282 commits

Author	SHA1	Message	Date
MaxUlysse	6a147b8aaa	chores: replace bcftools/bgzip by tabix/bgzip cf #179	2021-02-16 19:11:36 +01:00
MaxUlysse	3805eb2dd1	fix: remove bcftools/tabix from filters.yml	2021-02-16 18:38:20 +01:00
MaxUlysse	10524e3515	chores: add modules for htslib/tabix	2021-02-16 14:47:53 +01:00
MaxUlysse	bbee0efd75	fix: add suggestions from reviews	2021-02-16 13:59:21 +01:00
MaxUlysse	7f35a1742d	chores: add gatk/createsequencedictionary module	2021-02-16 13:40:06 +01:00
MaxUlysse	a285bfe8a6	fix: add guidelines to PRs and issues	2021-02-16 11:07:43 +01:00
Anders Goncalves da Silva	89f65e0875	Merge branch 'master' into ivar-variant	2021-02-15 20:50:35 -08:00
Harshil Patel	8eb3acc43f	Merge pull request #171 from JoseEspinosa/mosdepth ... Add mosdepth module	2021-02-15 23:13:01 +00:00
Anders Goncalves da Silva	4ab3ccc905	Add ivar variants	2021-02-15 09:28:10 -08:00
JoseEspinosa	6e92a6a080	Adding mosdepth module	2021-02-15 14:33:44 +01:00
Maxime Garcia	ec0bf0145e	Merge branch 'master' into master_bwa-mem2	2021-02-15 13:08:52 +01:00
Anders Goncalves da Silva	6dca7799e6	Add ivar trim	2021-02-12 16:02:10 -08:00
Harshil Patel	63a20e7b5c	Merge pull request #168 from JoseEspinosa/bcftools_merge ... Add bcftools merge module	2021-02-12 23:20:30 +00:00
JoseEspinosa	5313698705	Add bcftools merge module	2021-02-13 00:08:57 +01:00
Anders Goncalves da Silva	24b212318b	Merge branch 'master' into ivar-consensus	2021-02-12 11:51:24 -08:00
Anders Goncalves da Silva	e5a3e3a5b8	Add ivar consensus to filter.yml	2021-02-12 10:59:46 -08:00
JoseEspinosa	6e8b63fc26	Add cat fastq module	2021-02-12 17:22:07 +01:00
MaxUlysse	2f18750964	chores: update filters.yml	2021-02-12 13:53:49 +01:00
JoseEspinosa	68b85d9191	Merge remote-tracking branch 'upstream/master' into bedtools_getfasta	2021-02-09 18:23:24 +01:00
JoseEspinosa	1e9b88b33c	Fixing trailing slashes in .github/filters.yml	2021-02-09 18:16:16 +01:00
JoseEspinosa	e118bc049a	Add bedtools getfasta module	2021-02-09 17:56:51 +01:00
JoseEspinosa	9a11e90892	Fixing tests	2021-02-09 17:07:23 +01:00
JoseEspinosa	12ae7b0bff	Adding blast blastn module	2021-02-09 16:58:36 +01:00
JoseEspinosa	d0f09e26b6	Adding blast makeblastdb module to filters.yml	2021-02-09 15:47:53 +01:00
JoseEspinosa	c93e96101a	Add untar module	2021-02-09 11:50:32 +01:00
JoseEspinosa	f7f06dd6e8	Add gunzip module	2021-02-09 10:05:55 +01:00
Harshil Patel	46e5df2cf7	Merge pull request #151 from drpatelh/bedtools ... Follow up fixes for bedtools modules added in #79	2021-02-09 01:54:31 +00:00
Harshil Patel	84cf5ea2ef	Merge pull request #153 from JoseEspinosa/bedtools_maskfasta ... Add bedtools maskfasta module	2021-02-08 23:11:00 +00:00
JoseEspinosa	02d10c25a3	Add bedtools maskfasta module	2021-02-08 23:41:10 +01:00
Harshil Patel	13c1e908a3	Update .github/filters.yml	2021-02-08 21:48:21 +00:00
JoseEspinosa	58d28ed896	Fix copy/paste error :P	2021-02-08 21:57:31 +01:00
JoseEspinosa	7a0ba85843	Adding again bcftools modules to filters after solving conflict	2021-02-08 18:10:50 +01:00
drpatelh	c9cfdd31f3	Fix barfing linters	2021-02-08 00:57:06 +00:00
drpatelh	eeb496cf5c	Fix filters	2021-02-07 23:23:08 +00:00
drpatelh	83a50d8ae0	Rename SOFTWARE_TOOL to TOOL_SUBTOOL	2021-02-07 23:20:53 +00:00
drpatelh	418bd64e80	Test module with Conda	2021-02-07 21:33:42 +00:00
sruthipsuresh	93e414635b	Fixed md5sum, fixed filters, fixed slop input	2021-01-29 23:17:44 -06:00
sruthipsuresh	ac7f634675	Added complement test	2021-01-29 23:17:44 -06:00
sruthipsuresh	84b66e4f38	Fixed testing, rebased	2021-01-29 23:17:44 -06:00
sruthipsuresh	70de0331a5	Corrected pytest and config	2021-01-29 23:17:44 -06:00
sruthipsuresh	32564137fd	Corrected workflows and ran editor config	2021-01-29 23:17:44 -06:00
sruthipsuresh	672f94f2af	rebased and updated all bedtools testing and modules	2021-01-29 23:17:44 -06:00
Harshil Patel	b260192942	Merge pull request #149 from heuermh/minimap2 ... Add minimap2 align module	2021-02-07 16:37:26 +00:00
Kevin Menden	17dd0415f2	Merge pull request #146 from heuermh/bandage ... Add bandage image module	2021-02-05 08:00:44 +01:00
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
Edmund Miller	05c09429a3	ci: Fix artifact path ... Had to change it for singularity	2021-02-04 08:45:34 -06:00
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	0c88ff7458	Upgrade Singularity and change TMPDIR for pytest output	2021-02-03 20:03:43 -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	6901c7e830	ci: Fix bowtie_build names with ""	2021-02-03 12:37:14 -06:00
drpatelh	ff6f0642d2	Fix multiqc tests	2021-02-03 17:43:14 +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	3968c18fd7	Only run Docker tests	2021-02-03 14:04:58 +00:00
drpatelh	9e44b0f4f2	Add conda clean step to action	2021-02-03 12:57:55 +00:00
drpatelh	49fecaa4f0	Switch channel order	2021-02-03 12:07:39 +00:00
drpatelh	d783e2d535	Only test Docker and Conda	2021-02-03 09:02:12 +00:00
Edmund Miller	54bb0ae7a1	ci: Name logs	2021-02-02 17:51:20 -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	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	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