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nf-core / createpanelrefs

Generate Panel of Normals, models or other similar references from lots of samples
https://nf-co.re/createpanelrefs
MIT License
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pipeline does not generate cnv models #15

Open egenomics opened 9 months ago

egenomics commented 9 months ago

Description of the bug

The pipeline ends with error with ~120 samples: A USER ERROR has occurred: Bad input: Filtering removed all intervals. Select less strict filtering criteria.

However it does not generate cnv model or ploidy (a run in cohort mode with the samples provided). Only readcounts are available in folder readcounts (hdf5 format).

Command used and terminal output

nextflow run /playground/nf-core-createpanelrefs_dev/dev \
   -profile singularity \
   --input /playground/dataset_cnvs/samplesheets_sarek/samplesheet_bams_illumina.csv \
   --tools germlinecnvcaller \
   --fasta /corebm/tmp/bams/hg38.fa --dict /corebm/tmp/bams/hg38.dict --fai /corebm/tmp/bams/hg38.fa.fai \
   --outdir /playground/dataset_cnvs/germlinecnvcaller_illumina_reference_nochrM \
   --ploidy_priors /playground/dataset_cnvs/priors.table \
   --padding 250 \
   --bin_length 0 \
   --mappable_regions /playground/dataset_cnvs/Illumina-truseq-rapid-exome_v1.2_hg38_target_orig_nochrM.bed

Relevant files

next.log

System information

nextflow version 23.10.1.5891 Workstation local executor singularity ubuntu 22.04 nf-core/createpanelrefs dev (22/01/2024)

ramprasadn commented 7 months ago

Hi @egenomics Could you run the latest dev and see if it works now?