added fc_count_type parameter to biotype_qc command

[pcantalupo]

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[apeltzer]

Please also update CHANGELOG :-)

[apeltzer]

x-ref #440

[apeltzer]

Please update CHANGELOG.md in the FIXED section 👍

[ewels]

• params.fc_count_type needs to be initialised in nextflow.config
• If not set (eg. remains as default null) then we shouldn't include it in the command, as we will get -t null in the command

[pcantalupo]

* `params.fc_count_type` needs to be initialised in `nextflow.config`

* If not set (eg. remains as default `null`) then we shouldn't include it in the command, as we will get `-t null` in the command

Just checked...it is already set to a default value of 'exon': https://github.com/nf-core/rnaseq/blob/master/nextflow.config#L58

[ewels]

Ah I'm sorry - I only looked at the diff and assumed that you were adding a totally new parameter. Please ignore both of my comments then 👍

[apeltzer]

Thank you @pcantalupo - I'm merging this to the make-1-4-3-release branch now and will updatte it accordingly :-)