659 commits

Author	SHA1	Message	Date
Anders Goncalves da Silva	cb19c7b056	Fix trailing whitespace	2021-02-12 14:46:13 -08:00
Anders Goncalves da Silva	b08bf1ea5c	Remove ref to conda build and additional params	2021-02-12 14:43:50 -08:00
Anders Goncalves da Silva	24b212318b	Merge branch 'master' into ivar-consensus	2021-02-12 11:51:24 -08:00
Anders Goncalves da Silva	bfc13d3379	Add options to make samtools more flexible	2021-02-12 11:50:33 -08:00
Anders Goncalves da Silva	a4bba006bd	Add reference fasta as input	2021-02-12 11:26:55 -08:00
Anders Goncalves da Silva	6b22bb9782	Add meta.yml	2021-02-12 11:25:40 -08:00
JoseEspinosa	0688230863	Revert since fixes to test were not working ... This reverts commit d7a219e88d.	2021-02-12 18:02:32 +01:00
JoseEspinosa	8e23e1839d	Trying to fix tests	2021-02-12 17:56:51 +01:00
JoseEspinosa	6e8b63fc26	Add cat fastq module	2021-02-12 17:22:07 +01:00
MaxUlysse	9c98194d3c	chores: remove fasta file from bwamem2 mem process	2021-02-12 16:00:59 +01:00
MaxUlysse	0afddf6ca4	fix: CI is working	2021-02-12 15:24:09 +01:00
Maxime Garcia	c1ff201518	Apply suggestions from code review ... Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>	2021-02-12 13:24:10 +01:00
MaxUlysse	6b34ddf239	chores: bwa-mem2 -> bwamem2	2021-02-12 13:08:44 +01:00
MaxUlysse	a910d1a608	chores: add bwa-mem2 index + mem	2021-02-12 13:00:02 +01:00
Maxime Garcia	27be87ac72	Merge pull request #135 from drpatelh/bwa ... Update indices syntax for BWA index and mem modules	2021-02-12 12:45:38 +01:00
Anders Goncalves da Silva	e9aa037e7b	Add function to enable output of mpileup ... Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>	2021-02-10 10:02:06 -08:00
Anders Goncalves da Silva	06770d5f02	Specify the exact bioconda recipe build ... Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>	2021-02-10 10:01:25 -08:00
Anders Goncalves da Silva	362a630f8b	Change suffix of mpileup ouput file ... Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>	2021-02-10 10:00:54 -08:00
Anders Goncalves da Silva	884c4658b8	Make mpileup saving optional ... Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>	2021-02-10 10:00:22 -08:00
Jose Espinosa-Carrasco	1e771ac8a0	Merge pull request #164 from drpatelh/fixes ... Add missing build ids and rename *.txt channels	2021-02-10 14:19:00 +01:00
drpatelh	b9afca2b05	Underscore not .	2021-02-10 12:53:17 +00:00
drpatelh	d2508e3c03	Amend prefix for bcftools stats	2021-02-10 12:51:47 +00:00
drpatelh	e63279e6a2	Pin pangoLearn version	2021-02-10 10:28:27 +00:00
drpatelh	b03846600d	Tidy up	2021-02-09 23:26:45 +00:00
drpatelh	6795fe04b8	Rename output channel	2021-02-09 23:26:18 +00:00
drpatelh	2b9129b3f9	Change txt channel output	2021-02-09 23:09:22 +00:00
drpatelh	d50d070c06	Change txt channel output	2021-02-09 23:09:18 +00:00
drpatelh	0b33b6d081	Add missing build ids	2021-02-09 23:03:13 +00:00
JoseEspinosa	e8dc199dc8	Adding conda build to blast modules	2021-02-09 23:04:12 +01:00
JoseEspinosa	2fa14f2ec8	Adding conda build to bcftools modules	2021-02-09 23:00:19 +01:00
Harshil Patel	3f431014a4	Update software/bedtools/getfasta/main.nf	2021-02-09 21:34:40 +00:00
Anders Goncalves da Silva	8f546a1f95	Add ivar consensus	2021-02-09 10:26:35 -08:00
JoseEspinosa	68b85d9191	Merge remote-tracking branch 'upstream/master' into bedtools_getfasta	2021-02-09 18:23:24 +01:00
