ERROR nextflow.Nextflow - ERROR: No results report written!

[frahimov]

Description of the bug

The pipeline seems to fail at the last step, writing a report. But I cannot figure out from the log file what exactly goes wrong. The analysis was run on an HPC with SUSE OS. Thank you

Command used and terminal output

nextflow run pgscatalog/pgsc_calc -profile docker --input samplesheet.csv --target_build GRCh37 --min_overlap 0.0 --pgs_id PGS000754

Relevant files

nextflow.log

System information

HPC with SUSE OS

[smlmbrt]

By any chance do you have underscores or periods in your sampleset names in the samplesheet? I ran into that problem and pushed a check that will be in the next release. Until then (docs 1 2):

sampleset: A text string (no spaces, or reserved characters [ ‘.’ or ‘_’ ]) referring to the name of a target dataset of genotyping data containing at least one sample/individual (however cohort datasets will often contain many individuals with combined genotyped/imputed data).

[frahimov]

Yes. My sampleset names contained underscores. After removing the underscores the pipeline completed successfully. Somehow I missed the instruction to not include reserved characters in sampleset names. Thank you for your help. Much appreciated.