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
688cc05fe8
tests: Remove -profile in tests
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See ddbca7b467
for more info
2021-02-02 15:30:59 -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
Edmund Miller
ddbca7b467
test: Use profile ENV variable hack
...
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
JoseEspinosa
26829497d5
Fixing typo on path for md5 check
2021-02-02 12:19:57 +01:00
Maxime Garcia
e7474c3d98
Update main.nf
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Use same tag
2021-02-02 12:13:14 +01:00
JoseEspinosa
e7f15feccf
Adding --no-version
to bcftools_isec for tests md5 check
2021-02-02 11:00:02 +01:00
JoseEspinosa
3a40ec5664
Adding bcftools_isec taking a path with several vcfs and its tests
2021-02-02 10:50:45 +01:00
JoseEspinosa
8e4764b8ed
bcftools_filter adding argument to test to enable md5 check
2021-02-02 10:19:34 +01:00
JoseEspinosa
c25f8f0f6c
Fixing tests
2021-02-02 09:57:55 +01:00
JoseEspinosa
382ea31e7e
Adding bcftools test data
2021-02-02 09:18:28 +01:00
JoseEspinosa
cee37852cd
Merge remote-tracking branch 'upstream/master' into bcftools_viralrecon
2021-02-02 09:15:20 +01:00
JoseEspinosa
a3ce63c79c
Adding tests for bcftools
2021-02-02 09:14:00 +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
JoseEspinosa
579de3e038
bcftools_tabix generic for any TAB-delimited genome position file
2021-02-01 21:59:39 +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
...
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
...
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
...
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
JoseEspinosa
0a8915ae77
Adding bcftools_tabix module
2021-02-01 10:07:35 +01:00
JoseEspinosa
52b0b8094d
Adding bcftools_stats module
2021-02-01 10:03:25 +01:00
JoseEspinosa
0423e686a6
Adding bcftools_isec module
2021-02-01 09:46:24 +01:00
JoseEspinosa
da7598272e
Adding bcftools_filter module
2021-02-01 09:41:08 +01:00
JoseEspinosa
eb12f4610d
Fixing meta ymls
2021-02-01 09:28:51 +01:00
kevinmenden
956bf22a58
fixed bug; updated meta.yml
2021-02-01 07:44:26 +01:00
JoseEspinosa
b6ef06c6cd
Add bcftools_consensus module
2021-01-31 22:23:26 +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