JoseEspinosa	e118bc049a	Add bedtools getfasta module	2021-02-09 17:56:51 +01:00
JoseEspinosa	12ae7b0bff	Adding blast blastn module	2021-02-09 16:58:36 +01:00
JoseEspinosa	c23b355b35	Add blast makeblastdb module	2021-02-09 15:44:34 +01:00
JoseEspinosa	c93e96101a	Add untar module	2021-02-09 11:50:32 +01:00
JoseEspinosa	20771ae1bc	Remove meta from input/output meta.yml	2021-02-09 11:02:31 +01:00
JoseEspinosa	b09416a0d0	Correcting meta.yml	2021-02-09 10:51:57 +01:00
JoseEspinosa	f7f06dd6e8	Add gunzip module	2021-02-09 10:05:55 +01:00
Harshil Patel	46e5df2cf7	Merge pull request #151 from drpatelh/bedtools ... Follow up fixes for bedtools modules added in #79	2021-02-09 01:54:31 +00:00
Harshil Patel	84cf5ea2ef	Merge pull request #153 from JoseEspinosa/bedtools_maskfasta ... Add bedtools maskfasta module	2021-02-08 23:11:00 +00:00
JoseEspinosa	02d10c25a3	Add bedtools maskfasta module	2021-02-08 23:41:10 +01:00
JoseEspinosa	f4e322f88d	Merging upstream changes ... # Conflicts: # .github/filters.yml	2021-02-08 18:09:41 +01:00
JoseEspinosa	fe412797dd	Adressing general comments on PR #134	2021-02-08 15:11:36 +01:00
JoseEspinosa	5071bf5914	Merge remote-tracking branch 'upstream/master' into bcftools_viralrecon	2021-02-08 10:45:57 +01:00
drpatelh	c9cfdd31f3	Fix barfing linters	2021-02-08 00:57:06 +00:00
drpatelh	83a50d8ae0	Rename SOFTWARE_TOOL to TOOL_SUBTOOL	2021-02-07 23:20:53 +00:00
drpatelh	a34d74188d	Really fix Editor Config	2021-02-07 21:49:20 +00:00
drpatelh	ef0a984cc0	Fix Editor config tests	2021-02-07 21:44:45 +00:00
drpatelh	5779b180da	Fix bedtools sort module	2021-02-07 21:32:43 +00:00
drpatelh	f3b5af4ed5	Fix bedtools slip module	2021-02-07 21:32:20 +00:00
drpatelh	38964ecfc0	Fix bedtools intersect module	2021-02-07 21:32:01 +00:00
drpatelh	a37b116186	Fix bedtools merge module	2021-02-07 21:31:39 +00:00
drpatelh	4564ef0e54	Fix bedtools genomecov module	2021-02-07 21:31:21 +00:00
drpatelh	a0c08e0c06	Fix bedtools complement module	2021-02-07 21:31:02 +00:00
drpatelh	a9102c329c	Fix bedtools complement module	2021-02-07 20:55:12 +00:00
drpatelh	81ae0089bc	Fix merge conflicts	2021-02-05 10:06:39 +00:00
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
drpatelh	773d4d89f2	rseqc - add build to conda definition	2021-02-03 09:18:20 +00:00
drpatelh	383d35bc7d	samtools - add build to conda definition	2021-02-03 09:17:38 +00:00
drpatelh	ce3edcc994	deeptools - add build to conda definition	2021-02-03 09:16:59 +00:00
drpatelh	c089edc670	cutadapt - add build to conda definition	2021-02-03 09:16:33 +00:00
drpatelh	b41c3d63ec	bwa index - add build to conda definition	2021-02-03 09:16:22 +00:00
drpatelh	f913a55d85	bowtie2 build - add build to conda definition	2021-02-03 09:16:10 +00:00
drpatelh	a536c85ec0	bowtie - add build to conda definition	2021-02-03 08:49:18 +00:00
drpatelh	3ccf99d612	Fix module	2021-02-02 13:37:24 +00:00
drpatelh	6df54698d9	Remove fasta from input	2021-02-02 12:34:55 +00:00
drpatelh	dcb1dc5cd9	Remove fasta requirement from module	2021-02-02 12:34:42 +00:00
drpatelh	0d8bd42cca	Create index in bwa directory	2021-02-02 12:34:23 +00:00
Maxime Garcia	e7474c3d98	Update main.nf ... Use same tag	2021-02-02 12:13:14 +01:00
JoseEspinosa	3a40ec5664	Adding bcftools_isec taking a path with several vcfs and its tests	2021-02-02 10:50:45 +01:00
JoseEspinosa	c25f8f0f6c	Fixing tests	2021-02-02 09:57:55 +01:00
