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812 commits 30 branches 0 tags 142 MiB
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192 commits

Author SHA1 Message Date
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