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29 commits

Author SHA1 Message Date
Jose Espinosa-Carrasco
572abb00b3
Remove def from module options definition in main (#270) 
* Remove def from module options definition in main

* Fix bismark_deduplicate tests

* Fix bwameth_align tests

* Fixing gatk4 conda tests ("=" instead of ':' in build id)

* Same as previous commit (Fix gatk4 test)

* Fix qualimap bamqc test (no md5 check for pngs)

* Fix seqkit split2 tests. Changed to new test data

* Fix samtools tests. Some were missing initOptions include

* Removing TOOL SUBTOOL template module since now it is included on tools repo
 2021-03-15 12:16:43 +00:00
Kevin Menden
a552d97849
Exchange VCF data by sarscov2 data (#261) 
* added sarscov2 vcf data; adjusted bcftools tests

* updated README.md

* deleted old VCF files; fixed mergevcfs

* fixed tabix
 2021-03-09 10:04:08 +01:00
JoseEspinosa
ec674bb127 Add label to bcftools processes 2021-02-24 09:47:54 +01:00
JoseEspinosa
823a631afc Fix tools entry on yml 2021-02-24 09:47:36 +01:00
JoseEspinosa
af7bc743bf Correct yml file, add fasta to input and correct vcf on output 2021-02-24 09:15:18 +01:00
JoseEspinosa
138be9f918 Adding label to the bcftools-mpileup process 2021-02-23 21:52:15 +01:00
JoseEspinosa
035443b6e0 Add bcftools-mpileup module 2021-02-23 19:05:26 +01:00
drpatelh
dcc580e4fb Remove Conda build ids for all modules 2021-02-16 23:58:23 +00:00
Harshil Patel
412172cda6
Merge pull request #180 from MaxUlysse/master_tabix_bgzip 
Replace bcftools/bgzip by tabix/bgzip
 2021-02-16 23:32:23 +00:00
MaxUlysse
6a147b8aaa chores: replace bcftools/bgzip by tabix/bgzip cf #179 2021-02-16 19:11:36 +01:00
MaxUlysse
edf5fa3cf6 fix: merge bcftools/tabix and htslib/tabix into tabix/tabix 2021-02-16 18:27:13 +01:00
Harshil Patel
c0d128fd39
Update software/bcftools/merge/main.nf 2021-02-12 23:16:52 +00:00
JoseEspinosa
5313698705 Add bcftools merge module 2021-02-13 00:08:57 +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
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
2fa14f2ec8 Adding conda build to bcftools modules 2021-02-09 23:00:19 +01:00
JoseEspinosa
fe412797dd Adressing general comments on PR #134 2021-02-08 15:11:36 +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
579de3e038 bcftools_tabix generic for any TAB-delimited genome position file 2021-02-01 21:59:39 +01:00
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
JoseEspinosa
b6ef06c6cd Add bcftools_consensus module 2021-01-31 22:23:26 +01:00
JoseEspinosa
500481833f Adding bcftools_bgzip module 2021-01-30 11:22:25 +01:00