JoseEspinosa	cee37852cd	Merge remote-tracking branch 'upstream/master' into bcftools_viralrecon	2021-02-02 09:15:20 +01:00
JoseEspinosa	579de3e038	bcftools_tabix generic for any TAB-delimited genome position file	2021-02-01 21:59:39 +01:00
drpatelh	f84e5b59ca	Rename bowtie_index to bowtie_build	2021-02-01 17:53:31 +00:00
Harshil Patel	0a41130276	Merge pull request #131 from KevinMenden/fastp-module ... Adding fastp module	2021-02-01 13:43:35 +00:00
Harshil Patel	e851da8640	Merge pull request #130 from KevinMenden/master ... Adding a QUAST module	2021-02-01 13:17:57 +00:00
Kevin Menden	f6c4e9d9c1	Update software/quast/meta.yml ... Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>	2021-02-01 14:03:36 +01:00
Kevin Menden	9885da628e	Update software/quast/meta.yml ... Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>	2021-02-01 14:03:22 +01:00
Kevin Menden	c807c6c438	Update software/quast/main.nf ... Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>	2021-02-01 14:03:15 +01:00
Kevin Menden	d88bf3bdda	Update software/quast/main.nf ... Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>	2021-02-01 14:03:06 +01:00
Kevin Menden	c43fe85a0c	Update software/quast/main.nf ... Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>	2021-02-01 14:02:57 +01:00
kevinmenden	038381de99	added fastp module	2021-02-01 13:54:08 +01:00
kevinmenden	b5298f94d8	refactored quast module	2021-02-01 13:13:21 +01:00
Harshil Patel	2c962f34df	Merge pull request #110 from luslab/master ... Add SEACR module containing a single CALLPEAK process	2021-02-01 09:48:15 +00:00
JoseEspinosa	0a8915ae77	Adding bcftools_tabix module	2021-02-01 10:07:35 +01:00
JoseEspinosa	52b0b8094d	Adding bcftools_stats module	2021-02-01 10:03:25 +01:00
JoseEspinosa	0423e686a6	Adding bcftools_isec module	2021-02-01 09:46:24 +01:00
JoseEspinosa	da7598272e	Adding bcftools_filter module	2021-02-01 09:41:08 +01:00
JoseEspinosa	eb12f4610d	Fixing meta ymls	2021-02-01 09:28:51 +01:00
kevinmenden	956bf22a58	fixed bug; updated meta.yml	2021-02-01 07:44:26 +01:00
JoseEspinosa	b6ef06c6cd	Add bcftools_consensus module	2021-01-31 22:23:26 +01:00
Harshil Patel	eadbea4b83	Merge pull request #127 from JoseEspinosa/bowtie2_viralrecon ... Bowtie2 viralrecon	2021-01-30 13:22:30 +00:00
Harshil Patel	eab633776e	Update software/bowtie2/build/meta.yml	2021-01-30 13:21:56 +00:00
JoseEspinosa	500481833f	Adding bcftools_bgzip module	2021-01-30 11:22:25 +01:00
JoseEspinosa	986b72cee9	Fix error on previous commit	2021-01-30 09:35:25 +01:00
JoseEspinosa	29989035a5	Remove author entry from yml (copy-pasted :P)	2021-01-30 09:29:53 +01:00
sruthipsuresh	e360617ac6	Fixed images, genomecov	2021-01-29 23:17:44 -06:00
sruthipsuresh	e3bbbb48fc	Fixed slop file	2021-01-29 23:17:44 -06:00
sruthipsuresh	957983bd99	Fixed and tested 4 modules, keeping with fastp module syntax	2021-01-29 23:17:44 -06:00
sruthipsuresh	295fff35ec	Corrected containers and tested	2021-01-29 23:17:44 -06:00
sruthipsuresh	19b55fc67c	Fixed intersect, complement indentation issues	2021-01-29 23:17:44 -06:00
sruthipsuresh	3da39dfc88	Fixed bedtools complement module	2021-01-29 23:17:44 -06:00
sruthipsuresh	8496427c56	Update software/bedtools/complement/main.nf ... Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>	2021-01-29 23:17:44 -06:00
