feat: surface customized parameters for sub programs

[j23414]

Description

Allow users to pass in their customized params for:

• parallel
• gcpp_params
• freebayes_params
• purge_dups_params
• busco_params

The following params influence mapping/alignment, not indexing

• minimap2_params
• pbmm2_params
• bwamem2_params

Programs that are referenced multiple times in the pipeline will be difficult to parameterize without breaking something. These programs include samtools, bcftools, pbcstat, calcuts, split_fa, get_seqs, gzip

Testing

Ideally run this on a dataset to make sure parameters are being passed properly. However, for now can simply test a stub

Assuming reviewer has nextflow installed:

nextflow -version

Can test by creating empty input files, and running remotely the "params" branch.

mkdir data 
cd data
touch pri.fa alt.fa mit.fa ill_R1.fastq.bz2 ill_R2.fastq.bz2 pac.subreads.bam
cd ..

nextflow run isugifNF/polishCLR -r params \
            --primary_assembly data/pri.fa \
            --alternate_assembly data/alt.fa \
            --mitochondrial_assembly data/mit.fa \
            --illumina_reads "data/ill_{R1,R2}.fastq.bz2" \
            --pacbio_reads data/pac.subreads.bam \
            --species "BugName" \
            --k "21" \
            --falcon_unzip true \
            --step 1 \
            -stub-run \
            -profile local