Hi there!
On our nf-core/crisprseq pipeline tests’ are failing ever since a nextflow version change. It seems to be coming from the multiMap operator :
Channel.fromSamplesheet("input")
.multiMap { meta, fastq_1, fastq_2, reference, protospacer, template ->
// meta.condition is part of the screening workflow and we need to remove it
reads: [ meta.id, meta - meta.subMap('condition') + [ single_end:fastq_2?false:true, self_reference:reference?false:true, template:template?true:false ], fastq_2?[ fastq_1, fastq_2 ]:[ fastq_1 ] ]
reference: [meta - meta.subMap('condition') + [ single_end:fastq_2?false:true, self_reference:reference?false:true, template:template?true:false ], reference]
protospacer: [meta - meta.subMap('condition') + [ single_end:fastq_2?false:true, self_reference:reference?false:true, template:template?true:false ], protospacer]
template: [meta - meta.subMap('condition') + [ single_end:fastq_2?false:true, self_reference:reference?false:true, template:template?true:false ], template]
}
.set { ch_input }
as we use the operator in both workflows.
We now have this compilation error :
NXF_VER=24.01.0-edge nextflow run . -profile test_screening,docker --outdir ./results_screening
N E X T F L O W ~ version 24.01.0-edge
Launching `./main.nf` [sick_gates] DSL2 - revision: 23593e18ec
ERROR ~ Module compilation error
- file : /Users/laurencekuhlburger/Documents/crisprseq/crisprseq/./workflows/crisprseq_targeted.nf
- cause: Unexpected input: '{' @ line 133, column 29.
workflow CRISPRSEQ_TARGETED {
^
1 error
NOTE: If this is the beginning of a process or workflow, there may be a syntax error in the body, such as a missing or extra comma, for which a more specific error message could not be produced.
All tests are failing in our PRs such as here : Template update 2.12 by mirpedrol · Pull Request #115 · nf-core/crisprseq · GitHub
Thank you!
Laurence