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Author SHA1 Message Date
Edmund Miller
467d1595c4
test: Use docker image with singularity 2021-02-02 18:14:39 -06:00
Edmund Miller
54bb0ae7a1
ci: Name logs 2021-02-02 17:51:20 -06:00
Edmund Miller
72b4fb35aa
test: Fix profile logic order 2021-02-02 17:32:21 -06:00
Edmund Miller
67deb0d47a
ci: Add singularity tmp dir 
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
 2021-02-02 17:25:58 -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
6b675eef6d
ci: Set pull docker container to false 
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
 2021-02-02 17:00:40 -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
688cc05fe8
tests: Remove -profile in tests 
See ddbca7b467 for more info
 2021-02-02 15:30:59 -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
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 
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 
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 
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 
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 
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
Kevin Menden
0bd8506ea1
Update tests/software/quast/main.nf 
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 
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 
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 
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 
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