305 commits

Author	SHA1	Message	Date
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
drpatelh	238f43789e	Add tests for all samtools commands	2020-08-07 15:35:19 +01:00
drpatelh	14480affba	Add flagstat test	2020-08-07 15:32:09 +01:00
drpatelh	b5338efb7d	Add tests for BWA mem	2020-08-07 13:24:24 +01:00
drpatelh	cff81ef875	Add test data	2020-08-07 12:57:32 +01:00
drpatelh	9f4192d433	Add TrimGalore GitHub Actions test	2020-08-07 12:21:47 +01:00
drpatelh	49e37cb22c	Add profile docker	2020-08-07 10:07:20 +01:00
drpatelh	7efd46b489	Add nextflow.config	2020-08-07 09:59:19 +01:00
drpatelh	fab020461b	Add -with-docker	2020-08-07 09:44:16 +01:00
drpatelh	b0abd14135	Update tests	2020-08-07 09:31:27 +01:00
drpatelh	cb08a7326a	Change NF version	2020-08-07 00:38:56 +01:00
drpatelh	3e0c63a0a0	Update badge	2020-08-06 12:42:45 +01:00
drpatelh	3428157910	Add badges	2020-08-06 12:39:33 +01:00
drpatelh	3ec4f63fd8	Use correct link to fastqc	2020-08-05 16:28:42 +01:00
Phil Ewels	dcc4beacb1	Fix FastQC test	2020-07-17 11:26:50 +02:00
Phil Ewels	9b4634a426	Use latest edge version of NXF for FastQC test	2020-07-17 10:35:17 +02:00
Phil Ewels	e71bb92534	Workflows - trigger on change to workflow and test data too	2020-07-16 17:14:57 +02:00
Phil Ewels	aa24c8d175	Fix a bunch of stuff in GitHub Actions test workflows	2020-07-16 17:11:34 +02:00
Stephen Kelly	4957eb98e5	update GitHub actions for Fastqc	2020-07-16 08:49:08 -04:00
Stephen Kelly	61d44c34d0	update GitHub actions for Fastqc	2020-07-16 08:31:19 -04:00
Gregor Sturm	8f3718795b	Fix markdownlint ... Move markdownlint.yml to root directory. Like that it is automatically discovered and applied by most IDEs	2020-07-14 12:21:33 +02:00
Phil Ewels	31c0f617b9	Fix up cutadapt tests	2020-07-11 17:14:14 +02:00
Phil Ewels	905e842f36	Update more paths	2020-07-11 14:36:12 +02:00
Phil Ewels	263f48d520	Fix markdownlint	2020-07-11 13:48:11 +02:00
Phil Ewels	45fb2ff4f4	Remove verbose job names	2020-07-11 13:45:08 +02:00
Phil Ewels	fc53a6f0b5	Added markdown lint config file	2020-07-11 13:44:28 +02:00
Phil Ewels	a547f27f21	New GitHub Action to lint code style	2020-07-11 13:41:31 +02:00
Phil Ewels	8b6065764e	Merge branch 'master' into tcoffee_dev	2020-07-11 13:12:17 +02:00
Phil Ewels	dce77ce3f1	Merge branch 'master' of github.com:nf-core/modules	2020-07-11 13:08:33 +02:00
JoseEspinosa	787bf44c62	Name was fixed to tcoffee instead of FastQC (used as template)	2020-03-06 16:35:02 +01:00
Piotr Faba	6fd86ad9e5	2 tests	2020-03-06 14:56:33 +00:00
Piotr Faba	fa134a1196	fix path error	2020-03-06 14:54:26 +00:00
Piotr Faba	2646e55e2b	get test working	2020-03-06 14:50:29 +00:00
Piotr Faba	660be04708	fix test	2020-03-06 14:41:37 +00:00
Piotr Faba	36cad50593	test submodules checkout	2020-03-06 14:38:49 +00:00
Piotr Faba	977a9b3ee8	test fix	2020-03-06 14:34:34 +00:00
Phil Ewels	c8ceddfe77	Tidying, add samtools and trim_galore	2020-03-06 14:33:48 +00:00
Piotr Faba	f33dd2d2e9	add ci test	2020-03-06 14:31:44 +00:00
Phil Ewels	198e9a85eb	FastQC: add dockerfile and environment.yml	2020-03-06 14:04:18 +00:00
Phil Ewels	b3cc751e78	Build tool docker images: first attempt	2020-03-06 11:54:09 +00:00
JoseEspinosa	bcc89c27ca	Fixing command to run nxf	2020-03-06 12:47:55 +01:00
JoseEspinosa	7fe0a936f6	Fixing another typo on the yml for CI github actions	2020-03-06 12:41:07 +01:00
JoseEspinosa	36c0c56fdd	Fixing typo on the yml for CI github actions	2020-03-06 12:38:21 +01:00
JoseEspinosa	5f9cf40f5a	Changing publishDir to take params.outdir and modifying yml for github actions	2020-03-06 12:23:23 +01:00
JoseEspinosa	5de4c86bac	symlink working? (github actions error)	2020-03-06 12:02:40 +01:00
JoseEspinosa	4312ddc1fe	Is the file in the submodule? (github actions error)	2020-03-06 11:46:37 +01:00
JoseEspinosa	c8c2d0e659	Trying to fix git actions	2020-03-05 17:48:10 +01:00
JoseEspinosa	707d2855d6	Adding tcoffee module	2020-03-05 17:18:35 +01:00
JoseEspinosa	17ccbce67b	Update test-datasets with msa data	2020-03-05 17:17:14 +01:00
Phil Ewels	93f7b26aa2	Use submodules for test data	2019-12-06 09:24:33 +01:00
Phil Ewels	51bd2c0277	Ansi log false for tests	2019-12-05 22:20:02 +01:00
Phil Ewels	ef486a908b	Use empty dict instead for workflow	2019-12-05 16:09:28 +01:00
Phil Ewels	d682c6f7a8	Workflows: test everything on paths	2019-12-05 16:08:12 +01:00
Phil Ewels	a065ac3532	Actions: install nextflow	2019-12-05 16:03:00 +01:00
Phil Ewels	acc4eb0054	GitHub actions - run nextflow in a docker image	2019-12-05 15:57:32 +01:00
Phil Ewels	af766a9cc7	Added TrimGalore	2019-12-05 15:53:38 +01:00
Phil Ewels	497573fc5d	Refactor GitHub actions workflows	2019-12-05 15:44:10 +01:00
Phil Ewels	8837c2b81d	GitHub actions: paths, not path	2019-12-05 15:39:01 +01:00
Phil Ewels	97fbd32644	Added samtools sort + index ... Added container to FastQC	2019-12-05 15:36:35 +01:00
Phil Ewels	5e4c023edd	Start work on FastQC module files	2019-12-05 15:18:09 +01:00
Phil Ewels	4582ab344c	Add GitHub Actions, put FastQC in to a directory	2019-12-05 14:52:43 +01:00