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Command line: nextflow run nf-core/eager -c /bla/bla/screening_.config -profile eva,archgen,big_data,hops_phiX -r 2.4.2 --input /bla/bla/input.tsv --outdir /bla/bla/output --run_metagenomic_screening + all other parameters for metagenomics screening
See error: Please provide your error message [nf-core/eager] error: metagenomic classification can only run on unmapped reads. Please supply --bam_unmapped_type 'fastq'. Supplied: --bam_unmapped_type 'discard'.
Expected behaviour
When --run_metagenomic_screening is given however no bam filtering has been turn on, the message is unclear and it only mentions to set up the --bam_unmapped_type to 'fastq'. It should also remind you to turn on --run_bam_filtering
Log files
Have you provided the following extra information/files:
The command used to run the pipeline
The .nextflow.log file
The exact error:
System
Hardware:
Executor:
OS:
Version
Nextflow Installation
Version:
Container engine
Engine:
version:
Image tag:
Additional context
The text was updated successfully, but these errors were encountered:
Check Documentation
I have checked the following places for your error:
- nf-core/eager FAQ/troubleshooting can be found here
Description of the bug
Steps to reproduce
Steps to reproduce the behaviour:
nextflow run nf-core/eager -c /bla/bla/screening_.config -profile eva,archgen,big_data,hops_phiX -r 2.4.2 --input /bla/bla/input.tsv --outdir /bla/bla/output --run_metagenomic_screening
+ all other parameters for metagenomics screening[nf-core/eager] error: metagenomic classification can only run on unmapped reads. Please supply --bam_unmapped_type 'fastq'. Supplied: --bam_unmapped_type 'discard'.
Expected behaviour
When --run_metagenomic_screening is given however no bam filtering has been turn on, the message is unclear and it only mentions to set up the --bam_unmapped_type to 'fastq'. It should also remind you to turn on --run_bam_filtering
Log files
Have you provided the following extra information/files:
.nextflow.log
fileSystem
Nextflow Installation
Container engine
Additional context
The text was updated successfully, but these errors were encountered: