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print default values for --min_af_normal and --sigma_tumor
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tdelhomme committed Oct 24, 2016
1 parent 49ced4d commit b6a0cfd
Showing 1 changed file with 3 additions and 1 deletion.
4 changes: 3 additions & 1 deletion needlestack.nf
Original file line number Diff line number Diff line change
Expand Up @@ -282,6 +282,8 @@ if(params.input_vcf) {
log.info "Strand bias measure (--sb_type) : ${params.sb_type}"
log.info "Strand bias threshold for SNVs (--sb_snv) : ${params.sb_snv}"
log.info "Strand bias threshold for indels (--sb_indel) : ${params.sb_indel}"
log.info "Minimum allelic fraction for somatic (--min_af_tumor) : ${params.min_af_tumor}"
log.info "Sigma parameter for germline (--sigma) : ${params.sigma_normal}"
log.info "Samtools minimum mapping quality (--map_qual) : ${params.map_qual}"
log.info "Samtools minimum base quality (--base_qual) : ${params.base_qual}"
log.info "Samtools maximum coverage before downsampling (--max_DP) : ${params.max_DP}"
Expand Down Expand Up @@ -425,7 +427,7 @@ if(params.input_vcf) {
'''
# create a dummy empty pdf to avoid an error in the process when no variant is found
touch empty.pdf
needlestack.r --pairs_file=!{params.pairs_file} --source_path=!{baseDir}/bin/ --out_file=!{region_tag}.vcf --fasta_ref=!{fasta_ref} --GQ_threshold=!{params.min_qval} --min_coverage=!{params.min_dp} --min_reads=!{params.min_ao} --SB_type=!{params.sb_type} --SB_threshold_SNV=!{params.sb_snv} --SB_threshold_indel=!{params.sb_indel} --output_all_SNVs=!{params.all_SNVs} --do_plots=!{!params.no_plots} --plot_labels=!{!params.no_labels} --add_contours=!{!params.no_contours} --extra_rob=!{params.extra_robust_gl} --afmin=!{params.min_af_tumor} --sigma=!{params.sigma_normal}
needlestack.r --pairs_file=!{params.pairs_file} --source_path=!{baseDir}/bin/ --out_file=!{region_tag}.vcf --fasta_ref=!{fasta_ref} --GQ_threshold=!{params.min_qval} --min_coverage=!{params.min_dp} --min_reads=!{params.min_ao} --SB_type=!{params.sb_type} --SB_threshold_SNV=!{params.sb_snv} --SB_threshold_indel=!{params.sb_indel} --output_all_SNVs=!{params.all_SNVs} --do_plots=!{!params.no_plots} --plot_labels=!{!params.no_labels} --add_contours=!{!params.no_contours} --extra_rob=!{params.extra_robust_gl} --afmin=!{params.min_af_tumor} --sigma=!{params.sigma_normal}
'''
}

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@tdelhomme tdelhomme commented on b6a0cfd Oct 24, 2016

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part of #137

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