assembles bacterial plasmids
meta{:bash}
:map
Groovy Map containing sample information e.g. [ id:‘test’, single_end:false ]
scaffold{:bash}
:file
Fasta file containing scaffold
fasta{:bash}
FASTA reference file
*.{fasta,fa}
html{:bash}
${prefix}/*final_results.html{:bash}
html file with results rendered
*.{html}
tab{:bash}
${prefix}/*final_results.tab{:bash}
Results in a tabular file
*.{tab}
images{:bash}
${prefix}/images/{:bash}
:directory
Directory containing the images produced by plasmidid
images
logs{:bash}
${prefix}/logs/{:bash}
Directory containing the logs produced by plasmidid
logs
data{:bash}
${prefix}/data/{:bash}
Directory containing the data produced by plasmidid
data
database{:bash}
${prefix}/database/{:bash}
Directory containing the database produced by plasmidid
database
fasta_files{:bash}
${prefix}/fasta_files/{:bash}
Directory containing the fasta files produced by plasmidid
fasta_files
kmer{:bash}
${prefix}/kmer/{:bash}
Directory containing the kmer files produced by plasmidid
versions{:bash}
versions.yml{:bash}
File containing software versions
versions.yml
Pipeline for plasmid identification and reconstruction
