Fix publish error when remote path contains double slash

[bentsherman]

GCP doesn't accept paths that contain a double slash. Apparently this has been the case for a while, but we didn't realize it because publish errors were being ignored by default. Until recently when we made publish errors fatal.

The root cause appears to be that FileHelper.toCanonicalPath() does not normalize the path when it is remote. You can verify using this test case:

// local
outdir = 'results/'
filename = "${outdir}/bco.json"

println "local complete: ${(filename as Path).complete()}"
println "local canonical: ${nextflow.file.FileHelper.toCanonicalPath(filename)}"

// remote
outdir = 'gs://bucket/results/'
filename = "${outdir}/bco.json"

println "remote complete:  ${(filename as Path).complete().toUriString()}"
println "remote canonical: ${nextflow.file.FileHelper.toCanonicalPath(filename).toUriString()}"

Output:

local complete: /home/bent/projects/sketches/results/bco.json
local canonical: /home/bent/projects/sketches/results/bco.json
remote complete:  gs://bucket/results/bco.json
remote canonical: gs://bucket/results//bco.json

This will fix the specific issue with PublishDir, but long-term we should probably review the various ways in which strings are converted to paths across the codebase (which there are several) and try to use a uniform approach. The approach I used in this PR seems to be the most common one and the most robust.

See also: nextflow-io/nf-prov#34

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[pditommaso]

It may be better to fix this at level of toCanonicalPath method

[pditommaso]

Closing in favour of #5114