nf-core/createpanelrefs

Generate Panel of Normals, models or other similar references from lots of samples

createpanelrefs's Issues

panel of normals creation for Mutect2

Description of feature

With 40 normal samples a panel of normals file should be generated which can be used with Mutect2.

Create ploidy and cnv models for GATK's germline cnv calling pipeline

Description of feature

Running GATK's germline calling pipeline requires a ploidy model (created using GATK DetermineGermlineContigPloidy) and a cnv model (created using GATK GermlineCNVCaller). More details on how to create these models can be found here.

pipeline does not generate cnv models

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)

panel of normals creation for cnvkit

Description of feature

Given a number of normal samples a panel of normals file should be generated which can be used in cnvkit.

qDNAseq bin annotations

Description of feature

It might be worthwhile to integrate a flow to generate bin annotations for qDNAseq.
@nvnieuwk has already prepared a standalone workflow for this, but it might be a nice addition here.

https://github.com/CenterForMedicalGeneticsGhent/nf-cmgg-qdnaseq

Convert files for CNVKIT

          Why don't you also convert the CRAM files to BAM and add them here?

Originally posted by @nvnieuwk in #5 (comment)

Add dbnsfp computation and files

Description of feature

As discussed :) The instructions for it are here: https://www.ensembl.org/info/docs/tools/vep/script/vep_plugins.html#dbnsfp (click "more)
(slightly annoying it is different for 37 and 38)