Hackathon: build_minimap2_ont index && build_minimap2_sr_index

@cedric.laczny Maybe you can confirm this. The two rules build_minimap2_ont index and build_minimap2_sr_index give the following outputs in a dry-run. I've numbered them for discussion purposes.

• Aren't [#1 (closed),#2 (closed)] and [#4 (closed),#5] the same, so we could get rid of the redundancy maybe?
• #6 (closed), I'm assuming is so we can map SRs to the LR-contigs. Should we get rid of these extraneous runs at some point?

build_minimap2_ont_index

1) rule build_minimap2_ont_index:
    input: dbs/igc/igc.fna
    output: dbs/igc/igc-ont.mmi
    log: dbs/igc/igc.minimap2_ont_index
    jobid: 205
    wildcards: prefix=dbs/igc/igc

        (date &&        minimap2 -x map-ont -d dbs/igc/igc-ont.mmi dbs/igc/igc.fna &&        date) 2> >(tee dbs/igc/igc.minimap2_ont_index.stderr) > >(tee dbs/igc/igc.minimap2_ont_index.stdout)

2) rule build_minimap2_ont_index:
    input: dbs/hg38/hg38.fna
    output: dbs/hg38/hg38-ont.mmi
    log: dbs/hg38/hg38.minimap2_ont_index
    jobid: 206
    wildcards: prefix=dbs/hg38/hg38

        (date &&        minimap2 -x map-ont -d dbs/hg38/hg38-ont.mmi dbs/hg38/hg38.fna &&        date) 2> >(tee dbs/hg38/hg38.minimap2_ont_index.stderr) > >(tee dbs/hg38/hg38.minimap2_ont_index.stdout)

3) rule build_minimap2_ont_index:
    input: results/assembly/flye/lr/merged/no_barcode/assembly.fna
    output: results/assembly/flye/lr/merged/no_barcode/assembly-ont.mmi
    log: results/assembly/flye/lr/merged/no_barcode/assembly.minimap2_ont_index
    jobid: 176
    wildcards: prefix=results/assembly/flye/lr/merged/no_barcode/assembly

        (date &&        minimap2 -x map-ont -d results/assembly/flye/lr/merged/no_barcode/assembly-ont.mmi results/assembly/flye/lr/merged/no_barcode/assembly.fna &&        date) 2> >(tee results/assembly/flye/lr/merged/no_barcode/assembly.minimap2_ont_index.stderr) > >(tee results/assembly/flye/lr/merged/no_barcode/assembly.minimap2_ont_index.stdout)

build_minimap2_sr_index

4) rule build_minimap2_sr_index:
    input: dbs/igc/igc.fna
    output: dbs/igc/igc-sr.mmi
    log: dbs/igc/igc.minimap2_sr_index
    jobid: 199
    wildcards: prefix=dbs/igc/igc

        (date &&        minimap2 -x sr -d dbs/igc/igc-sr.mmi dbs/igc/igc.fna &&        date) 2> >(tee dbs/igc/igc.minimap2_sr_index.stderr) > >(tee dbs/igc/igc.minimap2_sr_index.stdout)

5) rule build_minimap2_sr_index:
    input: dbs/igc/igc.fna
    output: dbs/igc/igc-sr.mmi
    log: dbs/igc/igc.minimap2_sr_index
    jobid: 199
    wildcards: prefix=dbs/igc/igc

        (date &&        minimap2 -x sr -d dbs/igc/igc-sr.mmi dbs/igc/igc.fna &&        date) 2> >(tee dbs/igc/igc.minimap2_sr_index.stderr) > >(tee dbs/igc/igc.minimap2_sr_index.stdout)

6) rule build_minimap2_sr_index:
    input: results/assembly/flye/lr/merged/no_barcode/assembly.fna
    output: results/assembly/flye/lr/merged/no_barcode/assembly-sr.mmi
    log: results/assembly/flye/lr/merged/no_barcode/assembly.minimap2_sr_index
    jobid: 195
    wildcards: prefix=results/assembly/flye/lr/merged/no_barcode/assembly

        (date &&        minimap2 -x sr -d results/assembly/flye/lr/merged/no_barcode/assembly-sr.mmi results/assembly/flye/lr/merged/no_barcode/assembly.fna &&        date) 2> >(tee results/assembly/flye/lr/merged/no_barcode/assembly.minimap2_sr_index.stderr) > >(tee results/assembly/flye/lr/merged/no_barcode/assembly.minimap2_sr_index.stdout)