Message for metagenomic screening not clear

[aidaanva]

Check Documentation

I have checked the following places for your error:

• nf-core website: troubleshooting
• nf-core/eager pipeline documentation
  - nf-core/eager FAQ/troubleshooting can be found here

Description of the bug

Steps to reproduce

Steps to reproduce the behaviour:

1. 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
2. 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

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• OS:
• Version

Nextflow Installation

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Additional context

[jfy133]

If we need to do another patch release for a major bug, I'll throw this in. Otherwise we will make sure that this is fixed in our DSL2 conversion