Pretty-print tbprofiler_full_report.json file when writing file

[dfornika]

Our tbprofiler_full_report.json files don't have any newlines or indentation. They're fairly large/complex documents so this makes it difficult for a person to visually read the files directly. They can be re-formatted with a text editor, but it would be simpler and more convenient to write the files in "pretty-printed" form (with newlines and indentation).

One way to do this is to just stream the file through python's json.tool module before writing to disk:

On this line:

tbprofiler-nf/modules/tbprofiler.nf

Line 87 in 3f8a41d

cp results/${sample_id}.results.json ${sample_id}_tbprofiler_full_report.json

We could instead do:

cat results/${sample_id}.results.json | python -m json.tool > ${sample_id}_tbprofiler_full_report.json

[dfornika]

This isn't necessary with newer versions of tbprofiler.