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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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1 change: 1 addition & 0 deletions CHANGELOG.md
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Expand Up @@ -90,6 +90,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
- [#618](https://github.com/nf-core/sarek/pull/618) - Update test yml files
- [#644](https://github.com/nf-core/sarek/pull/644) - Use `-Y` for `bwa-mem(2)` and remove `-M`
- [#645](https://github.com/nf-core/sarek/pull/645) - Merge `tests/nextflow.config` in `conf/test.config`
- [#646](https://github.com/nf-core/sarek/pull/646) - Update `nextflow_schema.json` to reflect new parameters and functions, removes `--annotation_cache`, removes `--ascat_chromosomes`

### Fixed

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2 changes: 1 addition & 1 deletion conf/modules.config
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Expand Up @@ -944,7 +944,7 @@ process{
"purity": params.ascat_purity,
"ploidy": params.ploidy,
"minCounts": params.ascat_min_counts,
"chrom_names": meta.sex == 'XX' ? params.ascat_chromosomes : "c(1:22, 'X', 'Y')",
"chrom_names": meta.sex == 'XX' ? "c(1:22, 'X')" : "c(1:22, 'X', 'Y')",
"min_base_qual": params.ascat_min_base_qual,
"min_map_qual": params.ascat_min_map_qual
]}
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4 changes: 0 additions & 4 deletions nextflow.config
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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'
Expand All @@ -84,7 +81,6 @@ params {
spliceai_indel = null // No spliceai_indel file
spliceai_indel_tbi = null // No spliceai_indel file index
vep_spliceregion = null // spliceregion plugin disabled within VEP
annotation_cache = false // Annotation cache disabled
snpeff_cache = null // No directory for snpEff cache
vep_cache = null // No directory for VEP cache
vep_include_fasta = false // Don't use fasta file for annotation with VEP
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