund Miller
35ac5c5f15
ci: Add filters for new modules
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These snuck in after the 506ebe5
2021-02-02 15:27:45 -06:00
Edmund Miller
341fa43ae3
ci: Add PROFILE ahead of pytest run
2021-02-02 13:07:58 -06:00
Harshil Patel
e7b1241449
Merge pull request #120 from nf-core/composite-runs
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Universal CI job
2021-02-02 18:26:02 +00:00
Edmund Miller
ce2a5b32f5
refactor: Move away from composite-action
2021-02-02 12:21:36 -06:00
drpatelh
f84e5b59ca
Rename bowtie_index to bowtie_build
2021-02-01 17:53:31 +00:00
Harshil Patel
0a41130276
Merge pull request #131 from KevinMenden/fastp-module
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Adding fastp module
2021-02-01 13:43:35 +00:00
Harshil Patel
e851da8640
Merge pull request #130 from KevinMenden/master
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Adding a QUAST module
2021-02-01 13:17:57 +00:00
kevinmenden
e9e795633d
added fastp tests
2021-02-01 14:02:06 +01:00
Harshil Patel
c74d8a1711
Merge pull request #128 from JoseEspinosa/bowtie2_viralrecon
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Bowtie2 viralrecon 2
2021-02-01 09:56:11 +00:00
Harshil Patel
2c962f34df
Merge pull request #110 from luslab/master
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Add SEACR module containing a single CALLPEAK process
2021-02-01 09:48:15 +00:00
kevinmenden
956bf22a58
fixed bug; updated meta.yml
2021-02-01 07:44:26 +01:00
JoseEspinosa
177693de49
Adding worflow yml for bowtie2_align and bowtie2_build
2021-01-30 22:53:27 +01:00
Harshil Patel
bd59706d51
Merge pull request #118 from heuermh/dsh-bio
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Added dsh-bio filter-bed as dsh_filterbed
2021-01-29 18:15:24 +00:00
Harshil Patel
0fcbc4233c
Merge pull request #126 from JoseEspinosa/samtools_viralrecon
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Samtools viralrecon
2021-01-29 18:12:48 +00:00
JoseEspinosa
22dcdc692d
Adding samtools_mpileup module
2021-01-29 17:58:42 +01:00
JoseEspinosa
3eedca9bb4
Add samtools_view
2021-01-29 17:18:45 +01:00
kevinmenden
34cfc32c29
added quast workflow
2021-01-29 16:15:45 +01:00
kevinmenden
bacebdfb47
added pangolin workf
2021-01-29 12:53:51 +01:00
Harshil Patel
5da41ecb26
Merge pull request #122 from KevinMenden/master
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Added tests and meta.yml files for Salmon
2021-01-29 11:49:03 +00:00
kevinmenden
d91cd73e52
added test workflow
2021-01-29 09:41:24 +01:00
kevinmenden
431a2eb73b
added quant test workflow
2021-01-26 15:58:22 +01:00
