Kevin Menden
17dd0415f2
Merge pull request #146 from heuermh/bandage
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Add bandage image module
2021-02-05 08:00:44 +01:00
Michael L Heuer
d5f2f5e32d
Add minimap2 align module
2021-02-04 13:42:08 -06:00
Michael L Heuer
37a9f6f456
Address review comments
2021-02-04 12:10:54 -06:00
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
d48e865401
ci: Use bowtie filter
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This will cause a bit of duplication, but it appears to work. Still the
same logic, because any changes to bowtie*/build will run the align
modules also. So the bowtie_align tags may not even be necessary, since
we can't seem to get the bowtie*_build tags to kick off on their own
anyways. Thank you for coming to my TED talk.
2021-02-03 20:15:56 -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
Edmund Miller
431c699727
Revert "ci: Test bowtie-build instead of _"
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This reverts commit 9b454416d2
.
2021-02-03 20:06:05 -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
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"
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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
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
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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
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
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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
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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
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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
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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
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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
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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
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Added testing for Stringtie
2021-01-15 16:09:39 +00:00
Edmund Miller
a3ca757f4e
Update .github/workflows/phantompeakqualtools.yml
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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
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Add bowtie module
2020-12-18 14:56:29 +00:00
Edmund Miller
eb61638501
ci: Use verbose name for editorconfig-check
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I was getting confused myself with eclint
2020-12-17 17:48:19 -06:00
Edmund Miller
c6cf653f25
ci( #77 ): Ignore README for editorconfig
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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