sruthipsuresh	fc8cdde2b4	Apply suggestions from code review ... Add all initial suggestions from review (syntax issues) Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>	2021-01-29 23:17:44 -06:00
sruthipsuresh	e5c21d15a3	Update software/bedtools/complement/main.nf ... Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>	2021-01-29 23:17:44 -06:00
sruthipsuresh	bf2703f396	Update software/bedtools/complement/main.nf ... Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>	2021-01-29 23:17:44 -06:00
sruthipsuresh	93f640154a	Update software/bedtools/complement/main.nf ... Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>	2021-01-29 23:17:44 -06:00
sruthipsuresh	ced2458d78	Update software/bedtools/complement/main.nf ... Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>	2021-01-29 23:17:44 -06:00
sruthipsuresh	29639c522f	Corrected sort	2021-01-29 23:17:44 -06:00
sruthipsuresh	70de0331a5	Corrected pytest and config	2021-01-29 23:17:44 -06:00
sruthipsuresh	2f19b4279c	All modules corrected, TODO config	2021-01-29 23:17:44 -06:00
sruthipsuresh	6e7feb9e57	Update main.nf ... Fixed prefix	2021-01-29 23:17:44 -06:00
sruthipsuresh	672f94f2af	rebased and updated all bedtools testing and modules	2021-01-29 23:17:44 -06:00
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
JoseEspinosa	ddbe8055c2	Adding tests	2021-01-29 19:31:33 +01:00
JoseEspinosa	43f9815621	Adding module bowtie2 align	2021-01-29 19:29:32 +01:00
Harshil Patel	bd59706d51	Merge pull request #118 from heuermh/dsh-bio ... Added dsh-bio filter-bed as dsh_filterbed	2021-01-29 18:15:24 +00:00
Harshil Patel	7ab3217f16	Update software/dsh/filterbed/main.nf	2021-01-29 18:14:13 +00:00
Harshil Patel	cf5e38f48b	Update software/dsh/filterbed/main.nf	2021-01-29 18:14:08 +00:00
Harshil Patel	0fcbc4233c	Merge pull request #126 from JoseEspinosa/samtools_viralrecon ... Samtools viralrecon	2021-01-29 18:12:48 +00:00
Harshil Patel	eb7a3861db	Update software/samtools/mpileup/meta.yml	2021-01-29 18:12:17 +00:00
JoseEspinosa	2f9934c563	Adding bowtie2_build module	2021-01-29 18:57:27 +01:00
JoseEspinosa	13e9f81160	Fixing lint tests	2021-01-29 18:01:58 +01:00
JoseEspinosa	22dcdc692d	Adding samtools_mpileup module	2021-01-29 17:58:42 +01:00
JoseEspinosa	3eedca9bb4	Add samtools_view	2021-01-29 17:18:45 +01:00
kevinmenden	10bb80743a	started adding quast modules	2021-01-29 16:06:14 +01:00
Michael L Heuer	d2723408ad	Apply suggestions from code review ... Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>	2021-01-29 09:01:21 -06:00
kevinmenden	d30994c6ef	Merge branch 'pangolin-module' of https://github.com/KevinMenden/modules into pangolin-module	2021-01-29 12:54:38 +01:00
kevinmenden	44df90a795	Merge branch 'master' of https://github.com/nf-core/modules into pangolin-module	2021-01-29 12:50:24 +01:00
Harshil Patel	5da41ecb26	Merge pull request #122 from KevinMenden/master ... Added tests and meta.yml files for Salmon	2021-01-29 11:49:03 +00:00
Harshil Patel	59e3e8202b	Update software/pangolin/main.nf	2021-01-29 11:43:42 +00:00
Kevin Menden	afaef3c30d	Apply suggestions from code review ... Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>	2021-01-29 12:40:15 +01:00
kevinmenden	a22f430674	updated input description	2021-01-29 12:34:23 +01:00
Kevin Menden	8f2f936cd4	Apply suggestions from code review ... Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>	2021-01-29 12:33:37 +01:00
kevinmenden	69a41cadbc	added pangolin module	2021-01-29 11:03:54 +01:00
