161 commits

Author	SHA1	Message	Date
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	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
Harshil Patel	e7b1241449	Merge pull request #120 from nf-core/composite-runs ... 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
drpatelh	f84e5b59ca	Rename bowtie_index to bowtie_build	2021-02-01 17:53:31 +00:00
Harshil Patel	0a41130276	Merge pull request #131 from KevinMenden/fastp-module ... Adding fastp module	2021-02-01 13:43:35 +00:00
Harshil Patel	e851da8640	Merge pull request #130 from KevinMenden/master ... Adding a QUAST module	2021-02-01 13:17:57 +00:00
kevinmenden	e9e795633d	added fastp tests	2021-02-01 14:02:06 +01:00
Harshil Patel	c74d8a1711	Merge pull request #128 from JoseEspinosa/bowtie2_viralrecon ... Bowtie2 viralrecon 2	2021-02-01 09:56:11 +00:00
Harshil Patel	2c962f34df	Merge pull request #110 from luslab/master ... Add SEACR module containing a single CALLPEAK process	2021-02-01 09:48:15 +00:00
kevinmenden	956bf22a58	fixed bug; updated meta.yml	2021-02-01 07:44:26 +01:00
JoseEspinosa	177693de49	Adding worflow yml for bowtie2_align and bowtie2_build	2021-01-30 22:53:27 +01:00
Harshil Patel	bd59706d51	Merge pull request #118 from heuermh/dsh-bio ... Added dsh-bio filter-bed as dsh_filterbed	2021-01-29 18:15:24 +00:00
Harshil Patel	0fcbc4233c	Merge pull request #126 from JoseEspinosa/samtools_viralrecon ... Samtools viralrecon	2021-01-29 18:12:48 +00:00
JoseEspinosa	22dcdc692d	Adding samtools_mpileup module	2021-01-29 17:58:42 +01:00
JoseEspinosa	3eedca9bb4	Add samtools_view	2021-01-29 17:18:45 +01:00
kevinmenden	34cfc32c29	added quast workflow	2021-01-29 16:15:45 +01:00
kevinmenden	bacebdfb47	added pangolin workf	2021-01-29 12:53:51 +01:00
Harshil Patel	5da41ecb26	Merge pull request #122 from KevinMenden/master ... Added tests and meta.yml files for Salmon	2021-01-29 11:49:03 +00:00
kevinmenden	d91cd73e52	added test workflow	2021-01-29 09:41:24 +01:00
kevinmenden	431a2eb73b	added quant test workflow	2021-01-26 15:58:22 +01:00
kevinmenden	915e0574a2	added salmon index test workflow	2021-01-26 15:44:22 +01:00
kevinmenden	046444a736	added workflow files	2021-01-25 15:00:51 +01:00
kevinmenden	a1e1e27f67	updated test md5sums	2021-01-25 15:00:18 +01:00
Edmund Miller	6da00a8a1b	ci: Put python setup before cache ... 34cf8a3e0f	2021-01-24 11:38:29 -06:00
Edmund Miller	c7262e27d8	ci: Cache nextflow	2021-01-24 11:35:24 -06:00
Edmund Miller	73b572eede	ci: Cache pip	2021-01-24 11:25:13 -06:00
Edmund Miller	b048bf33e0	ci: Check to see if it's an example array	2021-01-24 11:14:48 -06:00
Edmund Miller	7a89902657	ci: Fix check for no checks ... https://github.community/t/needs-job-outputs-issue/149156 https://github.community/t/jobs-being-skipped-while-using-both-needs-and-if-unclear-why/18480	2021-01-24 10:34:40 -06:00
Edmund Miller	506ebe515e	ci: Move all files to filter file and delete old tests	2021-01-24 10:34:31 -06:00
Edmund Miller	b008afe2e6	ci(#119): Upload logs on failure	2021-01-24 10:33:45 -06:00
Edmund Miller	13539e1c1a	ci: Change name of pytest step	2021-01-24 10:33:45 -06:00
Edmund Miller	860a49d456	ci: Need to wrap matrix's in []	2021-01-24 10:33:45 -06:00
Edmund Miller	0f1016e4a3	ci: Remove any filter	2021-01-24 10:33:45 -06:00
Edmund Miller	9577f5dd64	ci: Reference output rather than a step ... The step wasn't there	2021-01-24 10:33:45 -06:00
Edmund Miller	939b1490b7	ci: Check if there's a change to anything	2021-01-24 10:33:45 -06:00
Edmund Miller	3aaacdde09	ci: Checkout code before looking for changes	2021-01-24 10:33:44 -06:00
Edmund Miller	f4316480c5	ci: Use paths-filter to make one CI test	2021-01-24 10:33:44 -06:00
Edmund Miller	474a6fad64	ci: Add python setup ... Cause apparently you can use an action inside of an action. Yet.	2021-01-24 10:33:44 -06:00
Edmund Miller	d00bd5f6b1	ci: v0.1 => master ... Living life on the edge	2021-01-24 10:33:44 -06:00
Edmund Miller	95270092b0	ci: Add universal CI Test	2021-01-24 10:33:44 -06:00
Edmund Miller	f05134e855	ci: Add nextflow.log	2021-01-22 12:18:45 -06:00
Edmund Miller	73bd2d499e	ci: Add keep-workflow-wd-on-fail	2021-01-22 12:07:59 -06:00
Edmund Miller	a1f4d53d3e	ci: Upload logs on failures	2021-01-22 12:04:41 -06:00
kevinmenden	f58c1c1e9e	added star genomegenerate test	2021-01-22 14:01:59 +01:00
Michael L Heuer	23f9284aae	Added dsh-bio split-bed as dsh_splitbed	2021-01-21 16:34:49 -06:00