drpatelh
0c88ff7458
Upgrade Singularity and change TMPDIR for pytest output
2021-02-03 20:03:43 -06:00
Edmund Miller
9b454416d2
ci: Test bowtie-build instead of _
2021-02-03 13:17:14 -06:00
Edmund Miller
7dbac4bdef
ci: Test adding another work to test name
2021-02-03 13:17:14 -06:00
Edmund Miller
b058da5856
ci: Test buil to see if build is special
2021-02-03 12:43:18 -06:00
Edmund Miller
6901c7e830
ci: Fix bowtie_build names with ""
2021-02-03 12:37:14 -06:00
drpatelh
ff6f0642d2
Fix multiqc tests
2021-02-03 17:43:14 +00:00
drpatelh
38c3ecfac6
Merge branch 'master' of https://github.com/nf-core/modules into split_tests
2021-02-03 16:05:06 +00:00
drpatelh
743ba37d4b
Update filters paths
2021-02-03 16:04:43 +00:00
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"
...
This reverts commit c63ba06777
.
2021-02-02 17:03:29 -06:00
Edmund Miller
c63ba06777
ci: Only test docker for now
...
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
...
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
...
It's not necessary in if statements
2021-02-02 15:40:30 -06:00
Edmund Miller
654c6225f0
ci: Setup multiple profiles for testing
...
Added conda and singularity
2021-02-02 15:38:51 -06:00
Edmund Miller
35ac5c5f15
ci: Add filters for new modules
...
These snuck in after the 506ebe5
was written
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
...
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
...
Adding fastp module
2021-02-01 13:43:35 +00:00
Harshil Patel
e851da8640
Merge pull request #130 from KevinMenden/master
...
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
...
Bowtie2 viralrecon 2
2021-02-01 09:56:11 +00:00
Harshil Patel
2c962f34df
Merge pull request #110 from luslab/master
...
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
...
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
...
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
...
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
kevinmenden
915e0574a2
added salmon index test workflow
2021-01-26 15:44:22 +01:00
kevinmenden
046444a736
added workflow files
2021-01-25 15:00:51 +01:00
kevinmenden
a1e1e27f67
updated test md5sums
2021-01-25 15:00:18 +01:00
Edmund Miller
6da00a8a1b
ci: Put python setup before cache
...
34cf8a3e0f
2021-01-24 11:38:29 -06:00
Edmund Miller
c7262e27d8
ci: Cache nextflow
2021-01-24 11:35:24 -06:00
Edmund Miller
73b572eede
ci: Cache pip
2021-01-24 11:25:13 -06:00
Edmund Miller
b048bf33e0
ci: Check to see if it's an example array
2021-01-24 11:14:48 -06:00
Edmund Miller
7a89902657
ci: Fix check for no checks
...
https://github.community/t/needs-job-outputs-issue/149156
https://github.community/t/jobs-being-skipped-while-using-both-needs-and-if-unclear-why/18480
2021-01-24 10:34:40 -06:00
Edmund Miller
506ebe515e
ci: Move all files to filter file and delete old tests
2021-01-24 10:34:31 -06:00
Edmund Miller
b008afe2e6
ci( #119 ): Upload logs on failure
2021-01-24 10:33:45 -06:00
Edmund Miller
13539e1c1a
ci: Change name of pytest step
2021-01-24 10:33:45 -06:00
Edmund Miller
860a49d456
ci: Need to wrap matrix's in []
2021-01-24 10:33:45 -06:00
Edmund Miller
0f1016e4a3
ci: Remove any filter
2021-01-24 10:33:45 -06:00
Edmund Miller
9577f5dd64
ci: Reference output rather than a step
...
The step wasn't there
2021-01-24 10:33:45 -06:00
Edmund Miller
939b1490b7
ci: Check if there's a change to anything
2021-01-24 10:33:45 -06:00
Edmund Miller
3aaacdde09
ci: Checkout code before looking for changes
2021-01-24 10:33:44 -06:00
Edmund Miller
f4316480c5
ci: Use paths-filter to make one CI test
2021-01-24 10:33:44 -06:00
Edmund Miller
474a6fad64
ci: Add python setup
...
Cause apparently you can use an action inside of an action. Yet.
2021-01-24 10:33:44 -06:00
Edmund Miller
d00bd5f6b1
ci: v0.1 => master
...
