Open hoelzer opened 1 year ago
Currently the output directory looks like this when all hands-on and solutions commands are finished running:
2023-08-nanopore-workshop-example-bacteria 2023-08-nanopore-workshop-example-bacteria.zip bacteria bacteria-filtered.fastq eco-consensus-mapping.sam eco-consensus-racon.fasta eco-consensus-racon.fasta.fai eco-consensus-racon.fasta.map-ont.mmi eco-fastqc eco-filtered.fastq ecoli-annotation.gff ecoli-reference.fna eco-mapping-ref.sam eco-mapping-ref.sorted.bam eco-mapping-ref.sorted.bam.bai eco-mapping.sam eco-mapping.sorted.bam eco-mapping.sorted.bam.bai eco-medaka envs flye_output flye-output-bacteria flye-output-sal1 hands-on.sh ideel input-data nanoplot sal1-filtered.fastq
This is a bit of a mess. It would be nice to properly organize the data into e.g. separate folders per pathogen, with clear naming of the output files depending on what tools were used to generate them (this last part is already not too bad).
Currently the output directory looks like this when all hands-on and solutions commands are finished running:
This is a bit of a mess. It would be nice to properly organize the data into e.g. separate folders per pathogen, with clear naming of the output files depending on what tools were used to generate them (this last part is already not too bad).