69 commits

Author	SHA1	Message	Date
drpatelh	fb697eca2f	Copy across test data and docs for bwa mem	2020-08-05 17:27:42 +01:00
drpatelh	da4dcee934	Copy across test data and docs for bwa index	2020-08-05 17:27:28 +01:00
drpatelh	5d224740cd	Change path	2020-08-05 17:17:58 +01:00
drpatelh	137db462a7	Add samtools	2020-08-05 17:17:47 +01:00
drpatelh	993d0d5743	Add picard	2020-08-05 17:17:41 +01:00
drpatelh	9d168cf29e	Add deeptools	2020-08-05 17:17:34 +01:00
drpatelh	f481899049	Add subread	2020-08-05 17:17:19 +01:00
drpatelh	20e6d847a3	Add trimgalore	2020-08-05 17:17:12 +01:00
drpatelh	c5bb9c2fde	Add macs2	2020-08-05 17:17:05 +01:00
drpatelh	f61ad7506a	Add homer	2020-08-05 17:16:56 +01:00
drpatelh	71d7aecf74	Add preseq	2020-08-05 17:16:45 +01:00
drpatelh	e94676a2b2	Add phantompeakqualtools	2020-08-05 17:16:34 +01:00
drpatelh	6fe4ec16df	Add ucsc	2020-08-05 17:16:23 +01:00
drpatelh	3b1669c317	Add bwa mem	2020-08-05 17:16:08 +01:00
drpatelh	7938a60a02	Add bwa index	2020-08-05 17:15:56 +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
Harshil Patel	95a91032ce	Merge pull request #42 from JoseEspinosa/bedtools_dev ... Add modules complement, genomecov, intersect, merge, sort for bedtools	2020-08-05 15:45:17 +01:00
Paolo Di Tommaso	70daf8be30	Minor style improvents ... This commit provides a minor refactoring with som Nextflow code style improvments: - Replaces `.toGiga()` with `.giga` - Replaces `tag { foo }` with `tag "$foo"` - Move publishDir before input declarations. Directives should be before the first input. Tho this is not enforced, it may be in future versions. - Replaces input `file` with `path` - Remove unnecessary parentheses	2020-07-27 12:11:42 +02:00
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
JoseEspinosa	a09e3a633d	I forgot to uncomment output	2020-07-16 16:38:37 +02:00
JoseEspinosa	d30089f12d	Very preliminary implementation of passing optional params to bedtools/intersect modules	2020-07-16 16:37:33 +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
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