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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.
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
The text was updated successfully, but these errors were encountered:
Check Documentation
I have checked the following places for the error:
- 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:
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
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:
.nextflow.log
fileSystem
Nextflow Installation
Container engine
The text was updated successfully, but these errors were encountered: