Don't need to call fastqc twice

[swzCuroverse]

There seems to be an extra step calling fastqc twice. Fastqc is designed to both fastqcs, you don't have to call it twice.
(1)

quality_control_forward:
run: bio-cwl-tools/fastqc/fastqc_2.cwl
in:
reads_file: rna_reads_fruitfly_forward
out: [html_file]

quality_control_reverse:
run: bio-cwl-tools/fastqc/fastqc_2.cwl
in:
reads_file: rna_reads_fruitfly_reverse
out: [html_file]

https://github.com/common-workflow-library/bio-cwl-tools/blob/release/fastqc/fastqc_1.cwl -- would allow you to do both. Not sure why we are using fastqc_2? Perhaps it is documented. This would make the workflow much easier to understand.

[swzCuroverse]

I think when fastqc_2 was written, it limits which data can be put in for some reasons but I believe fastqc can still be run on an array of files - as shown in fastqc_1.