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Author SHA1 Message Date
drpatelh
743ba37d4b Update filters paths 2021-02-03 16:04:43 +00:00
drpatelh
ff23473e82 Restructure tests to run individually for each module 2021-02-03 16:02:58 +00:00
Harshil Patel
bffe3bb7b5
Merge pull request #140 from drpatelh/containers 
Add build ids for all Conda packages defined in modules
 2021-02-03 15:49:45 +00:00
drpatelh
3968c18fd7 Only run Docker tests 2021-02-03 14:04:58 +00:00
drpatelh
8be5e05111 Remove bam md5sum check for bowtie 2021-02-03 13:46:44 +00:00
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 
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