Updated cutadapt parameters

[vicasze]

Summary

I added a new parameter to be able to provide additional cutadapt arguments for the forward and/or reverse primer. This is needed for the ITS database preparation, because the presence of the primer needs to be set as "optional" according to their presence/absence on the DB. On the other hand, I remove this optional primer trimming in zamp run and zamp insilico, because the read data should always contain primers and be trimmed.

In zamp run, cutadapt is called directly on the rules file, and not as an script.

I added usage example to prepare a fungal ITS database.

Details

Additions

• 38ac9f7c18dec29e2fce5cfb7203d894b86795f2 Add parameter for additional cutadapt arguments for forward and reverse primers.
• af41bee8dd1903dc558cef0a9a0666bffcf15c17 Update docu with usage cases for zamp db

Changes

• 2e0dcc0b37367533abcbfbae46d799db6659986e cutadapt called from snakemake rules files; not as a script.

Fixes

• b0dd769f812c7b561f8d27446daf28da6df31508 Remove optional primer trimming in insilico and run module. Drop amplicon parameter.

[farchaab]

Can you add commit hashes and their description in the Details section ?

[vicasze]

@farchaab as suggested, cutadapt is called directly on the snakemake rules files, and not as an outside script. Tested on data/sra-samples.tsv