Commit graph

2067 commits

Author SHA1 Message Date
drpatelh
9b153f296d Add check to see if bowtie bam files exists 2021-02-03 16:26:10 +00:00
drpatelh
239cbe17ad Fix relative paths 2021-02-03 16:20:02 +00:00
drpatelh
38c3ecfac6 Merge branch 'master' of https://github.com/nf-core/modules into split_tests 2021-02-03 16:05:06 +00:00
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