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)