improve documentation to point out that when using ASCAT and the Format in the BAM file is chr, one has to change the loci ascat reference file to be also in the chr format

[rgraus]

Description of the bug

Running Ascat on the dev. branch of the SAREK pipeline in tumor-normal mode with WES data raised an error, because chromosome format in BAM file (e.g. chr1) did not match format of acat loci reference file (e.g. 1). This is mentioned in the ascat documentation (https://github.com/VanLoo-lab/ascat/tree/master/ReferenceFiles/WES), but is should be also made clear in the Sarek documentation.

Command used and terminal output

export NXF_OPTS='-Xms1g -Xmx10g'
sudo nextflow run nf-core/sarek \
	-r 3.4.0 \
	--input ./sampleSheetShort.csv \
	--outdir ./results \
	--genome GATK.GRCh38 \
	--tools freebayes,mutect2,strelka,manta,tiddit,cnvkit,controlfreec,ascat,snpeff,vep,merge \
	-profile docker \


##############################Error Output###########################################
ERROR ~ Error executing process > 'NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_ASCAT:ASCAT (VUC133_1_
vs_VUC133_0)'

Caused by:
  Process `NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_ASCAT:ASCAT (VUC133_1_vs_VUC133_0)` terminated
 with an error exit status (1)

Command executed:

  #!/usr/bin/env Rscript
  library(RColorBrewer)
  library(ASCAT)
  options(bitmapType='cairo')
 
  #build prefixes: <abspath_to_files/prefix_chr>
  allele_path = normalizePath("battenberg_alleles_on_target_hg38")
  allele_prefix = paste0(allele_path, "/", "battenberg_alleles_on_target_hg38", "_chr")
 
  loci_path = normalizePath("battenberg_loci_on_target_hg38")
  loci_prefix = paste0(loci_path, "/", "battenberg_loci_on_target_hg38", "_chr")
 
  #prepare from BAM files
  ascat.prepareHTS(
      tumourseqfile = "VUC133_1.recal.cram",
      normalseqfile = "VUC133_0.recal.cram",
      tumourname = paste0("VUC133_1_vs_VUC133_0", ".tumour"),
      normalname = paste0("VUC133_1_vs_VUC133_0", ".normal"),
      allelecounter_exe = "alleleCounter",
      alleles.prefix = allele_prefix,
      loci.prefix = loci_prefix,
      gender = "XY",
      genomeVersion = "hg38",
      nthreads = 6
      ,minCounts = 10
      ,BED_file = 'Twist_Exome_RefSeq_targets_hg38_c3.bed'
      ,chrom_names = c(1:22, 'X', 'Y')
      ,min_base_qual = 20
      ,min_map_qual = 35
      ,ref.fasta = 'Homo_sapiens_assembly38.fasta'
 
      ,
      seed = 42
  )
	--wes \
	--intervals "/scratch/rgraus29/projects/wes_emily/emilyDataVsc/Grubb/supporting_files/gatk/Twist_Exome_RefSeq_targets_hg38_c3.bed" \
	--ascat_alleles "/localmirror_sata/ascat/correctionFiles/1000G_alleles_hg38/battenberg_alleles_on_target_hg38/battenberg_alleles_on_target_hg38.zip" \
	--ascat_loci "/localmirror_sata/ascat/correctionFiles/1000G_loci_hg38/battenberg_loci_on_target_hg38/battenberg_loci_on_target_hg38.zip" \
	--ascat_loci_gc "/localmirror_sata/ascat/correctionFiles/GC_G1000_on_target_hg38.zip" \
	--ascat_loci_rt "/localmirror_sata/ascat/correctionFiles/RT_G1000_on_target_hg38.zip" \
	-c nextflow.config \
	-resume

Relevant files

nextflow.log

System information

No response