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nf-core / sarek

Analysis pipeline to detect germline or somatic variants (pre-processing, variant calling and annotation) from WGS / targeted sequencing
https://nf-co.re/sarek
MIT License
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Need to document snpeff_cache/vep_cache clashes with snpeff_version/vep_version #984

Open FriederikeHanssen opened 1 year ago

FriederikeHanssen commented 1 year ago

Description of feature

When using 

nextflow run nf-core/sarek -r 3.1.1 -profile cfc \
--input 'sampleSheet_sarek.csv' \
--genome null \
--save_reference \
--fasta './Synechocystis_sp_pcc_6803_gca_000009725.ASM972v1.dna.toplevel.fa' \
--skip_tools baserecalibrator \
--split_fastq 0 \
--igenomes_ignore \
--snpeff_cache './snpeff_cache' \
--tools 'freebayes,snpeff,vep' \
--snpeff_version '5.0-1' \
--annotation_cache true \
--snpeff_db 'Synechocystis_sp_pcc_6803_substr_gt_i' \
--vep_cache './vep_cache' \
--vep_genome 'Synechocystis_sp_pcc_6803_gca_000009725' \
-c custom.config \
--outdir 'results_sarek' \
-resume

The snpeff container was not actually updated but still container 5.1 was used

maxulysse commented 1 year ago

This is not a params anymore: annotation_cache When using snpeff_cache we remove the usage of the home made custom containers with cache and version, so we revert to the snpeff version specified in the modules file hence snpeff_version is useless in that case. We should add warnings for that.