Living life on the edge
2021-01-24 10:33:44 -06:00
Edmund Miller
95270092b0
ci: Add universal CI Test
2021-01-24 10:33:44 -06:00
Edmund Miller
f05134e855
ci: Add nextflow.log
2021-01-22 12:18:45 -06:00
Edmund Miller
73bd2d499e
ci: Add keep-workflow-wd-on-fail
2021-01-22 12:07:59 -06:00
Edmund Miller
a1f4d53d3e
ci: Upload logs on failures
2021-01-22 12:04:41 -06:00
kevinmenden
f58c1c1e9e
added star genomegenerate test
2021-01-22 14:01:59 +01:00
Michael L Heuer
23f9284aae
Added dsh-bio split-bed as dsh_splitbed
2021-01-21 16:34:49 -06:00
Michael L Heuer
eb6408f3dc
Added dsh-bio filter-bed as dsh_filterbed
2021-01-21 15:16:20 -06:00
Edmund Miller
daa25b9329
Merge branch 'preseq_test'
2021-01-15 17:41:13 -06:00
Edmund Miller
4f0c34bbfb
ci: Bump nextflow version
...
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-01-15 10:32:20 -06:00
sruthipsuresh
7729fee5a9
Added gffread and gff3 file for testing
2021-01-15 10:32:20 -06:00
sruthipsuresh
b95bd37780
Added ucsc module
2021-01-15 10:28:11 -06:00
Harshil Patel
27dbe8b52a
Merge pull request #115 from Functional-Genomics-Lab/stringtie_test
...
Added testing for Stringtie
2021-01-15 16:09:39 +00:00
Edmund Miller
a3ca757f4e
Update .github/workflows/phantompeakqualtools.yml
...
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-01-15 09:38:13 -06:00
sruthipsuresh
3f814d1e2f
Workflow and md5sums added
2021-01-15 09:38:13 -06:00
sruthipsuresh
2d2f15af0f
Delete phantompeakqualtools.yml
2021-01-13 21:23:24 -06:00
sruthipsuresh
b297f7aea1
Fixed test and removed phantompeak tests
2021-01-12 18:04:12 -06:00
sruthipsuresh
0a04c96357
Added module, TODO data
2021-01-12 09:13:37 -06:00
sruthipsuresh
cb39fcb915
Added preseq module and workflow
2021-01-12 08:41:09 -06:00
Chris Cheshire
7e9cbfc8d1
Merge remote-tracking branch 'nf-core/master'
2021-01-05 09:10:11 +00:00
sruthipsuresh
522b896534
Workflow and md5sums added
2020-12-19 06:09:04 -06:00
Harshil Patel
c98f9284a2
Merge pull request #89 from KevinMenden/master
...
Add bowtie module
2020-12-18 14:56:29 +00:00
Edmund Miller
eb61638501
ci: Use verbose name for editorconfig-check
...
I was getting confused myself with eclint
2020-12-17 17:48:19 -06:00
Edmund Miller
c6cf653f25
ci( #77 ): Ignore README for editorconfig
...
Because of the nf-core examples it throws errors.
2020-12-17 17:48:02 -06:00
Edmund Miller
0b6f117d2a
ci( #77 ): eclint => editorconfig-checker
2020-12-17 17:48:02 -06:00
Chris Cheshire
4436f59a1c
seacr | Syntax error
2020-12-17 14:27:37 +00:00
Chris Cheshire
15e1b860f9
seacr | added github action workflow
2020-12-17 14:25:42 +00:00
kevinmenden
8d3fc30eb3
fixed yml formatting
2020-12-17 07:39:34 +01:00
kevinmenden
d75cb75111
added singularity; edge NXF version
2020-12-17 07:33:44 +01:00
drpatelh
992232b340
Bump NF version to 20.11.0-edge
2020-12-14 00:14:28 +00:00
Edmund Miller
8d27ff53c5
ci: Support multiple nextflow versions
2020-12-09 09:56:40 -06:00
Edmund Miller
f994d55c18
style: Fix indent on workflows
2020-12-09 09:56:11 -06:00
Harshil Patel
79a0ce79ab
Merge pull request #82 from abhi18av/master
...
Add multiqc module
2020-12-09 11:31:07 +00:00
kevinmenden
fee0707af1
added bowtie_align workflow test
2020-12-08 14:19:34 +01:00
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
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