Generalizable split

[j23414]

Description

Concatenate and split a combination of fasta files

Different steps of the pipeline requires concatenating and separating a combination of fasta files:

• --primary_assembly -> and add a header prefix with pri
• --alternative_assembly -> and add a header prefix with alt
• --mitochondrial_assembly -> and add a header prefix with mit

Originally we had specialized merge and split processes to deal with Case 1, 2, or 3 depending on if some or all of the above input files were provided. To clean up the code base, created generalized and reusable functions:

• PREFIX_FASTA
• CONCATINATE_FASTAS
• SPLIT_FASTAS

Setting the publish directories

Other changes include moving

process taskname {
  publishDir "params.outdir/subdirectoryname"
  ...
}

into a separate configs/publishdir.config file, so that it is easier to restructure the final output folders.

Other changes

Put parameter variables in the help statement "[default $params.variablename]" to avoid a situation such that the help statement becomes out of sync with the actual default values.

Testing

• [x] Test with PGOS or test data

[Sivanandan]

This passed on PGOS, so merged it.