Fix for nocontrol #44
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kubranarci
commented
Nov 12, 2024
kubranarci
commented
- add cram/crai files to input list (assets/schema_input.json)
- add only a warn about the indices does not exists in converttovcf.json (bin/convertToStdVCF.py)
- change default arg for ENSEMBL VEP (conf/modules.config)
- upgrade samtools version for cram handling (modules/local/grep_samplename.nf)
- edit nextflow version to latest (nextflow.config)
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@kubranarci, Could you also add an update to the changelog? |
NagaComBio
requested changes
Nov 12, 2024
conf/modules.config
Outdated
| @@ -166,7 +166,7 @@ process { | |||
| ] | |||
| } | |||
| withName: 'ENSEMBLVEP_VEP' { | |||
| //ext.args ='--everything --filter_common --per_gene --total_length --offline' | |||
| ext.args ='--everything --filter_common --per_gene --total_length --offline' | |||
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Please exclude --filter_common and --per_gene, as we need all annotations for all variants, regardless of MAF. We also require all consensus data, not just the 'most severe' consensus for each variant.
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these parameters are mainly default settings, update on those parameters has to be given by local config. But I will this as well for now.
NagaComBio
approved these changes
Nov 12, 2024
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