Edmund Miller
ddbca7b467
test: Use profile ENV variable hack
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The user will now set the env variable and pass it to pytest. You also
can't set the env variable ahead of time, it has to be run with pytest.
Example:
PROFILE=conda pytest --tag fastqc --symlink --kwd
2021-02-02 12:44:30 -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
Harshil Patel
f126200610
Merge pull request #133 from nf-core/MaxUlysse-patch-1-1
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Update bwa/index container
2021-02-02 12:26:31 +00:00
Maxime Garcia
e7474c3d98
Update main.nf
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Use same tag
2021-02-02 12:13:14 +01:00
Kevin Menden
4301afb771
Merge pull request #132 from drpatelh/bowtie
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Rename bowtie_index to bowtie_build
2021-02-02 07:47:37 +01:00
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
Kevin Menden
0bd8506ea1
Update tests/software/quast/main.nf
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Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-02-01 14:04:08 +01:00
Kevin Menden
05370b5e16
Update tests/software/quast/main.nf
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Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-02-01 14:03:49 +01:00
Kevin Menden
f6c4e9d9c1
Update software/quast/meta.yml
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Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-02-01 14:03:36 +01:00
Kevin Menden
9885da628e
Update software/quast/meta.yml
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Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-02-01 14:03:22 +01:00
Kevin Menden
c807c6c438
Update software/quast/main.nf
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Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-02-01 14:03:15 +01:00
Kevin Menden
d88bf3bdda
Update software/quast/main.nf
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Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-02-01 14:03:06 +01:00
Kevin Menden
c43fe85a0c
Update software/quast/main.nf
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Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-02-01 14:02:57 +01:00
kevinmenden
e9e795633d
added fastp tests
2021-02-01 14:02:06 +01:00
kevinmenden
038381de99
added fastp module
2021-02-01 13:54:08 +01:00
kevinmenden
a342296d70
fixed test md5s
2021-02-01 13:36:25 +01:00
kevinmenden
b5298f94d8
refactored quast module
2021-02-01 13:13:21 +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
Chris Cheshire
41233763ae
Removed test-datasets submodule
2021-02-01 09:46:24 +00:00
kevinmenden
956bf22a58
fixed bug; updated meta.yml
2021-02-01 07:44:26 +01:00
JoseEspinosa
8fb6b80abd
Fixing some md5 hashes
2021-01-30 23:08:17 +01:00
JoseEspinosa
3c95af9e50
Merge branch 'bowtie2_viralrecon' of https://github.com/JoseEspinosa/modules into bowtie2_viralrecon
2021-01-30 22:53:53 +01:00
JoseEspinosa
177693de49
Adding worflow yml for bowtie2_align and bowtie2_build
2021-01-30 22:53:27 +01:00
Harshil Patel
eadbea4b83
Merge pull request #127 from JoseEspinosa/bowtie2_viralrecon
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Bowtie2 viralrecon
2021-01-30 13:22:30 +00:00
Harshil Patel
eab633776e
Update software/bowtie2/build/meta.yml
2021-01-30 13:21:56 +00:00
JoseEspinosa
986b72cee9
Fix error on previous commit
2021-01-30 09:35:25 +01:00
JoseEspinosa
29989035a5
Remove author entry from yml (copy-pasted :P)
2021-01-30 09:29:53 +01:00
sruthipsuresh
7a1c2a2eb5
Fixed slop module
2021-01-29 23:17:44 -06:00
sruthipsuresh
93e414635b
Fixed md5sum, fixed filters, fixed slop input
2021-01-29 23:17:44 -06:00
sruthipsuresh
78ac4435be
Added new tests, todo: fix md5sums
2021-01-29 23:17:44 -06:00
Edmund Miller
2b0d51ca9c
test(bedtools): Remove old style tests
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AKA how the tests were done last week.
2021-01-29 23:17:44 -06:00
Edmund Miller
7d52907d1c
test(bedtools): Fix typo on yaml indentation
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
e360617ac6
Fixed images, genomecov
2021-01-29 23:17:44 -06:00
sruthipsuresh
e3bbbb48fc
Fixed slop file
2021-01-29 23:17:44 -06:00
sruthipsuresh
957983bd99
Fixed and tested 4 modules, keeping with fastp module syntax
2021-01-29 23:17:44 -06:00
sruthipsuresh
295fff35ec
Corrected containers and tested
2021-01-29 23:17:44 -06:00
sruthipsuresh
19b55fc67c
Fixed intersect, complement indentation issues
2021-01-29 23:17:44 -06:00
sruthipsuresh
3da39dfc88
Fixed bedtools complement module
2021-01-29 23:17:44 -06:00
sruthipsuresh
8496427c56
Update software/bedtools/complement/main.nf
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Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-01-29 23:17:44 -06:00
sruthipsuresh
fc8cdde2b4
Apply suggestions from code review
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Add all initial suggestions from review (syntax issues)
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-01-29 23:17:44 -06:00
sruthipsuresh
e5c21d15a3
Update software/bedtools/complement/main.nf
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Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-01-29 23:17:44 -06:00
sruthipsuresh
bf2703f396
Update software/bedtools/complement/main.nf
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Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-01-29 23:17:44 -06:00
sruthipsuresh
93f640154a
Update software/bedtools/complement/main.nf
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Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-01-29 23:17:44 -06:00
sruthipsuresh
ced2458d78
Update software/bedtools/complement/main.nf
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Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-01-29 23:17:44 -06:00
