87 commits

Author	SHA1	Message	Date
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
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
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