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Nextflow_schema.json updates #646

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Merged
maxulysse merged 12 commits into from
Jul 17, 2022
Merged

Nextflow_schema.json updates #646

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3fa628b
add descriptions for tools
FriederikeHanssen Jul 17, 2022
5491bea
update icons, (it's important:joy: :sparkle:
FriederikeHanssen Jul 17, 2022
52a9237
Update nextflow_schema.json
FriederikeHanssen Jul 17, 2022
e6743e7
since ascat_chrom parameter isn't doing anything at the moment, remov…
FriederikeHanssen Jul 17, 2022
759ade6
since ascat_chrom parameter isn't doing anything at the moment, remov…
FriederikeHanssen Jul 17, 2022
b6ccbfd
Update nextflow_schema.json
FriederikeHanssen Jul 17, 2022
2c9e7a5
update changelog
FriederikeHanssen Jul 17, 2022
ed37174
update changelog
FriederikeHanssen Jul 17, 2022
2f87020
Update nextflow_schema.json
FriederikeHanssen Jul 17, 2022
10c9281
a bit more coherence with formatting
FriederikeHanssen Jul 17, 2022
7269a06
remove enum list, resolve merge conflicts
FriederikeHanssen Jul 17, 2022
093a35f
remove enum list
FriederikeHanssen Jul 17, 2022
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3 changes: 0 additions & 3 deletions nextflow.config
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Original file line number Diff line number Diff line change
Expand Up @@ -51,7 +51,6 @@ params {
// Variant Calling
only_paired_variant_calling = false //if true, skips germline variant calling for normal-paired samples
ploidy = 2 //null (in ascat, test this works) // Use default value, you can use 2,3,4
ascat_chromosomes = "c(1:22, 'X')" // default value for ASCAT
ascat_min_base_qual = 20 // default value for ASCAT
ascat_min_counts = 10 // default value for ASCAT
ascat_min_map_qual = 35 // default value for ASCAT
Expand All @@ -67,8 +66,6 @@ params {
pon_tbi = null // No default PON index for GATK Mutect2
ignore_soft_clipped_bases = false // no --dont-use-soft-clipped-bases for GATK Mutect2
wes = false // Set to true, if data is exome/targeted sequencing data. Used to use correct models in various variant callers
joint_germline = false // g.vcf & joint germline calling are not run by default if HaplotypeCaller is selected


// Annotation
vep_out_format = 'vcf'
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