Fix kraken db loading fromPath

[maxibor]

Kraken database loading fixed to fromPath method for channel creation

PR checklist

• This comment contains a description of changes (with reason).
• Make sure your code lints (nf-core lint .).
• Ensure the test suite passes (nextflow run . -profile test,docker).
• CHANGELOG.md is updated.

[jfy133]

CI fail :(

Error executing process > 'decomp_kraken'
Caused by:
  Process `decomp_kraken` terminated with an error exit status (1)
Command executed:
  tar xvzf eager_test.tar.gz
  mkdir -p eager_test
  mv *.k2d eager_test
Command exit status:
  1
Command output:
  eager_test/
  eager_test/opts.k2d
  eager_test/seqid2taxid.map
  eager_test/taxo.k2d
  eager_test/hash.k2d
Command error:
  mv: cannot stat '*.k2d': No such file or directory

[jfy133]

See comment above about CI fail

[apeltzer]

Guessing from the conversation still some fixes required no ?

[jfy133]

This in principle to me now looks good. CI tests do pass (the one fail is the flakiness on the BAM filtering thing).

@maxibor please decide if you want to change fromPath to file() (see Harshil's comment), and then proceed with merging!

[maxibor]

As I can't see file() anywhere in the doc for channel creation, I think for my future self, it's better to keep fromPath() to understand what I did

[jfy133]

As I can't see file() anywhere in the doc for channel creation, I think for my future self, it's better to keep fromPath() to understand what I did

Feel free to merge! <- SCRAP THAT!

See Slack - only one sample was run, needs a .collect() somewhere

[apeltzer]

Yeah add either file() or an additional collect() in the respective process to get past this 👍🏻

[maxibor]

Went with .first() 😉
It has the same effect: transforms a queue channel to a value channel (There is anyway only a single item in this channel, the kraken db directory)

[apeltzer]

See slack - solves the issue 👍🏻