Missing output file(s) error when centroiding data

[plashmore]

Description of the bug

After centroiding first data file the workflow gives an error and stops, saying it can't find the centroided data file it just created.

It appears that changing line 48 in modules.config to be

ext.prefix = { " ${meta.id}.centroided " }

fixes the issue. The workflow appears to create a new centroided file with the original filename.mzML instead of filename.centroided.mzML which is what the workflow looks for in future steps

Command used and terminal output

No response

Relevant files

No response

System information

Nextflow version: 23.10.01
Metaboigniter version: 2.0.0
Hardware: Desktop
Executor: Local
Container Engine: Docker
OS: Linux (Fedora 39)

[plashmore]

the above fix broke later steps in the pipeline, the proper fix was to change lin 14 of openms_peakpickerhires.nf to be

tuple val(meta), path("output/*.mzML"), emit: mzml

instead of the original

tuple val(meta), path("output/*.centroided.mzML"), emit: mzml

this both fixes the error during centroiding as well as prevents errors further down the pipeline without any adjustments to the modules.config file

[PayamEmami]

Thanks for the report. Fixing now.

[PayamEmami]

It has now been resolved.