111 commits

Author	SHA1	Message	Date
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
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
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
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