when file not found in DEEPCELL_MESMER test, the test is not run, so the issue isn't reported #76
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PR checklist
nf-core pipelines lint
).nextflow run . -profile test,docker --outdir <OUTDIR>
).nextflow run . -profile debug,test,docker --outdir <OUTDIR>
).I've changed to the tonsil file we usually use and new it's giving a new error, so looking into that as well.
So to be clear, there seem to be 2 issues.