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Author	SHA1	Message	Date
Anders Goncalves da Silva	9268851cde	Remove samtools option ... Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>	2021-02-12 15:09:50 -08:00
Anders Goncalves da Silva	1f66954180	Relabel input parameter ... Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>	2021-02-12 15:09:35 -08:00
JoseEspinosa	5313698705	Add bcftools merge module	2021-02-13 00:08:57 +01:00
Harshil Patel	96d3b0a18b	Update tests/software/ivar/consensus/main.nf	2021-02-12 23:02:25 +00:00
Harshil Patel	f8916060f8	Update tests/software/ivar/consensus/main.nf	2021-02-12 23:02:19 +00:00
Harshil Patel	0580fd8ded	Update software/ivar/consensus/main.nf	2021-02-12 23:02:04 +00:00
Harshil Patel	9e4539473e	Update software/ivar/consensus/main.nf	2021-02-12 23:01:53 +00:00
Harshil Patel	bc5e073cdb	Update software/ivar/consensus/main.nf	2021-02-12 22:57:06 +00:00
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	ffc849761d	Edit test to output mpileup and passing args to samtools	2021-02-12 14:43:19 -08:00
Anders Goncalves da Silva	487ec7b793	Fix test.yml	2021-02-12 14:42:42 -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	8b3c16a518	Add ref FASTA to test main.nf	2021-02-12 11:29:16 -08:00
Anders Goncalves da Silva	0a6e8400ac	Add reference SC2 genome to test data	2021-02-12 11:27:12 -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
Anders Goncalves da Silva	e5a3e3a5b8	Add ivar consensus to filter.yml	2021-02-12 10:59:46 -08:00
Harshil Patel	0b5b8957f4	Merge pull request #167 from JoseEspinosa/cat_fastq ... Add cat fastq module	2021-02-12 18:02:10 +00:00
JoseEspinosa	fafe068192	Fixing test tags	2021-02-12 18:49:57 +01:00
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	d7a219e88d	Fix test.yml	2021-02-12 17:37:49 +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
MaxUlysse	2f18750964	chores: update filters.yml	2021-02-12 13:53:49 +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	df9125b46a	Fix test name ... Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>	2021-02-10 12:05:01 -08:00
Anders Goncalves da Silva	40bbf94ef9	Update filename for outputted mpileup file in test ... Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>	2021-02-10 12:04:46 -08:00
Anders Goncalves da Silva	68de6fef0d	Fix indentation ... Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>	2021-02-10 12:04:15 -08:00
Anders Goncalves da Silva	ffa9cf85b1	Clean up header params ... I used these for testing and forgot to remove them Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>	2021-02-10 12:03:50 -08:00
Anders Goncalves da Silva	1f6419f8f5	Fix indentation ... Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>	2021-02-10 10:55:24 -08:00
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
Harshil Patel	9069ed5921	Merge pull request #165 from drpatelh/pangolin ... Bump Pangolin version and minor amendments	2021-02-10 11:22:47 +00:00
drpatelh	e63279e6a2	Pin pangoLearn version	2021-02-10 10:28:27 +00:00
drpatelh	1d00a4a11c	Update md5sum	2021-02-09 23:31:39 +00:00
drpatelh	79d730f2c3	Change output name	2021-02-09 23:27:08 +00:00
drpatelh	7f629bca45	OCDness	2021-02-09 23:26:55 +00:00
drpatelh	b03846600d	Tidy up	2021-02-09 23:26:45 +00:00