kevinmenden	0780155dc4	added cutadapt module and tests	2021-01-29 09:33:45 +01:00
kevinmenden	3750bea2dd	fixed typo	2021-01-26 16:18:46 +01:00
kevinmenden	a3185732ff	added meta.yml files	2021-01-26 16:12:41 +01:00
kevinmenden	84355f674d	added optional output files	2021-01-26 13:31:30 +01:00
Kevin Menden	8e2749beb7	Apply suggestions from code review ... Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>	2021-01-26 12:46:30 +01:00
kevinmenden	272de7c021	Added meta.yml files for align and genomegenerate	2021-01-25 15:14:57 +01:00
kevinmenden	71e0de733c	adapdted star for mutliple output BAMs	2021-01-25 14:09:03 +01:00
kevinmenden	6444af7b36	star module tests	2021-01-25 09:02:03 +01:00
Michael L Heuer	e6547d5b16	Update dsh-bio version to 2.0	2021-01-22 12:12:56 -06:00
Michael L Heuer	23f9284aae	Added dsh-bio split-bed as dsh_splitbed	2021-01-21 16:34:49 -06:00
Michael L Heuer	eb6408f3dc	Added dsh-bio filter-bed as dsh_filterbed	2021-01-21 15:16:20 -06:00
Chris Cheshire	f6432d3c9c	seacr | updated whitespace	2021-01-05 10:22:37 +00:00
Chris Cheshire	d9818cf3ab	seacr | updated whitespace	2021-01-05 10:21:32 +00:00
Chris Cheshire	6d34e6964f	seacr | added new line at end	2021-01-05 10:20:13 +00:00
Chris Cheshire	e25edbf7b8	seacr | Added meta file	2021-01-05 10:18:11 +00:00
Chris Cheshire	c110088b5e	Updated line endings	2021-01-05 09:56:15 +00:00
Chris Cheshire	37840b3855	seacr | updated trailing whitespace	2021-01-05 09:54:44 +00:00
Chris Cheshire	9c00d1722c	seacr | PR review changes	2021-01-05 09:50:47 +00:00
Chris Cheshire	7e9cbfc8d1	Merge remote-tracking branch 'nf-core/master'	2021-01-05 09:10:11 +00:00
Harshil Patel	c98f9284a2	Merge pull request #89 from KevinMenden/master ... Add bowtie module	2020-12-18 14:56:29 +00:00
kevinmenden	32f6191ff3	editorconfig	2020-12-18 11:11:19 +01:00
kevinmenden	db0b631906	removed index from test output	2020-12-18 11:06:02 +01:00
kevinmenden	299a3fa07e	adding .index back	2020-12-18 10:58:37 +01:00
kevinmenden	0be13edc52	next try at editorconfig	2020-12-18 09:52:38 +01:00
kevinmenden	07f0a2476a	fixed linting errors	2020-12-18 09:50:05 +01:00
kevinmenden	0eb20c14bf	fixed unaligned output	2020-12-18 09:20:35 +01:00
kevinmenden	1c89c9717b	Merge branch 'master' of https://github.com/KevinMenden/modules	2020-12-18 09:16:17 +01:00
kevinmenden	f840325ead	added unaligned output	2020-12-18 09:14:40 +01:00
Kevin Menden	7805d25cc5	Update software/bowtie/align/meta.yml ... Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>	2020-12-18 09:13:48 +01:00
Kevin Menden	a7f1ff29d7	Update software/bowtie/align/meta.yml ... Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>	2020-12-18 09:13:42 +01:00
Kevin Menden	dc4108fd9b	Update software/bowtie/align/meta.yml ... Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>	2020-12-18 09:13:35 +01:00
Kevin Menden	41329b8982	Apply suggestions from code review ... Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>	2020-12-18 08:16:18 +01:00
Edmund Miller	d76638d6f8	style(#77): Fix editorconfig errors	2020-12-17 17:50:24 -06:00
Chris Cheshire	6f1c66f22f	Merge remote-tracking branch 'nf-core/master'	2020-12-17 14:29:20 +00:00
Chris Cheshire	b24834dfce	seacr | local testing implimented	2020-12-17 14:20:24 +00:00
Chris Cheshire	74e7b5385f	seacr | Added main process structure	2020-12-17 13:54:48 +00:00
