fix the collision between input and output filename for single read

[piplus2]

PR checklist

Closes #11302

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Now when single read input is passed to the process, the output filename gets a _filtered suffix so that there's no collision with the input filename.
No changes for paired reads.
Also now the test for single read checks that some seqs are actually filtered.

[vagkaratzas]

You can just override the ext.prefix on the pipeline's module.args instead.

[piplus2]

Yes, but that means the user is already aware of the collision. At the moment, there's no feedback so there's a chance of a silent bug.

[piplus2]

I've included the error message following https://nf-co.re/docs/specifications/components/modules/naming-conventions#command-file-output-naming