Data type in MQC report is always "Paired End" for TSV input, regardless of SeqType in TSV.

[TCLamnidis]

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

When TSV input is used, the parameter single_end is left as false. It seems that within MQC it is that parameter that is checked to report the "Data Type" in the "Workflow Summary" section, leading to mixed messages when TSV input is used on SE or mixed data.

Steps to reproduce

Steps to reproduce the behaviour:

1. Command line: nextflow run --input <any TSV with SE data>
2. See error: None. The pipeline does not fail, simply misreports a field in MQC.

Expected behaviour

For the "Data Type" field in the MQC report, it should ideally say "Single End" if a TSV of SE data is provided, and/or "Mixed/Unknown" if the TSV has a mix of PE and SE data.

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: HPC
• Executor: slurm
• OS: Linux Ubuntu
• Version 18.04.5

Nextflow Installation

• Version: 20.10.0

Container engine

• Engine: Singularity
• version: 3.5.1+124-g54a90cd63+dirty
• Image tag: nfcore-eager-2.3.{3,4}.img

Additional context

[jfy133]

Ooof... This is a tricky one... I'm not sure how we can get around this one unfortunately given its a Boolean parameter... Can look into it though.