cutadapt (#7)

* First commit, clone of cutadapt in htrnaseq + help.txt

* Add config

* Don't allow multiple: true when providing a FASTA file with adapters

* First version of script

* Updates and fixes - se/pe

* Add tests and fix --json argument

* Add software version

* Better consistency in using snake_case

* Update src/cutadapt/config.vsh.yaml

Co-authored-by: Robrecht Cannoodt <[email protected]>

* Update src/cutadapt/config.vsh.yaml

Co-authored-by: Robrecht Cannoodt <[email protected]>

* Update src/cutadapt/config.vsh.yaml

Co-authored-by: Robrecht Cannoodt <[email protected]>

* Specify --input and --input_r2 as separate arguments

* Avoid specifying default arg values

* Add more information to `--minimum_length` and `maximum_length`

* Add --cpus by means of $meta_cpus and set proper default

* Allow multiple for adapters/fasta and add test

* change multiple_sep to ';'

* add example

* simplify code with a helper function

* create directories in test

* use a different output extension if --fasta is provided

* decrease code duplication by separating optional outputs from paired/unpaired output arguments

* write custom tests for cutadapt

* fix _r2 arguments

* add debug flag as not to always print the cli command

* remove comment

* Update to Viash 0.9.0-RC4

* Ability to specify output globbing patterns

* Avoid the need for both output_dir and output

* Move fields from `info` to `links`

Co-authored-by: Robrecht Cannoodt <[email protected]>

* Move references back to the info field

* apologies, I proposed a wrong syntax

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Co-authored-by: Robrecht Cannoodt <[email protected]>