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226 commits

Author SHA1 Message Date
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