319 commits

Author	SHA1	Message	Date
sruthipsuresh	78473edb72	Removed large testing files, will convert to updated testing	2021-01-29 23:17:44 -06:00
Sruthi Suresh	4fca435120	Fixed naming issues and links in meta.yml	2021-01-29 23:17:44 -06:00
Edmund Miller	178becdd69	style: Run yaml-lint against files	2021-01-29 23:17:44 -06:00
Edmund Miller	b16226c09c	fix(bedtools): Add header param	2021-01-29 23:17:44 -06:00
Sruthi Suresh	a984c1be7c	Added all modules with basic functionality and updated meta.yml files.	2021-01-29 23:17:44 -06:00
Sruthi Suresh	89e5473b44	Updated modules with the changed container format	2021-01-29 23:17:44 -06:00
Sruthi Suresh	6677c98b11	Updated complement and completed slop module with all parameters available.	2021-01-29 23:17:44 -06:00
Sruthi Suresh	199dfc5ea3	Added complement module with necessary test dir/parameters	2021-01-29 23:17:44 -06:00
Sruthi Suresh	709970e9af	Completed slop module for modules with test directory and updated meta.yml file	2021-01-29 23:17:44 -06:00
Sruthi Suresh	5205ce286a	Added all modules using bedtools in the enhancer transcript identification section	2021-01-29 23:17:44 -06:00
Sruthi Suresh	637b545168	Removed extraneous modules and updated removegenes module	2021-01-29 23:17:44 -06:00
Sruthi Suresh	1426d89440	Completed sloprefseq and removegenes modules (main.nf, meta.yml and functiosn.nf file). Also added the test directory with input/output/main.nf files.	2021-01-29 23:17:44 -06:00
Sruthi Suresh	5b2633757e	updated test file and main.nf file	2021-01-29 23:17:44 -06:00
sruthipsuresh	521c87f999	Updated test.mainnf file. ... Added the necessary chrom sizes input and changed test file to directory (as specified in nfcore).	2021-01-29 23:17:44 -06:00
sruthipsuresh	fefbdb9893	Created test file for checking code. ... Still need to add parameters map and chrom sizes path.	2021-01-29 23:17:44 -06:00
Sruthi Suresh	185ca19930	Added module for slopRefseq, including meta.yml, functions and main	2021-01-29 23:17:44 -06:00
Sruthi Suresh	352a48741f	updated test file and main.nf file	2021-01-29 23:17:44 -06:00
Sruthi Suresh	5a997c5ac6	Updated module, need to fix cardinality of tuple	2021-01-29 23:17:44 -06:00
Sruthi Suresh	022b0bfe54	Updated test directory with input files, corrected main.nf and config. Additionally, main.nf for the process was updated.	2021-01-29 23:17:44 -06:00
sruthipsuresh	74f1a62fa4	Corrected errors in naming.	2021-01-29 23:17:44 -06:00
sruthipsuresh	ec6ebe086f	Updated test.mainnf file. ... Added the necessary chrom sizes input and changed test file to directory (as specified in nfcore).	2021-01-29 23:17:44 -06:00
sruthipsuresh	898c0775c6	Main.nf for bedtools module added.	2021-01-29 23:17:44 -06:00
sruthipsuresh	a654c0f5fa	Created fixbedcoordinates functions.nf file	2021-01-29 23:17:44 -06:00
sruthipsuresh	c8f30720a1	Created meta file for the fixbedcoordinates module.	2021-01-29 23:17:44 -06:00
sruthipsuresh	8d6d48f067	Created test file for checking code. ... Still need to add parameters map and chrom sizes path.	2021-01-29 23:17:44 -06:00
sruthipsuresh	5f705f69e1	Fixed version error in bedtools.	2021-01-29 23:17:44 -06:00
sruthipsuresh	fe2e27c793	Update main.nf ... Updated bedtools module with updated container version and upstream/downstream values.	2021-01-29 23:17:44 -06:00
Sruthi Suresh	69f9f1cc89	Updated with removegenes folder (with meta, main and generic function file).	2021-01-29 23:17:44 -06:00
Sruthi Suresh	cfe8a490d8	Added module for slopRefseq, including meta.yml, functions and main	2021-01-29 23:17:44 -06:00
Harshil Patel	b260192942	Merge pull request #149 from heuermh/minimap2 ... Add minimap2 align module	2021-02-07 16:37:26 +00:00
Michael L Heuer	35ed09b06e	Fix CI test failure	2021-02-05 11:41:36 -06:00
Michael L Heuer	6b873d7d33	Remove single_end if/else	2021-02-05 11:35:11 -06:00
Harshil Patel	31520fce97	Update software/minimap2/align/main.nf	2021-02-05 10:45:34 +00:00
Michael L Heuer	bbc8c725a2	Fix lint errors	2021-02-04 13:45:39 -06:00
Michael L Heuer	d5f2f5e32d	Add minimap2 align module	2021-02-04 13:42:08 -06:00
Michael L Heuer	37a9f6f456	Address review comments	2021-02-04 12:10:54 -06:00
Kevin Menden	f298c594fe	Update meta.yml ... Just a small edit, we want to keep this consistent for linting	2021-02-04 07:34:08 +01:00
Michael L Heuer	05d257e8f5	Fix lint errors	2021-02-03 19:34:25 -06:00
Michael L Heuer	c466255f6f	Add bandage image module	2021-02-03 19:31:58 -06:00
drpatelh	673d463208	bowtie - add mulled build info	2021-02-03 11:33:31 +00:00
drpatelh	423144808c	seacr - add build info for mulled container	2021-02-03 11:05:10 +00:00
drpatelh	34e451dd2e	rsem - add build info for mulled container	2021-02-03 11:04:59 +00:00
drpatelh	26e04dd298	rsem - add build info for mulled container	2021-02-03 11:04:51 +00:00
drpatelh	3d1b9371f2	hisat2 - add build info for mulled container	2021-02-03 11:04:35 +00:00
drpatelh	98158064a7	bwa - add build info for mulled container	2021-02-03 11:04:25 +00:00
drpatelh	630b4be938	bowtie2 - add build info for mulled container	2021-02-03 11:04:02 +00:00
drpatelh	415d0265db	Add build to Conda	2021-02-03 11:03:36 +00:00
drpatelh	3ae4c51f42	various - add build to conda definition	2021-02-03 09:20:34 +00:00
drpatelh	c0926b0b6b	various - add build to conda definition	2021-02-03 09:19:46 +00:00
drpatelh	daab19a849	picard - add build to conda definition	2021-02-03 09:18:37 +00:00