58 commits

Author	SHA1	Message	Date
Edmund Miller	d76638d6f8	style(#77): Fix editorconfig errors	2020-12-17 17:50:24 -06:00
drpatelh	200c946693	Add --singularity_pull_docker_container to module yml	2020-12-14 00:34:24 +00:00
drpatelh	047dbde0af	Add singularity containers for rnaseq pipeline modules	2020-12-13 23:41:53 +00:00
Edmund Miller	ba681c6f27	refactor(pytest-workflow): Move fastqc tests to tests/	2020-11-24 20:26:04 +00:00
Edmund Miller	c264c66a49	test(fastqc): Use -entry to speed up tests ... `--wt, --workflow-threads` is now an option and can be used to run tests simultaneously.	2020-11-16 13:41:59 -06:00
Edmund Miller	a4544a11ad	chore(fastqc): Remove test output	2020-11-16 10:22:19 -06:00
drpatelh	a3f46865ff	Remove Singularity image path	2020-11-12 14:55:16 +00:00
drpatelh	29f9b05433	Update docs	2020-10-15 11:13:54 +01:00
drpatelh	530789ba85	Get tests passing	2020-10-15 10:47:15 +01:00
drpatelh	14525ed50d	Remove functions file	2020-10-14 18:29:50 +01:00
drpatelh	e438d026bd	Unify syntax	2020-09-10 16:45:11 +01:00
drpatelh	473f1b192f	Update functions script	2020-09-10 15:59:26 +01:00
Jeremy1805	789dc4f09a	Changed options.publish_files definition in functions.nf/initOptions	2020-08-20 11:57:10 +01:00
drpatelh	736a0aa43c	Update indents and syntax	2020-08-07 15:05:25 +01:00
drpatelh	375af1428e	Minor change	2020-08-07 12:38:10 +01:00
drpatelh	2c0f552908	Add output files	2020-08-07 12:18:43 +01:00
drpatelh	9296897009	Define options as input	2020-08-07 10:58:24 +01:00
drpatelh	4f76bb6b03	Add nextflow.config	2020-08-07 10:06:45 +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	111b1505fa	Add basedir	2020-08-07 09:40:02 +01:00
drpatelh	75e7e1573c	Add output files	2020-08-07 09:32:28 +01:00
drpatelh	754fad7c8e	Update output paths	2020-08-07 09:32:03 +01:00
drpatelh	b0abd14135	Update tests	2020-08-07 09:31:27 +01:00
drpatelh	0466d5249b	Update docs	2020-08-07 00:50:49 +01:00
drpatelh	f014e67de6	Remove old outputs	2020-08-07 00:37:13 +01:00
drpatelh	2c7abca088	Move unit tests to deprecated	2020-08-07 00:36:05 +01:00
drpatelh	16d3ad5d06	Adapt script for meta	2020-08-07 00:35:34 +01:00
drpatelh	f315a7b3c4	Hard copy files	2020-08-05 18:38:27 +01:00
drpatelh	5d224740cd	Change path	2020-08-05 17:17:58 +01:00
drpatelh	7f5ca56413	Soft-link functions to top-level module dir	2020-08-05 17:03:04 +01:00
drpatelh	3ec4f63fd8	Use correct link to fastqc	2020-08-05 16:28:42 +01:00
drpatelh	c08e6959a5	Reorganise everything	2020-08-05 16:09:25 +01:00
Phil Ewels	3406ed4da0	Merge branch 'master' into fastqc-unit-test	2020-07-17 16:00:59 +02:00
Phil Ewels	f01b3f13a6	Remove debugging statement	2020-07-17 16:00:08 +02:00
Phil Ewels	2d1252c804	FastQC tests - disable hash check	2020-07-17 11:30:28 +02:00
Phil Ewels	dcc4beacb1	Fix FastQC test	2020-07-17 11:26:50 +02:00
Stephen Kelly	846a862513	move md5 function to lib dir and symlink to fastqc test dir, rename md5 function	2020-07-16 09:17:48 -04:00
Phil Ewels	9dfafb4a19	Merge pull request #46 from stevekm/fastqc-unit-test ... add FastQC output validation and md5 checksum hash checks	2020-07-16 15:13:44 +02:00
Stephen Kelly	45fbbb538c	add FastQC output validation and md5 checksum hash checks	2020-07-16 08:20:37 -04:00
FelixKrueger	e90164dd0b	Adding back tool specific input output and index files	2020-07-15 15:46:45 +01:00
drpatelh	532859d437	Update path	2020-07-15 14:07:19 +01:00
Gregor Sturm	a2bcb5c36a	Update module according to discussion on Slack	2020-07-15 13:04:49 +02:00
Gregor Sturm	01a926866e	Update software/fastqc/test/main.nf ... Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>	2020-07-15 12:48:21 +02:00
Gregor Sturm	9d7cece077	Update software/fastqc/meta.yml ... Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>	2020-07-15 12:48:11 +02:00
Gregor Sturm	5a8803ee2f	Update software/fastqc/meta.yml ... Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>	2020-07-15 12:48:03 +02:00
Gregor Sturm	a3db769a93	Update software/fastqc/meta.yml ... Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>	2020-07-15 12:47:52 +02:00
Gregor Sturm	180310bf0a	Update software/fastqc/meta.yml ... Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>	2020-07-15 12:47:42 +02:00
Gregor Sturm	6ad2b570c2	Update software/fastqc/meta.yml ... Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>	2020-07-15 12:47:30 +02:00
Gregor Sturm	53897f4d97	Update software/fastqc/meta.yml ... Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>	2020-07-15 12:47:19 +02:00