Missing output file(s) expected by process

The task ran, but nothing matched the output pattern it declared

why

The output: declaration is a promise about filenames. If the tool wrote a different name, wrote into a subdirectory, or wrote nothing because it failed quietly, the pattern matches nothing and the workflow stops here — even though the tool itself may have exited 0.

what to do

Go to the Work dir: and simply list it: what is actually there tells you immediately whether the name differs or nothing was produced. Also check .command.err — a tool that failed but exited 0 is common, and this is where it shows up.

Nextflow output declaration
This is one entry from BioErrors, a catalogue of bioinformatics error messages that point at the wrong thing. Every entry was traced to its real cause before it was written down.
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