GTDBTK_SUMMARY: Not a valid path ...

[muniheart]

Description of the bug

[commit e728900 (tag: 2.5.1, origin/master)]
From output below it appears that process GTDBTK_SUMMARY is being passed the wrong channel as one of the inputs.

Command used and terminal output

nextflow run nf-core/mag -profile debug,singularity --input samplesheet.csv --max_memory 125.GB --max_cpus 32 --max_time 168h --skip_concoct -resume

Dec-04 19:59:37.833 [Actor Thread 76] DEBUG nextflow.processor.TaskProcessor - Handling unexpected condition for
  task: name=NFCORE_MAG:MAG:GTDBTK:GTDBTK_SUMMARY; work-dir=null
  error [nextflow.exception.ProcessUnrecoverableException]: Not a valid path value type: java.util.LinkedHashMap ([id:sample_063, group:0, single_end:false, assembler:MEGAHIT, binner:MaxBin2, domain:unclassified, refinement:unrefined])
Dec-04 19:59:37.948 [Actor Thread 76] ERROR nextflow.processor.TaskProcessor - Error executing process > 'NFCORE_MAG:MAG:GTDBTK:GTDBTK_SUMMARY'

Caused by:
  Not a valid path value type: java.util.LinkedHashMap ([id:sample_063, group:0, single_end:false, assembler:MEGAHIT, binner:MaxBin2, domain:unclassified, refinement:unrefined])

Relevant files

No response

System information

No response

[jfy133]

Thank you @muniheart for this and the previous issue.

I have seen them, but currently on parental leave and have some other issues so I'm quite slow in replying.

There is a PR open currently which I believe may address the issues and I'll try to get to asap

[muniheart]

Thanks @jfy133. I logged the 2 channels that are passed to GTDBTK_SUMMARY. In my case they have the same structure,
[ [ meta, file ], ... ]. The first channel is modified by '.map{it[1]}' to pull the paths and it seems the 2nd channel should be, too. It works in my case.

[Peter-Kille]

Thanks @jfy133. I logged the 2 channels that are passed to GTDBTK_SUMMARY. In my case they have the same structure, [ [ meta, file ], ... ]. The first channel is modified by '.map{it[1]}' to pull the paths and it seems the 2nd channel should be, too. It works in my case.

Just to clarify the fix that muniheart identified.
Under subworkflows/local/gtdbtk.nf
Line 88:
GTDBTK_CLASSIFYWF.out.summary.collect().ifEmpty([]),
replaced by:
GTDBTK_CLASSIFYWF.out.summary.map{it[1]}.collect().ifEmpty([]),

This fixed the issue for me.

[jfy133]

@maxibor has included this here:

mag/subworkflows/local/gtdbtk.nf

Line 88 in 3f3505a

GTDBTK_CLASSIFYWF.out.summary.map{it[1]}.collect().ifEmpty([]),

[jfy133]

Thanks everyone!