Harshil Patel
a282ecd8c7
Merge pull request #172 from andersgs/ivar-variant
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Add ivar variants
2021-02-16 23:20:30 +00:00
Harshil Patel
b07ad23efa
Merge pull request #179 from MaxUlysse/master_htslib_tabix
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Replace bcftools/tabix by tabix/tabix
2021-02-16 22:30:45 +00:00
Harshil Patel
759079796a
Update .github/filters.yml
2021-02-16 22:24:49 +00:00
MaxUlysse
6a147b8aaa
chores: replace bcftools/bgzip by tabix/bgzip cf #179
2021-02-16 19:11:36 +01:00
MaxUlysse
3805eb2dd1
fix: remove bcftools/tabix from filters.yml
2021-02-16 18:38:20 +01:00
MaxUlysse
10524e3515
chores: add modules for htslib/tabix
2021-02-16 14:47:53 +01:00
MaxUlysse
bbee0efd75
fix: add suggestions from reviews
2021-02-16 13:59:21 +01:00
MaxUlysse
7f35a1742d
chores: add gatk/createsequencedictionary module
2021-02-16 13:40:06 +01:00
MaxUlysse
a285bfe8a6
fix: add guidelines to PRs and issues
2021-02-16 11:07:43 +01:00
Anders Goncalves da Silva
89f65e0875
Merge branch 'master' into ivar-variant
2021-02-15 20:50:35 -08:00
Harshil Patel
8eb3acc43f
Merge pull request #171 from JoseEspinosa/mosdepth
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Add mosdepth module
2021-02-15 23:13:01 +00:00
Anders Goncalves da Silva
4ab3ccc905
Add ivar variants
2021-02-15 09:28:10 -08:00
JoseEspinosa
6e92a6a080
Adding mosdepth module
2021-02-15 14:33:44 +01:00
Maxime Garcia
ec0bf0145e
Merge branch 'master' into master_bwa-mem2
2021-02-15 13:08:52 +01:00
Anders Goncalves da Silva
6dca7799e6
Add ivar trim
2021-02-12 16:02:10 -08:00
Harshil Patel
63a20e7b5c
Merge pull request #168 from JoseEspinosa/bcftools_merge
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Add bcftools merge module
2021-02-12 23:20:30 +00:00
JoseEspinosa
5313698705
Add bcftools merge module
2021-02-13 00:08:57 +01:00
Anders Goncalves da Silva
24b212318b
Merge branch 'master' into ivar-consensus
2021-02-12 11:51:24 -08:00
Anders Goncalves da Silva
e5a3e3a5b8
Add ivar consensus to filter.yml
2021-02-12 10:59:46 -08:00
JoseEspinosa
6e8b63fc26
Add cat fastq module
2021-02-12 17:22:07 +01:00
MaxUlysse
2f18750964
chores: update filters.yml
2021-02-12 13:53:49 +01:00
JoseEspinosa
68b85d9191
Merge remote-tracking branch 'upstream/master' into bedtools_getfasta
2021-02-09 18:23:24 +01:00
JoseEspinosa
1e9b88b33c
Fixing trailing slashes in .github/filters.yml
2021-02-09 18:16:16 +01:00
JoseEspinosa
e118bc049a
Add bedtools getfasta module
2021-02-09 17:56:51 +01:00
JoseEspinosa
9a11e90892
Fixing tests
2021-02-09 17:07:23 +01:00
JoseEspinosa
12ae7b0bff
Adding blast blastn module
2021-02-09 16:58:36 +01:00
JoseEspinosa
d0f09e26b6
Adding blast makeblastdb module to filters.yml
2021-02-09 15:47:53 +01:00
JoseEspinosa
c93e96101a
Add untar module
2021-02-09 11:50:32 +01:00
JoseEspinosa
f7f06dd6e8
Add gunzip module
2021-02-09 10:05:55 +01:00
Harshil Patel
46e5df2cf7
Merge pull request #151 from drpatelh/bedtools
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Follow up fixes for bedtools modules added in #79
2021-02-09 01:54:31 +00:00
Harshil Patel
84cf5ea2ef
Merge pull request #153 from JoseEspinosa/bedtools_maskfasta
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Add bedtools maskfasta module
2021-02-08 23:11:00 +00:00
JoseEspinosa
02d10c25a3
Add bedtools maskfasta module
2021-02-08 23:41:10 +01:00
Harshil Patel
13c1e908a3
Update .github/filters.yml
2021-02-08 21:48:21 +00:00
JoseEspinosa
58d28ed896
Fix copy/paste error :P
2021-02-08 21:57:31 +01:00
JoseEspinosa
7a0ba85843
Adding again bcftools modules to filters after solving conflict
2021-02-08 18:10:50 +01:00
drpatelh
c9cfdd31f3
Fix barfing linters
2021-02-08 00:57:06 +00:00
drpatelh
eeb496cf5c
Fix filters
2021-02-07 23:23:08 +00:00
drpatelh
83a50d8ae0
Rename SOFTWARE_TOOL to TOOL_SUBTOOL
2021-02-07 23:20:53 +00:00
drpatelh
418bd64e80
Test module with Conda
2021-02-07 21:33:42 +00:00
sruthipsuresh
93e414635b
Fixed md5sum, fixed filters, fixed slop input
2021-01-29 23:17:44 -06:00
sruthipsuresh
ac7f634675
Added complement test
2021-01-29 23:17:44 -06:00
sruthipsuresh
84b66e4f38
Fixed testing, rebased
2021-01-29 23:17:44 -06:00
sruthipsuresh
70de0331a5
Corrected pytest and config
2021-01-29 23:17:44 -06:00
sruthipsuresh
32564137fd
Corrected workflows and ran editor config
2021-01-29 23:17:44 -06:00
sruthipsuresh
672f94f2af
rebased and updated all bedtools testing and modules
2021-01-29 23:17:44 -06:00
Harshil Patel
b260192942
Merge pull request #149 from heuermh/minimap2
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Add minimap2 align module
2021-02-07 16:37:26 +00:00
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