785 commits

This branch

This branch

All branches

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