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Author SHA1 Message Date
Harshil Patel
c0d128fd39
Update software/bcftools/merge/main.nf 2021-02-12 23:16:52 +00:00
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