Small update, local test results

• Short read test looks good
• Long read running

I note that in both cases both FASTQCs/NANOPLOTs run - is that to be expected?

Code looks good! Testing again...

• ✅ nextflow run ../main.nf -profile test_hybrid,docker --outdir ./results --skip_shortread_qc --skip_longread_qc --ansi-log false --> no FILTERED fastqc/nonplot
• ✅ nextflow run ../main.nf -profile test_hybrid,docker --outdir ./results --skip_shortread_qc -ansi-log false --> no filtered FASTQC / yes filtered nonplot
• ✅ nextflow run ../main.nf -profile test_hybrid,docker --outdir ./results --skip_longread_qc -ansi-log false --> no Nanoplot / Yes filtered fastqcx
• ✅ nextflow run ../main.nf -profile test_hybrid,docker --outdir ./results -ansi-log false

(ffs really need to make proper nf-tests...)

• ✅ nextflow run ../main.nf -profile test,docker --outdir ./results -ansi-log false --> three trimmed
• ✅ nextflow run ../main.nf -profile test,docker --outdir ./results -ansi-log false --skip_shortread_qc --> no trimmed
• ✅ nextflow run ../main.nf -profile test_host_rm,docker --outdir ./results -ansi-log false --sk ip_shortread_qc --> DO run fastqc_trimmed because host removal
• ✅ nextflow run ../main.nf -profile test_longread,docker --outdir ./results -ansi-log false --s kip_longread_qc didn't run nanoplot raw at all (went striaght to assembly... maybe scheduling reasons... will see if will execute after assembly) --> it did
• ✅ nextflow run ../main.nf -profile test_longread,docker --outdir ./results -ansi-log false --> runs timmed
• nextflow run ../main.nf -profile test_longread,docker --outdir ./results -ansi-log false --skip_longread_qc --host_fasta --> run trimmed even if skip_qc, because host removal

We are good to go - thank you very much @erikrikarddaniel !