438 commits

Author	SHA1	Message	Date
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