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Fix input channels for variantrecalibrator #1022

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merged 5 commits into from
May 16, 2023
Merged

Fix input channels for variantrecalibrator #1022

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260e927
fix snps_resource_label and indels_resource_label
asp8200 May 14, 2023
46b20e9
Again trying to get mix operator working with known_indels_vqsr known…
asp8200 May 15, 2023
00aafa5
Trying to make sure that dbsnp_vqsr known_indels_vqsr and known_snps_…
asp8200 May 15, 2023
3dfe4d6
Fixing copy-paste mistake
asp8200 May 15, 2023
c026ee3
Updating changelog
asp8200 May 16, 2023
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6 changes: 3 additions & 3 deletions workflows/sarek.nf
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Original file line number Diff line number Diff line change
Expand Up @@ -153,9 +153,9 @@ pon = params.pon ? Channel.fromPath(params.pon).co

// Initialize value channels based on params, defined in the params.genomes[params.genome] scope
ascat_genome = params.ascat_genome ?: Channel.empty()
dbsnp_vqsr = params.dbsnp_vqsr ?: Channel.empty()
known_indels_vqsr = params.known_indels_vqsr ?: Channel.empty()
known_snps_vqsr = params.known_snps_vqsr ?: Channel.empty()
dbsnp_vqsr = params.dbsnp_vqsr ? Channel.value(params.known_snps_vqsr) : Channel.empty()
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@FriederikeHanssen and @maxulysse : The joint-germline genotyping now seems to work both when known_snps_vqsr etc. are set and when they are not.

Should we do a similar initialisation of the other channels in this section?

known_indels_vqsr = params.known_indels_vqsr ? Channel.value(params.known_snps_vqsr) : Channel.empty()
known_snps_vqsr = params.known_snps_vqsr ? Channel.value(params.known_snps_vqsr) : Channel.empty()
snpeff_db = params.snpeff_db ?: Channel.empty()
vep_cache_version = params.vep_cache_version ?: Channel.empty()
vep_genome = params.vep_genome ?: Channel.empty()
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