Hello! I'm trying to run the pipeline on HPC with LSF. I'm using following command

nextflow run nf-core/oncoanalyser -profile singularity -revision dev --mode wgts --genome GRCh38_hmf --input samplesheet2.csv --outdir ./output2 -c nextflow.config

but I'm getting following error

Execution cancelled -- Finishing pending tasks before exit
-[nf-core/oncoanalyser] Pipeline completed with errors-
ERROR ~ Error executing process > 'NFCORE_ONCOANALYSER:WGTS:READ_ALIGNMENT_DNA:FASTP (1)'

Caused by:
  Path value cannot be null

I checked that all the fastq file in samplesheet exists. Did I miss anything else? Thanks!

Hi @Livana Z, I would think this is related to the input samplesheet - would you be able to post that and .nextflow.log from the above run?

Thanks for the response! Here is the .nextflow.log, samplesheet, and nextflow.config.

Thanks for the extra files @Livana Z. The problem is caused when using single FASTQ files as input - oncoanalyser currently expects non-interleaved paired-end reads in gziped FASTQ

Thank you! does the pipeline work with bam input aligned from single end reads?

I’ve spoken with the Hartwig team briefly and there seems to be reasonable support for single end reads. I’ve never run this library format myself but it’s probably worth attempting