Pipeline finishes without running DeepVariant when fasta file named with .fa not .fasta - Githubissues

sanger-tol / variantcalling

This Nextflow DSL2 pipeline calls variants on long read alignment. It is run after sanger-tol/readmapping in the Sanger ToL production suite but with options to run on unaligned reads.

https://pipelines.tol.sanger.ac.uk/variantcalling

MIT License

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Pipeline finishes without running DeepVariant when fasta file named with .fa not .fasta #68

Closed gq1 closed 7 months ago

gq1 commented 8 months ago

Description of the bug

finish successfully but without DeepVariant subworkflow.

Problem at this line: https://github.com/sanger-tol/variantcalling/blob/15a147594240fbb545936b85f444b303989c7048/subworkflows/local/input_filter_split.nf#L57

Command used and terminal output

nextflow run sanger-tol/variantcalling -r 1.1.0 --input input_file_Tithorea_tarricina.csv --fasta /lustre/scratch125/tol/teams/meier/analysis/karin/ithomiini_clade/01_data/data_renamed/ilTitTari1.1.primary.fa -profile singularity,sanger --align

Relevant files

No response

System information

No response