3169 commits

This branch

This branch

All branches

Author	SHA1	Message	Date
drpatelh	a9102c329c	Fix bedtools complement module	2021-02-07 20:55:12 +00:00
Harshil Patel	e4adb8ab53	Merge pull request #79 from Functional-Genomics-Lab/bedtools-general ... Bring bedtools up to speed	2021-02-07 20:49:17 +00:00
Harshil Patel	0393d39105	Update tests/software/bedtools/complement/main.nf	2021-02-07 20:35:51 +00:00
Harshil Patel	5269c1ec60	Update tests/software/bedtools/intersect/main.nf	2021-02-07 20:35:12 +00:00
Harshil Patel	8841af1267	Update tests/software/bedtools/merge/main.nf	2021-02-07 20:34:30 +00:00
Harshil Patel	b068f2fc53	Update tests/software/bedtools/sort/main.nf	2021-02-07 20:33:02 +00:00
Harshil Patel	b260192942	Merge pull request #149 from heuermh/minimap2 ... Add minimap2 align module	2021-02-07 16:37:26 +00:00
Michael L Heuer	35ed09b06e	Fix CI test failure	2021-02-05 11:41:36 -06:00
Michael L Heuer	6b873d7d33	Remove single_end if/else	2021-02-05 11:35:11 -06:00
Edmund Miller	e51d0bdf5e	Apply suggestions from code review ... Co-authored-by: Kevin Menden <kevin.menden@t-online.de>	2021-02-05 09:26:45 -06:00
Harshil Patel	31520fce97	Update software/minimap2/align/main.nf	2021-02-05 10:45:34 +00:00
drpatelh	137d00b523	Fix tests	2021-02-05 10:44:08 +00:00
drpatelh	81ae0089bc	Fix merge conflicts	2021-02-05 10:06:39 +00:00
Kevin Menden	17dd0415f2	Merge pull request #146 from heuermh/bandage ... Add bandage image module	2021-02-05 08:00:44 +01:00
Edmund Miller	f065476d36	docs: Add testing documentation	2021-02-04 16:00:31 -06:00
Michael L Heuer	50bebac136	Remove pairwise test	2021-02-04 15:22:12 -06:00
Michael L Heuer	061b13bf25	Fix md5 --> md5sum	2021-02-04 13:48:56 -06:00
Michael L Heuer	bbc8c725a2	Fix lint errors	2021-02-04 13:45:39 -06:00
Michael L Heuer	d5f2f5e32d	Add minimap2 align module	2021-02-04 13:42:08 -06:00
Michael L Heuer	37a9f6f456	Address review comments	2021-02-04 12:10:54 -06:00
Kevin Menden	089af956fb	Merge pull request #148 from nf-core/fix-artifact-path ... ci: Fix artifact path	2021-02-04 15:48:52 +01:00
Edmund Miller	05c09429a3	ci: Fix artifact path ... Had to change it for singularity	2021-02-04 08:45:34 -06:00
Harshil Patel	08d8443510	Merge pull request #143 from nf-core/ci-fixes ... Get Singularity CI tests working	2021-02-04 11:28:49 +00:00
Harshil Patel	5aa920eb53	Update tests/software/bowtie/align/test.yml	2021-02-04 10:19:28 +00:00
Harshil Patel	68f9a0b711	Update tests/software/bowtie/build/test.yml	2021-02-04 10:08:01 +00:00
Harshil Patel	eb45368a35	Update tests/software/bowtie2/build/test.yml	2021-02-04 10:07:44 +00:00
Kevin Menden	f298c594fe	Update meta.yml ... Just a small edit, we want to keep this consistent for linting	2021-02-04 07:34:08 +01:00
Edmund Miller	d48e865401	ci: Use bowtie filter ... This will cause a bit of duplication, but it appears to work. Still the same logic, because any changes to bowtie*/build will run the align modules also. So the bowtie_align tags may not even be necessary, since we can't seem to get the bowtie*_build tags to kick off on their own anyways. Thank you for coming to my TED talk.	2021-02-03 20:15:56 -06:00
Edmund Miller	6fe7b48b5b	Revert "Run alllll the testsgit add .github/workflows/pytest-workflow.yml" ... This reverts commit ffc218e51b.	2021-02-03 20:08:11 -06:00
Edmund Miller	431c699727	Revert "ci: Test bowtie-build instead of _" ... This reverts commit 9b454416d2.	2021-02-03 20:06:05 -06:00
drpatelh	ffc218e51b	Run alllll the testsgit add .github/workflows/pytest-workflow.yml	2021-02-03 20:03:45 -06:00
drpatelh	fe3cb87f6d	Direct download Singularity containers	2021-02-03 20:03:45 -06:00
drpatelh	0c88ff7458	Upgrade Singularity and change TMPDIR for pytest output	2021-02-03 20:03:43 -06:00
Michael L Heuer	05d257e8f5	Fix lint errors	2021-02-03 19:34:25 -06:00
Michael L Heuer	c466255f6f	Add bandage image module	2021-02-03 19:31:58 -06:00
Edmund Miller	9b454416d2	ci: Test bowtie-build instead of _	2021-02-03 13:17:14 -06:00
Edmund Miller	7dbac4bdef	ci: Test adding another work to test name	2021-02-03 13:17:14 -06:00
Edmund Miller	b058da5856	ci: Test buil to see if build is special	2021-02-03 12:43:18 -06:00
Edmund Miller	4d58a037f6	test(bowtie_align): Fix md5sum	2021-02-03 12:37:19 -06:00
Edmund Miller	6901c7e830	ci: Fix bowtie_build names with ""	2021-02-03 12:37:14 -06:00
Harshil Patel	5f810beaa4	Merge pull request #142 from drpatelh/split_tests ... Split tests	2021-02-03 18:09:30 +00:00
drpatelh	e71b3eaaa5	Rename workflows	2021-02-03 17:48:17 +00:00
drpatelh	ff6f0642d2	Fix multiqc tests	2021-02-03 17:43:14 +00:00
drpatelh	0683efc679	Fix salmon quant tests	2021-02-03 17:36:06 +00:00
drpatelh	550494cbd1	Fix picard mergesamfiles test	2021-02-03 17:31:41 +00:00
drpatelh	f079ce9d1f	Fix preseq tests	2021-02-03 17:28:44 +00:00
drpatelh	f37fb66f40	Fix bwa mem tests	2021-02-03 17:26:43 +00:00
drpatelh	8a15852756	Fix salmon index tests	2021-02-03 17:13:47 +00:00
drpatelh	058d7b397c	Fix fastqc test	2021-02-03 17:03:30 +00:00
drpatelh	39b8600dbb	Fix trimgalore test	2021-02-03 17:02:52 +00:00