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nf-core_modules/tests/modules/gatk4
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santiagorevale 1a4c7cec1b
New modules added: issues #200 and #310 (#884) 
* New modules added: issues #200 and #310

* Update main.nf

* Update meta.yml

* Update tests/modules/gatk4/genotypegvcfs/main.nf

* Apply suggestions from code review

* Update main.nf

* Updating tests for GenomicsDB input and adding the path for this test resource to test_data.config

* Some minor changes on one of the test files I forgot to include

Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
Co-authored-by: GCJMackenzie <43276267+GCJMackenzie@users.noreply.github.com>
2021-11-15 15:43:06 +00:00
..
applybqsr feat: update gatk4 from 4.2.0.0 to 4.2.3.0 (#1059) 2021-11-11 08:58:59 +01:00
baserecalibrator Update to allow cram + update needed to use the gatk4 modules in sarek (#976) 2021-10-29 13:01:05 +02:00
bedtointervallist Rename software/ directory to modules/ to re-organise module structure (#567) 2021-07-07 10:10:18 +01:00
calculatecontamination feat: update gatk4 from 4.2.0.0 to 4.2.3.0 (#1059) 2021-11-11 08:58:59 +01:00
createsequencedictionary Rename software/ directory to modules/ to re-organise module structure (#567) 2021-07-07 10:10:18 +01:00
createsomaticpanelofnormals feat: update gatk4 from 4.2.0.0 to 4.2.3.0 (#1059) 2021-11-11 08:58:59 +01:00
estimatelibrarycomplexity Add gatk4/estimatelibrarycomplexity (#965) 2021-10-28 17:49:27 +02:00
fastqtosam feat: update gatk4 from 4.2.0.0 to 4.2.3.0 (#1059) 2021-11-11 08:58:59 +01:00
filtermutectcalls feat: update gatk4 from 4.2.0.0 to 4.2.3.0 (#1059) 2021-11-11 08:58:59 +01:00
genomicsdbimport bug fixes: genomicsdbimport (#1035) 2021-11-06 15:51:15 +00:00
genotypegvcfs New modules added: issues #200 and #310 (#884) 2021-11-15 15:43:06 +00:00
getpileupsummaries feat: update gatk4 from 4.2.0.0 to 4.2.3.0 (#1059) 2021-11-11 08:58:59 +01:00
haplotypecaller Update to allow cram + update needed to use the gatk4 modules in sarek (#976) 2021-10-29 13:01:05 +02:00
indexfeaturefile New modules added: issues #200 and #310 (#884) 2021-11-15 15:43:06 +00:00
intervallisttools Rename software/ directory to modules/ to re-organise module structure (#567) 2021-07-07 10:10:18 +01:00
learnreadorientationmodel Learnreadorientationmodel (#794) 2021-10-07 13:55:06 +01:00
markduplicates feat: update gatk4 from 4.2.0.0 to 4.2.3.0 (#1059) 2021-11-11 08:58:59 +01:00
mergebamalignment feat: update gatk4 from 4.2.0.0 to 4.2.3.0 (#1059) 2021-11-11 08:58:59 +01:00
mergevcfs feat: update gatk4 from 4.2.0.0 to 4.2.3.0 (#1059) 2021-11-11 08:58:59 +01:00
mutect2 Mutect2 add mitochondria mode and update tests (#967) 2021-10-29 11:27:56 +01:00
revertsam feat: update gatk4 from 4.2.0.0 to 4.2.3.0 (#1059) 2021-11-11 08:58:59 +01:00
samtofastq Rename software/ directory to modules/ to re-organise module structure (#567) 2021-07-07 10:10:18 +01:00
splitncigarreads feat: update gatk4 from 4.2.0.0 to 4.2.3.0 (#1059) 2021-11-11 08:58:59 +01:00
variantfiltration Rename software/ directory to modules/ to re-organise module structure (#567) 2021-07-07 10:10:18 +01:00