Library merge filename collision for a mixture of UDG treatments with several libraries per treatment

[alexandregilardet]

Check Documentation

I have checked the following places for the error:

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

Description of the bug

When processing a sample constituted of a mixture of different UDG treatments with several libraries per different UDG treatment, there is a file name collision at the additonal_library_merge step. It works fine if there's only one library per UDG treatment or only 1 treatment type has several libraries.

Steps to reproduce

Steps to reproduce the behaviour:

1. Command line: nextflow run nf-core/eager -r 2.3.3 -profile production,crick -params-file nf-post_externalSE.json -c /camp/lab/skoglundp/working/alexandre/bin/custom.config
2. See error: Error executing process > 'additional_library_merge (KGH6)'
   Caused by:
   Process additional_library_merge input file name collision -- There are multiple input files for each of the following file names: KGH6_libmerged_rg_rmdup.bam.bai, KGH6_libmerged_rg_rmdup.bam

(files were provided on Slack)

Expected behaviour

The libraries-merged BAMs should have different names eg. containing the UDG treatment it refers to.

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

Nextflow Installation

• Version: 20.07.1

Container engine

• Engine: Singularity
• version: 3.4.2
• Image tag: 2.3.3

[jfy133]

Solution is to insert UDG treatment at the first library merging step (as additional library merge happens after UDG-specific BAM trimming).