641 commits

Author	SHA1	Message	Date
Stephen Kelly	45fbbb538c	add FastQC output validation and md5 checksum hash checks	2020-07-16 08:20:37 -04:00
JoseEspinosa	759dd85c92	Removing biocontainer in favor of nf-core container	2020-07-16 10:22:09 +02:00
JoseEspinosa	6d8b616975	Bedtools sort adapted to the current module standard	2020-07-15 18:16:12 +02:00
JoseEspinosa	4d2e375a0d	Bedtools merge adapted to the current module standard	2020-07-15 18:16:01 +02:00
JoseEspinosa	98c8f44130	Bedtools intersect adapted to the current module standard	2020-07-15 18:15:49 +02:00
JoseEspinosa	0b123f9e13	Bedtools genomecov adapted to the current module standard	2020-07-15 18:15:32 +02:00
JoseEspinosa	2cbc988d5f	Bedtools complement adapted to the current module standard	2020-07-15 18:15:16 +02:00
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
JoseEspinosa	7f8b8189f8	Merge remote-tracking branch 'upstream/master' into bedtools_dev	2020-07-15 15:05:26 +02:00
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
Gregor Sturm	b00bb83532	Document params	2020-07-15 11:01:15 +02:00
Gregor Sturm	86d6daf9de	Implement publish_results parameter	2020-07-15 10:55:52 +02:00
Gregor Sturm	1dc47e7cd3	Make publishDir more flexible	2020-07-15 10:16:48 +02:00
Gregor Sturm	dd34fa5853	Use moduleDir for conda env	2020-07-15 09:48:17 +02:00
Gregor Sturm	f7c42ac4fd	Add tests for fastqc module	2020-07-15 09:48:14 +02:00
Gregor Sturm	167067a92e	Clean up module file	2020-07-15 09:47:41 +02:00
JoseEspinosa	c485d56972	Indentation error in yml	2020-07-14 18:00:23 +02:00
JoseEspinosa	562fc74550	Indentation error in yml	2020-07-14 17:57:42 +02:00
JoseEspinosa	39b9ca205c	Correcting path to test data	2020-07-14 17:42:03 +02:00
JoseEspinosa	b38135ff6b	Moving bedtools/intersectbed to bedtools/intersect	2020-07-14 17:40:17 +02:00
JoseEspinosa	c059a485b9	Using bedtools{_,-}genomecov instead of genomecov alone	2020-07-14 17:31:40 +02:00
JoseEspinosa	71eaa83bf6	bedtoools/complementBed changed to bedtools/complement	2020-07-14 17:26:45 +02:00
JoseEspinosa	8c3d7aa2d8	Standardizing process names to BEDTOOLS_FOO and same with some variables	2020-07-14 17:25:32 +02:00
JoseEspinosa	99a8196776	Module bedtools-sort added	2020-07-14 17:20:12 +02:00
JoseEspinosa	cf9d87c977	Module bedtools-merge added	2020-07-14 16:49:06 +02:00
JoseEspinosa	708cee9cae	Module bedtools-intersectbed added	2020-07-14 16:49:05 +02:00
JoseEspinosa	5f80a900e9	Changing fasta_sizes by chrom_sizes input path for genomecov	2020-07-14 16:47:27 +02:00
JoseEspinosa	f2eb3f68c0	Module bedtools-genomecov added	2020-07-14 16:47:26 +02:00
JoseEspinosa	f6894c7d3a	Module complementbed added	2020-07-14 15:50:35 +02:00
Phil Ewels	31c0f617b9	Fix up cutadapt tests	2020-07-11 17:14:14 +02:00
Phil Ewels	f36902b9af	Cutadapt - merge tests into one	2020-07-11 17:09:06 +02:00
Phil Ewels	d3f3432451	Update test file imports	2020-07-11 14:33:12 +02:00
Phil Ewels	014fef2e92	Rename tools to software	2020-07-11 14:27:21 +02:00