Harshil Patel	b236d0c834	Update main.nf	2020-12-17 10:24:01 +00:00
kevinmenden	57ab6dbcbf	groovy formatting	2020-12-17 10:24:48 +01:00
kevinmenden	d75cb75111	added singularity; edge NXF version	2020-12-17 07:33:44 +01:00
Chris Cheshire	3ff2b558e0	seacr | Added callpeak skeleton	2020-12-16 11:05:06 +00:00
kevinmenden	f35850bf14	bowtie bam output	2020-12-16 11:02:58 +01:00
drpatelh	200c946693	Add --singularity_pull_docker_container to module yml	2020-12-14 00:34:24 +00:00
drpatelh	99a2364a26	Update all other modules	2020-12-14 00:05:48 +00:00
drpatelh	047dbde0af	Add singularity containers for rnaseq pipeline modules	2020-12-13 23:41:53 +00:00
drpatelh	115efec15c	Update Salmon quant to use BAM input	2020-12-09 21:20:52 +00:00
drpatelh	37b8b82c98	Fix tyop	2020-12-09 21:20:26 +00:00
drpatelh	42f318fe75	Update Salmon modules	2020-12-09 21:20:11 +00:00
kevinmenden	42020ce5ac	added tests for bowtie paired-end alignment; resolved index bug	2020-12-09 16:39:05 +01:00
kevinmenden	cc72028d3d	output index as directory	2020-12-09 15:58:56 +01:00
Kevin Menden	560a6a578b	Apply suggestions from code review ... Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>	2020-12-09 15:45:05 +01:00
Harshil Patel	79a0ce79ab	Merge pull request #82 from abhi18av/master ... Add multiqc module	2020-12-09 11:31:07 +00:00
Abhinav Sharma	0c9f29e0a2	Give finishing touches after the review	2020-12-08 19:08:00 +05:30
Abhinav Sharma	b56a0322ab	Apply suggestions from code review by @drpatelh ... Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>	2020-12-08 18:57:14 +05:30
kevinmenden	9d67da2b2c	added module yml files	2020-12-08 13:40:32 +01:00
kevinmenden	508761e05c	Added bowtie index and align modules	2020-12-08 12:57:00 +01:00
Harshil Patel	cd2cf9cf2f	Merge pull request #85 from nf-core/pytest-workflow-refactor ... Refactor all tests to use pytest-workflow	2020-12-04 14:30:00 +00:00
Abhinav Sharma	3da7aec183	Update the signatures	2020-12-04 12:25:16 +05:30
Abhinav Sharma	a30df8a59b	Iterate again on MultiQC	2020-12-04 12:11:17 +05:30
Abhinav Sharma	5fd3ba3ce6	Update the tests for MultiQC	2020-12-02 13:09:32 +05:30
Abhinav Sharma	4e657c82e2	Move the MultiQC test files to data folder	2020-12-01 12:27:31 +05:30
Abhinav Sharma	b43c1f3937	Refactor the multiqc test code	2020-12-01 12:19:52 +05:30
Abhinav Sharma	131609dc05	Tweak the output section to make the tests pass	2020-12-01 12:03:37 +05:30
Paolo Cozzi	835ac48565	Fixing MULTIQC module and adding tests (#1) ... * fix multiqc process * fix multiqc tests * move multiqc test input data into tests/data/fastqc/ folder Move input tests data into tests/data/fastqc/ and linking those files into software/multiqc/test/input/ as stated from the project documentation * add multiqc github workflow * remove unused file * generalize multiqc input data User must collect all desidered files in a channel (as described in https://seqera.io/training/#_multiqc_report * update meta information	2020-12-01 12:03:37 +05:30
Abhinav Sharma	2783913122	initial attempt for multiqc module	2020-12-01 12:03:37 +05:30
drpatelh	e5c7ecc89c	Use STAR to build initial index for RSEM	2020-11-30 11:29:24 +00:00
Edmund Miller	6eeb930bdb	chore: Remove test directory from dummy tool	2020-11-24 21:09:55 -06:00
Edmund Miller	2fc39e02e2	test(trimgalore): Refactor se and pe to use pytest-workflow	2020-11-24 21:08:34 -06:00
