An nf-core module for the OATK
meta{:bash}
:map
Groovy Map containing sample information e.g. [ id:‘Cladonia_norvegica’ ]
reads{:bash}
:file
HiFi reads in FASTA format
*.{fasta,fasta.gz,fa,fa.gz}
meta2{:bash}
mito_hmm_files{:bash}
HMM profile for mitochondrial gene annotation, with corresponding .h3i, h3f, .h3p, .h3m files from hmmpress
*.{fam,h3i,h3f,h3p,h3m}
meta3{:bash}
pltd_hmm_files{:bash}
HMM profile for plastid gene annotation, with corresponding .h3i, h3f, .h3p, .h3m files from hmmpress
mito_fasta{:bash}
Groovy Map containing sample information e.g. [ id:‘test’, single_end:false ]
*mito.ctg.fasta{:bash}
the structure-solved MT contigs
*mito.ctg.fasta
pltd_fasta{:bash}
*pltd.ctg.fasta{:bash}
the structure-solved PT contigs
*pltd.ctg.fasta
mito_bed{:bash}
*mito.ctg.bed{:bash}
the gene annotation for the MT sequences
*mito.ctg.bed
pltd_bed{:bash}
*pltd.ctg.bed{:bash}
the gene annotation for the PT sequences
*pltd.ctg.bed
mito_gfa{:bash}
*mito.gfa{:bash}
the subgraph for the MT genome
*mito.gfa
pltd_gfa{:bash}
*pltd.gfa{:bash}
the subgraph for the PT genome
*pltd.gfa
annot_mito_txt{:bash}
*annot_mito.txt{:bash}
the MT gene annotation file over all assembled sequences
*annot_mito.txt
annot_pltd_txt{:bash}
*annot_pltd.txt{:bash}
the PT gene annotation file over all assembled sequences
*annot_pltd.txt
final_gfa{:bash}
*utg.final.gfa{:bash}
the GFA file for the final genome assembly
*utg.final.gfa
initial_gfa{:bash}
*utg.gfa{:bash}
the GFA file for the initial genome assembly
*utg.gfa
log{:bash}
*.log{:bash}
log file describing oatk run
*.log
versions_oatk{:bash}
${task.process}{:bash}
:string
The name of the process
oatk{:bash}
The name of the tool
oatk --version 2>&1{:bash}
:eval
The expression to obtain the version of the tool
versions{:bash}
An organelle genome assembly toolkit
