Kraken breaks with missing output if 0 sequences

alexandregilardet commented 2 years ago

Check Documentation

I have checked the following places for your error:

[x] nf-core website: troubleshooting
[x] nf-core/eager pipeline documentation
[x] nf-core/eager FAQ/troubleshooting can be found here

Description of the bug

When having eg. a negative control, Kraken will break because of a missing output since no sequences were found. No complexity filtering applied. The unmapped FASTQ is basically empty.

Steps to reproduce

Steps to reproduce the behaviour:

nextflow run nf-core/eager -r 2.3.3 -profile production,crick -params-file nf-params.json -c $alexandre/bin/custom.config

Missing output file(s) *.kraken.out expected by process `kraken ...

Loading database information... done. 0 sequences (0.00 Mbp) processed in 0.009s (0.0 Kseq/m, 0.00 Mbp/m). 0 sequences classified (-nan%) 0 sequences unclassified (-nan%)

Expected behaviour

Pipeline shouldn't break because of missing Kraken output.

Log files

Have you provided the following extra information/files:

[x] The command used to run the pipeline
[ ] The .nextflow.log file
[x] The exact error

System

Hardware: HPC
Executor: slurm
OS: macOS
Version

Nextflow Installation

Version: 20.07.1

Container engine

Engine: Singularity
version: 3.4.2
Image tag: 2.3.3

Additional context

jfy133 commented 2 years ago

@alexandregilardet could you try with -r kraken2-emptyfastq-fix and see if that works?

TODO: update docuemntation to say you may not always get kraken2 output

alexandregilardet commented 2 years ago

Tested and works, thanks! Sorry didn't spot that fix.

jfy133 commented 2 years ago

Will be in the next patch release :)

nf-core / eager