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Author SHA1 Message Date
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
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
Harshil Patel
6765db81be
Merge pull request #163 from JoseEspinosa/fix_conda_build 
Add conda build id
 2021-02-09 22:47:15 +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
6319fb242e
Merge pull request #161 from JoseEspinosa/bedtools_getfasta 
Add bedtools getfasta module
 2021-02-09 21:42:16 +00:00
Harshil Patel
28866f3dc7
Update tests/software/bedtools/maskfasta/main.nf 2021-02-09 21:36:38 +00:00
Harshil Patel
3f431014a4
Update software/bedtools/getfasta/main.nf 2021-02-09 21:34:40 +00:00
Harshil Patel
aaa088dba8
Update tests/software/bedtools/getfasta/main.nf 2021-02-09 21:34:29 +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
Jose Espinosa-Carrasco
1baca83f00
Merge pull request #160 from JoseEspinosa/blast_blastn 
Add blast blastn module
 2021-02-09 18:22:23 +01:00
JoseEspinosa
1e9b88b33c Fixing trailing slashes in .github/filters.yml 2021-02-09 18:16:16 +01:00
JoseEspinosa
e118bc049a Add bedtools getfasta module 2021-02-09 17:56:51 +01:00
JoseEspinosa
7536b386a5 Correct channel declaration on bedtools_maskfasta 2021-02-09 17:56:01 +01:00
JoseEspinosa
9a11e90892 Fixing tests 2021-02-09 17:07:23 +01:00
JoseEspinosa
12ae7b0bff Adding blast blastn module 2021-02-09 16:58:36 +01:00
Harshil Patel
25db9bc648
Merge pull request #159 from JoseEspinosa/blast_makeblastdb 
Add blast makeblastdb module
 2021-02-09 15:36:25 +00:00
JoseEspinosa
d0f09e26b6 Adding blast makeblastdb module to filters.yml 2021-02-09 15:47:53 +01:00