310 commits

Author	SHA1	Message	Date
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
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
Michael L Heuer	eb6408f3dc	Added dsh-bio filter-bed as dsh_filterbed	2021-01-21 15:16:20 -06:00
Edmund Miller	daa25b9329	Merge branch 'preseq_test'	2021-01-15 17:41:13 -06:00
Edmund Miller	4f0c34bbfb	ci: Bump nextflow version ... Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>	2021-01-15 10:32:20 -06:00
sruthipsuresh	7729fee5a9	Added gffread and gff3 file for testing	2021-01-15 10:32:20 -06:00
sruthipsuresh	b95bd37780	Added ucsc module	2021-01-15 10:28:11 -06:00
Harshil Patel	27dbe8b52a	Merge pull request #115 from Functional-Genomics-Lab/stringtie_test ... Added testing for Stringtie	2021-01-15 16:09:39 +00:00
Edmund Miller	a3ca757f4e	Update .github/workflows/phantompeakqualtools.yml ... Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>	2021-01-15 09:38:13 -06:00
sruthipsuresh	3f814d1e2f	Workflow and md5sums added	2021-01-15 09:38:13 -06:00
sruthipsuresh	2d2f15af0f	Delete phantompeakqualtools.yml	2021-01-13 21:23:24 -06:00
sruthipsuresh	b297f7aea1	Fixed test and removed phantompeak tests	2021-01-12 18:04:12 -06:00
sruthipsuresh	0a04c96357	Added module, TODO data	2021-01-12 09:13:37 -06:00
sruthipsuresh	cb39fcb915	Added preseq module and workflow	2021-01-12 08:41:09 -06:00
Chris Cheshire	7e9cbfc8d1	Merge remote-tracking branch 'nf-core/master'	2021-01-05 09:10:11 +00:00
sruthipsuresh	522b896534	Workflow and md5sums added	2020-12-19 06:09:04 -06:00
Harshil Patel	c98f9284a2	Merge pull request #89 from KevinMenden/master ... Add bowtie module	2020-12-18 14:56:29 +00:00
Edmund Miller	eb61638501	ci: Use verbose name for editorconfig-check ... I was getting confused myself with eclint	2020-12-17 17:48:19 -06:00
Edmund Miller	c6cf653f25	ci(#77): Ignore README for editorconfig ... Because of the nf-core examples it throws errors.	2020-12-17 17:48:02 -06:00
Edmund Miller	0b6f117d2a	ci(#77): eclint => editorconfig-checker	2020-12-17 17:48:02 -06:00
Chris Cheshire	4436f59a1c	seacr | Syntax error	2020-12-17 14:27:37 +00:00
Chris Cheshire	15e1b860f9	seacr | added github action workflow	2020-12-17 14:25:42 +00:00
kevinmenden	8d3fc30eb3	fixed yml formatting	2020-12-17 07:39:34 +01:00
kevinmenden	d75cb75111	added singularity; edge NXF version	2020-12-17 07:33:44 +01:00
drpatelh	992232b340	Bump NF version to 20.11.0-edge	2020-12-14 00:14:28 +00:00
Edmund Miller	8d27ff53c5	ci: Support multiple nextflow versions	2020-12-09 09:56:40 -06:00
Edmund Miller	f994d55c18	style: Fix indent on workflows	2020-12-09 09:56:11 -06:00
Harshil Patel	79a0ce79ab	Merge pull request #82 from abhi18av/master ... Add multiqc module	2020-12-09 11:31:07 +00:00
kevinmenden	fee0707af1	added bowtie_align workflow test	2020-12-08 14:19:34 +01:00
kevinmenden	73530e8df7	added bowtie index test github workflow	2020-12-08 14:13:30 +01:00
Abhinav Sharma	27b4b29976	Remove the extra data files	2020-12-04 20:20:59 +05:30
Edmund Miller	6d8ba714d5	ci(fastqc): Use 20.10.0 => ''	2020-12-04 08:23:19 -06:00
Abhinav Sharma	5fd3ba3ce6	Update the tests for MultiQC	2020-12-02 13:09:32 +05:30
Edmund Miller	65697532a1	ci: Get rid of software folder	2020-12-01 11:40:16 -06:00
Edmund Miller	8cd635f757	ci(fastqc): Fix test matrix	2020-12-01 11:13:43 -06:00
Paolo Cozzi	835ac48565	Fixing MULTIQC module and adding tests (#1) ... * fix multiqc process * fix multiqc tests * move multiqc test input data into tests/data/fastqc/ folder Move input tests data into tests/data/fastqc/ and linking those files into software/multiqc/test/input/ as stated from the project documentation * add multiqc github workflow * remove unused file * generalize multiqc input data User must collect all desidered files in a channel (as described in https://seqera.io/training/#_multiqc_report * update meta information	2020-12-01 12:03:37 +05:30
Edmund Miller	98c629583a	ci: Test whether subdirectories are breaking workflows	2020-11-30 19:03:56 -06:00
Edmund Miller	7d2b74a5f7	ci(fastqc): Use a test matrix for NXF versions	2020-11-30 18:57:56 -06:00
Edmund Miller	036427d73c	ci(pytest-workflow): Fix trigger paths	2020-11-24 21:24:55 -06:00
Edmund Miller	86219a586b	ci(trimgalore): Use pytest-workflow	2020-11-24 21:08:34 -06:00
Edmund Miller	445498d0c3	ci(samtools): Run tests with pytest-workflow	2020-11-24 21:08:34 -06:00
Edmund Miller	34d86427a6	test(samtools): Refactor flagstat to use pytest-workflow	2020-11-24 21:08:33 -06:00
Edmund Miller	ebf3a4529f	ci(picard): Update markduplicates	2020-11-24 21:08:33 -06:00
Edmund Miller	939f5ca744	test(picard): Refactor collectmultiplemetrics to use pytest-workflow	2020-11-24 21:03:40 -06:00
Edmund Miller	234e85bdce	test(picard): Refactor mergesamfiles to use pytest-workflow	2020-11-24 19:01:12 -06:00
Edmund Miller	016d8684f3	test(bwa): Refactor to use pytest-workflow	2020-11-24 19:00:11 -06:00
Edmund Miller	dfc8528df9	ci: Remove docker workflow ... This only applies to deprecated software	2020-11-24 18:58:02 -06:00
Edmund Miller	691df9d469	style(actions): Create seperate software dir ... For future subworkflows	2020-11-24 18:57:53 -06:00
Edmund Miller	f235732a58	ci(fastqc): Use both threads in GitHub runner	2020-11-16 13:45:00 -06:00
Edmund Miller	6d857a2584	ci(fastqc): Run pytest-workflow instead of workflow ... This will check for the actual output files and their contents not just whether the module runs or not.	2020-11-16 09:37:45 -06:00
drpatelh	082c582258	Remove EClint for now	2020-11-12 15:22:15 +00:00
drpatelh	b22ec332e9	Add GitHub Actions	2020-08-07 16:42:56 +01:00
drpatelh	50a628ad0a	Remove deprecated tests	2020-08-07 15:55:23 +01:00