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controlfreec with multiple ploidy values results in plotting error
Description of the bug
When running nf-core/sarek 3.0.2
with --cf_ploidy "2,3,4"
controlfreec
runs and produces output but the makeGraph.R
script to plot the results crashes, as it expects a single number for the ploidy
parameter.
Suggested solution: if --cf_ploidy
is used with more than one ploidy option, extract the Output_Ploidy
from the tumour_vs_normal.tumor.mpileup.gz_info.txt
file (attached) that is produced and pass this to the makeGraph.R
script.
Command used and terminal output
run nf-core/sarek -r 3.0.2 -profile singularity \
-c nextflow.config \
--step variant_calling \
--outdir ./results_3.0.2 \
-w /scratch/wsspaces/sarek_3.0.2_cfascat-0/work/ \
--genome GATK.GRCh38 \
--wes \
--intervals /data/exome_targets/truseq-dna-exome-targeted-regions-manifest-v1-2_GRCh38_sorted_unique_controlFREEC.bed \
--cf_chrom_len /data/reference_genomes/custom_references/custom_Homo_sapiens_assembly38.fasta.fai \
--tools controlfreec,ascat \
--cf_contamination_adjustment true \
--cf_ploidy "2,3,4" \
--schema_ignore_params cf_ploidy,genomes \
-resume admiring_noether
Relevant files
command.err.txt tumour_vs_normal_p30.tumor.mpileup.gz_info.txt
System information
- Nextflow version 21.10.5
- HPC
- PBS torque
- Singularity
- Scientific Linux 7.5 (Nitrogen)
- nf-core/sarek 3.0.2
Thank you for reporting! will look into a fix