drpatelh
9e44b0f4f2
Add conda clean step to action
2021-02-03 12:57:55 +00:00
drpatelh
1512c9af74
Unable to test BAM due to command
2021-02-03 12:26:10 +00:00
drpatelh
49fecaa4f0
Switch channel order
2021-02-03 12:07:39 +00:00
drpatelh
16b32495e4
Remove deprecated modules that have now been added
2021-02-03 11:38:15 +00:00
drpatelh
9d097e7aeb
Remove unrequired file
2021-02-03 11:34:05 +00:00
drpatelh
673d463208
bowtie - add mulled build info
2021-02-03 11:33:31 +00:00
drpatelh
423144808c
seacr - add build info for mulled container
2021-02-03 11:05:10 +00:00
drpatelh
34e451dd2e
rsem - add build info for mulled container
2021-02-03 11:04:59 +00:00
drpatelh
26e04dd298
rsem - add build info for mulled container
2021-02-03 11:04:51 +00:00
drpatelh
3d1b9371f2
hisat2 - add build info for mulled container
2021-02-03 11:04:35 +00:00
drpatelh
98158064a7
bwa - add build info for mulled container
2021-02-03 11:04:25 +00:00
drpatelh
630b4be938
bowtie2 - add build info for mulled container
2021-02-03 11:04:02 +00:00
drpatelh
415d0265db
Add build to Conda
2021-02-03 11:03:36 +00:00
drpatelh
3ae4c51f42
various - add build to conda definition
2021-02-03 09:20:34 +00:00
drpatelh
c0926b0b6b
various - add build to conda definition
2021-02-03 09:19:46 +00:00
drpatelh
daab19a849
picard - add build to conda definition
2021-02-03 09:18:37 +00:00
drpatelh
773d4d89f2
rseqc - add build to conda definition
2021-02-03 09:18:20 +00:00
drpatelh
383d35bc7d
samtools - add build to conda definition
2021-02-03 09:17:38 +00:00
drpatelh
ce3edcc994
deeptools - add build to conda definition
2021-02-03 09:16:59 +00:00
drpatelh
c089edc670
cutadapt - add build to conda definition
2021-02-03 09:16:33 +00:00
drpatelh
b41c3d63ec
bwa index - add build to conda definition
2021-02-03 09:16:22 +00:00
drpatelh
f913a55d85
bowtie2 build - add build to conda definition
2021-02-03 09:16:10 +00:00
drpatelh
d783e2d535
Only test Docker and Conda
2021-02-03 09:02:12 +00:00
drpatelh
a536c85ec0
bowtie - add build to conda definition
2021-02-03 08:49:18 +00:00
Harshil Patel
93775f3262
Merge pull request #138 from nf-core/pytest-profiles
...
Pytest profiles
2021-02-03 08:35:05 +00:00
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
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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
...
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