nf-core_modules/tests/modules/gatk4
GCJMackenzie 61376425fb
BugFix: add missing tbi output channel to genotypeGVCFs (#1153)
* initial commit to setup branch

* workflow finished

* Update nextflow.config

* tumour to tumor, getpileup passed as nomral and tumor

* paired_somatic renamed to tumor_normal_somatic

* Apply suggestions from code review

Co-authored-by: Maxime U. Garcia <maxime.garcia@scilifelab.se>

* Update subworkflows/nf-core/gatk_tumor_normal_somatic_variant_calling/main.nf

Co-authored-by: Maxime U. Garcia <maxime.garcia@scilifelab.se>

* updated index names in meta.yml

* changed index file names in main script and test

* Apply suggestions from code review

Co-authored-by: Maxime U. Garcia <maxime.garcia@scilifelab.se>

* Apply suggestions from code review

* fixed bug from changes

* Apply suggestions from code review

* modified yml to allow new subworkflow testing

* Update test.yml

* Update test.yml

* added output channel for tbi files, tweaked method of adding blank inputs for gendb tests

* Update main.nf

* Update main.nf

Co-authored-by: GCJMackenzie <gavin.mackenzie@nibsc.org>
Co-authored-by: Maxime U. Garcia <maxime.garcia@scilifelab.se>
2021-12-14 16:10:08 +00:00
..
applybqsr Update all modules to new NF DSL2 syntax (#1099) 2021-11-26 07:58:40 +00:00
baserecalibrator Update all modules to new NF DSL2 syntax (#1099) 2021-11-26 07:58:40 +00:00
bedtointervallist Update all modules to new NF DSL2 syntax (#1099) 2021-11-26 07:58:40 +00:00
calculatecontamination Update all modules to new NF DSL2 syntax (#1099) 2021-11-26 07:58:40 +00:00
createsequencedictionary Update all modules to new NF DSL2 syntax (#1099) 2021-11-26 07:58:40 +00:00
createsomaticpanelofnormals Change syntax from task.ext.suffix to tast.ext.prefix in all modules (#1110) 2021-12-02 12:39:55 +00:00
estimatelibrarycomplexity Update all modules to new NF DSL2 syntax (#1099) 2021-11-26 07:58:40 +00:00
fastqtosam Update all modules to new NF DSL2 syntax (#1099) 2021-11-26 07:58:40 +00:00
filtermutectcalls Change syntax from task.ext.suffix to tast.ext.prefix in all modules (#1110) 2021-12-02 12:39:55 +00:00
gatherbqsrreports add gatk4/gatherbqsr (#1130) 2021-12-08 23:43:36 +01:00
genomicsdbimport Update all modules to new NF DSL2 syntax (#1099) 2021-11-26 07:58:40 +00:00
genotypegvcfs BugFix: add missing tbi output channel to genotypeGVCFs (#1153) 2021-12-14 16:10:08 +00:00
getpileupsummaries Update all modules to new NF DSL2 syntax (#1099) 2021-11-26 07:58:40 +00:00
haplotypecaller Update all modules to new NF DSL2 syntax (#1099) 2021-11-26 07:58:40 +00:00
indexfeaturefile Update all modules to new NF DSL2 syntax (#1099) 2021-11-26 07:58:40 +00:00
intervallisttools Update all modules to new NF DSL2 syntax (#1099) 2021-11-26 07:58:40 +00:00
learnreadorientationmodel Change syntax from task.ext.suffix to tast.ext.prefix in all modules (#1110) 2021-12-02 12:39:55 +00:00
markduplicates Update all modules to new NF DSL2 syntax (#1099) 2021-11-26 07:58:40 +00:00
mergebamalignment Update all modules to new NF DSL2 syntax (#1099) 2021-11-26 07:58:40 +00:00
mergevcfs Update all modules to new NF DSL2 syntax (#1099) 2021-11-26 07:58:40 +00:00
mutect2 Update all modules to new NF DSL2 syntax (#1099) 2021-11-26 07:58:40 +00:00
revertsam Update all modules to new NF DSL2 syntax (#1099) 2021-11-26 07:58:40 +00:00
samtofastq Update all modules to new NF DSL2 syntax (#1099) 2021-11-26 07:58:40 +00:00
splitncigarreads Update all modules to new NF DSL2 syntax (#1099) 2021-11-26 07:58:40 +00:00
variantfiltration Change syntax from task.ext.suffix to tast.ext.prefix in all modules (#1110) 2021-12-02 12:39:55 +00:00