Edmund Miller
a3684d9594
Lint modules ci ( #389 )
...
* ci: Add modules lint step
Moved it ahead of the nextflow install so ideally it'll fail before we
bother doing any more setup
* ci: _ => /
* Update tests/config/pytest_software.yml
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-04-08 09:10:52 +01:00
Mark-S-Hill
889465cb2b
update test data paths ( #373 )
...
* update test data paths
* Update test md5sums
* gatk test fixes & update variantfiltration main
* few extra fixes after review
* fix suspected format error
* Update software/gatk4/variantfiltration/main.nf
* Update software/gatk4/variantfiltration/main.nf
* Apply suggestions from code review
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-03-24 18:14:11 +00:00
Harshil Patel
acb1a12a56
Re-organise all test data ( #354 )
...
* Re-organise all test data
* Fix ECLint
* Fix ECLint agaaainn
* Now is not the time EClint
2021-03-24 09:53:41 +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
e9d90007c5
Adding arguments to make md5 hashes stable
2021-02-23 19:39:24 +01:00
JoseEspinosa
4b3c86ed9f
Add tests for bcftools-mpileup
2021-02-23 19:05:57 +01:00
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
5a144d6213
fix: merge bcftools/tabix and htslib/tabix tests into tabix/tabix
2021-02-16 18:35:32 +01:00
JoseEspinosa
5313698705
Add bcftools merge module
2021-02-13 00:08:57 +01:00
Harshil Patel
0f6830f7cc
Update tests/software/bcftools/consensus/main.nf
2021-02-08 21:41:24 +00:00
JoseEspinosa
f8882de456
Renaming test ymls just to: software tool
2021-02-08 21:56:53 +01:00
JoseEspinosa
4fa38ebb7a
Separate test data to break dependencies between bcftools modules tests
2021-02-08 16:51:21 +01:00
JoseEspinosa
83cc25860d
Rearranging tests to test each module separately
2021-02-08 15:16:51 +01:00
JoseEspinosa
26829497d5
Fixing typo on path for md5 check
2021-02-02 12:19:57 +01:00
JoseEspinosa
e7f15feccf
Adding --no-version to bcftools_isec for tests md5 check
2021-02-02 11:00:02 +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
8e4764b8ed
bcftools_filter adding argument to test to enable md5 check
2021-02-02 10:19:34 +01:00
JoseEspinosa
c25f8f0f6c
Fixing tests
2021-02-02 09:57:55 +01:00
JoseEspinosa
a3ce63c79c
Adding tests for bcftools
2021-02-02 09:14:00 +01:00
