plotsr failed on memverge with the error "Path value cannot be null"

[SarahBailey1998]

Description of the bug

My memverge run of assemblyqc failed with the error "ERROR ~ Error executing process > 'PLANTFOODRESEARCHOPEN_ASSEMBLYQC:ASSEMBLYQC:FASTA_SYNTENY:PLOTSR (1)'
Caused by:
Path value cannot be null"
As far as we could tell all of the paths specified in the params file were correct so decided to exclude plotsr from the run as a temporary work around.
For more details see the aws-utilities repo.

Command used and terminal output

No response

Relevant files

No response

System information

No response

[GallVp]

This failure occurs because of a bug in the pipeline code where the Syri files are created in a different order and then fed to PLOTSR in the wrong order,

assemblyqc/subworkflows/local/fasta_synteny.nf

Line 347 in 0141925

def proposed_order = plotsr_assembly_order ? plotsr_assembly_order.tokenize(' ') : syri_tags.sort(false)

Here, syri_tags.sort(false) should be syri_tags.sort(false) { it.toUpperCase() } to match the order created for minimap2 alignment,

assemblyqc/subworkflows/local/fasta_synteny.nf

Line 276 in 0141925

return list.sort(false) { it[0].id.toUpperCase() }