Commit graph

1952 commits

Author SHA1 Message Date
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
cff3ac7e5f
ci: Make an edit to test pipeline trigger
Plus this got clean up in 0c9f29e0a2
2021-01-24 10:37:29 -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
Michael L Heuer
e6547d5b16 Update dsh-bio version to 2.0 2021-01-22 12:12:56 -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
86850dc8a4 style: Remove old comment
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-01-15 10:32:20 -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
Edmund Miller
d7a78fa127 style: Fix indent
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-01-15 10:28:11 -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
53830e05c7
test: Fix typo
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-01-15 10:07:44 -06:00
Edmund Miller
fe39c7822f
style: Fix indentation 2021-01-15 10:01:02 -06:00
Edmund Miller
b9e8f959b3
style: Standardize process names
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-01-15 10:00:40 -06:00
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
ec91171152 Corrected naming to ensure test checks work 2021-01-15 09:38:13 -06:00
sruthipsuresh
5a1c1f90e5 removed md5sums for pdf, rdata 2021-01-15 09:38:13 -06:00
sruthipsuresh
3f814d1e2f Workflow and md5sums added 2021-01-15 09:38:13 -06:00
sruthipsuresh
269d9888fe Corrected bash error, tested process 2021-01-15 09:38:13 -06:00
Sruthi Suresh
b7435b0159 added test file for phantompeakqualtools for testing 2021-01-15 09:38:13 -06:00
sruthipsuresh
09d56efe12 Fixed with mr file for size issues 2021-01-14 02:12:57 -06:00
sruthipsuresh
00ef1d3863
Changed input to bed files 2021-01-15 16:52:17 -06:00
Edmund Miller
4181a7356c
Remove -bam flag
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-01-15 09:39:32 -06:00
sruthipsuresh
2d2f15af0f
Delete phantompeakqualtools.yml 2021-01-13 21:23:24 -06:00
sruthipsuresh
a66618be98
Delete tests/software/phantompeakqualtools directory 2021-01-13 21:23:02 -06:00
sruthipsuresh
6f3cbfcd9a Fixed test.yml 2021-01-12 18:14:28 -06:00
sruthipsuresh
b297f7aea1 Fixed test and removed phantompeak tests 2021-01-12 18:04:12 -06:00
sruthipsuresh
7c88cf4f67 Finished module with md5sums 2021-01-12 09:29:31 -06:00
sruthipsuresh
0a04c96357 Added module, TODO data 2021-01-12 09:13:37 -06:00
sruthipsuresh
3b581d1912 Updated test.yml 2021-01-12 08:56:11 -06:00