48 commits

Author	SHA1	Message	Date
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
drpatelh	c08e6959a5	Reorganise everything	2020-08-05 16:09:25 +01:00
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
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
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