Edmund Miller	b2cd464ad3	test(samtools): Refactor stats to use pytest-workflow	2020-11-24 21:08:34 -06:00
Edmund Miller	36bbf6baa3	test(samtools): Refactor sort to use pytest-workflow ... Pretty sure this is passing it a sorted bam though?	2020-11-24 21:08:34 -06:00
Edmund Miller	6448638b55	test(samtools): Refactor index to use pytest-workflow	2020-11-24 21:08:34 -06:00
Edmund Miller	16cb794892	test(samtools): Refactor idxstats to use pytest-workflow	2020-11-24 21:08:34 -06:00
Edmund Miller	34d86427a6	test(samtools): Refactor flagstat to use pytest-workflow	2020-11-24 21:08:33 -06:00
Edmund Miller	7848019cdb	test(picard): Refactor markduplicates to use pytest-workflow	2020-11-24 21:08:33 -06:00
Edmund Miller	939f5ca744	test(picard): Refactor collectmultiplemetrics to use pytest-workflow	2020-11-24 21:03:40 -06:00
Edmund Miller	234e85bdce	test(picard): Refactor mergesamfiles to use pytest-workflow	2020-11-24 19:01:12 -06:00
Edmund Miller	016d8684f3	test(bwa): Refactor to use pytest-workflow	2020-11-24 19:00:11 -06:00
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	47d390772c	Update picard version command and default container	2020-10-19 15:17:19 +01:00
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	1d30e2c21a	Update tools not in rnaseq pipeline too	2020-10-14 18:59:25 +01:00
drpatelh	14525ed50d	Remove functions file	2020-10-14 18:29:50 +01:00
drpatelh	e9e81e8691	Revert RSeQC version	2020-10-12 17:47:13 +01:00
drpatelh	6bb3d5caea	Update container	2020-10-12 16:20:35 +01:00
drpatelh	64377d4035	Bug fixes	2020-10-12 16:20:22 +01:00
drpatelh	a1b705d412	Update RSeQC version	2020-10-12 16:04:04 +01:00
drpatelh	436a1f983c	Update trimgalore version	2020-10-12 15:59:46 +01:00
drpatelh	d19a8c702d	Update picard version	2020-10-12 15:58:09 +01:00
drpatelh	74f27803b4	Update stringtie version	2020-10-12 15:55:07 +01:00
drpatelh	f4f96ff792	Update gffread version	2020-10-12 15:52:05 +01:00
Harshil Patel	0e11679748	Update main.nf	2020-09-18 10:39:41 +01:00
Harshil Patel	fb44f36f66	Update main.nf	2020-09-16 19:08:24 +01:00
drpatelh	e438d026bd	Unify syntax	2020-09-10 16:45:11 +01:00
drpatelh	cbf8329ffd	Add new modules	2020-09-10 16:09:54 +01:00
drpatelh	46edf8ae4c	Update featurecounts module	2020-09-10 16:07:21 +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	08723c9d61	Add tests for mergesamfiles	2020-08-07 16:39:16 +01:00
drpatelh	3547b64eab	Add docs and tests for markduplicates	2020-08-07 16:30:28 +01:00
drpatelh	cb85acddf0	Add docs and tests for collectmultiplemetrics	2020-08-07 16:29:37 +01:00
drpatelh	d6f7bb055b	Fix indents	2020-08-07 15:27:35 +01:00
drpatelh	e648dc335c	Add samtools stats commands	2020-08-07 15:23:39 +01:00
drpatelh	d5b16db27d	Add samtools sort	2020-08-07 15:21:28 +01:00
drpatelh	0287cad1f8	Add samtools index tests	2020-08-07 15:17:46 +01:00
drpatelh	17b5f5ef3b	Get samtools idxstats tests passing	2020-08-07 15:14:45 +01:00
drpatelh	46e4d35ec3	Get samtools flagstat passing	2020-08-07 15:12:03 +01:00
drpatelh	cf5cb8945c	Get samtools flagstat passing	2020-08-07 15:11:31 +01:00
drpatelh	736a0aa43c	Update indents and syntax	2020-08-07 15:05:25 +01:00
drpatelh	6333786d62	Add test BAM files	2020-08-07 14:04:39 +01:00
drpatelh	0ad26e3b19	Add output files	2020-08-07 13:28:18 +01:00
drpatelh	d10878f19d	Change to SE	2020-08-07 13:27:06 +01:00
drpatelh	7ab1245eb5	Add test data	2020-08-07 13:24:39 +01:00