Dear all, one question: how is it possible to integrate the argument

-fastaProt z.prot.fa

when running snpeff within the command? Thanks! here my command:

LOGFILE="/data/myname/projects/rnavar_test/logs/rnavar_run_$(date +%Y%m%d_%H%M%S).log"

nextflow run nf-core/rnavar \
  -profile singularity \
  -resume \
  -c /data/myname/bins/custom.config3 \
  --input /data/myname/projects/rnavar_test/samplesheet_test.csv \
  --outdir /data/myname/projects/rnavar_test/results_test \
  --genome Olea_europaea \
  --skip_baserecalibration \
  --tools snpeff \
  &> "$LOGFILE"

here my config:

process {
  // Shell robusta
  shell = 'bash -euo pipefail'

  // Risorse di default
  cpus = 8
  memory = '28 GB'
  beforeScript = 'chmod +x .command.run || true'

  // Profili per label
  withLabel: process_low {
    cpus = 4
    memory = '8 GB'
  }

  withLabel: process_medium {
    cpus = 6
    memory = '16 GB'
  }

  withLabel: process_high {
    cpus = 8
    memory = '28 GB'
  }

  withLabel: process_long {
    cpus = 8
    memory = '28 GB'
  }

  // ⚙️ Processo STAR genomeGenerate → alto uso di RAM
  withName: 'NFCORE_RNASEQ:PREPARE_GENOME:STAR_GENOMEGENERATE' {
    cpus = 8
    memory = '28 GB'
  }

  // ⚙️ Processo fastp + umi-tools → medio uso di RAM
  withName: 'NFCORE_RNASEQ:RNASEQ:FASTQ_QC_TRIM_FILTER_SETSTRANDEDNESS:FASTQ_FASTQC_UMITOOLS_FASTP:FASTP' {
    cpus = 6
    memory = '16 GB'
  }

  // 🧪 PATCH: usa container aggiornato per snpEff
  withName: SNPEFF_SNPEFF {
    container = '<https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/37/37a5be8afdc2e112fd1bb4aa226e009a437e6537f50a51ed909fe2018fd62e99/data>'
  }
}

executor {
  queueSize = 2
  maxForks = 2
}

params {
  genome = 'Olea_europaea'
  params.snpeff_db         = 'Olea_europaea'
  params.snpeff_cache      = '/data/myname/bins/snpEff/data'  

  genomes {
    'Olea_europaea' {
      fasta      = '/data/myname/refs/genomes/Olea_europaea/Olea_europaea.OLEA9.dna.toplevel.fa'
      gtf        = '/data/myname/refs/genomes/Olea_europaea/Olea_europaea.OLEA9.62.gtf'
      star_index = '/data/myname/refs/STAR/Olea_europaea'
    }
  }
}

where would this z.prot.fa come from?

https://pcingola.github.io/SnpEff/snpeff/faq/ within Creating a protein sequence FASTA file, please check

-fastaProt

ok, so you want to publish this file as well too then I assume?

Its nice to get the modified protein directly. But I actually need also other files i.e. modified transcripts, cds.. so I'm obliged to use another pipeline to get to that point.

ok, so at the moment, it won't possible to do that, but we can always make some modifications upstream to the snpeff_snpeff module -> https://github.com/nf-core/modules/blob/master/modules/nf-core/snpeff/snpeff/main.nf And report back these changes in the pipeline

Dear, you helped me already a lot! No worries, I've found a turnaround to do this and other steps I needed as I mentioned in my previous message. Thanks!

I do see the appeal of such an addition, if we had a variant annotation only pipeline that we could pipe in after #C01NHS4CC91 or #CGFUX04HZ instead of bundling it in the pipelines