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}
mito_hmm{:bash}
mitochondria gene annotation HMM profile database
*.{fa,fam}
mito_hmm_h3f{:bash}
mitochondria gene annotation HMM profile binary auxfile
*.{h3f}
mito_hmm_h3i{:bash}
*.{h3i}
mito_hmm_h3m{:bash}
*.{h3m}
mito_hmm_h3p{:bash}
*.{h3p}
pltd_hmm{:bash}
plastid gene annotation HMM profile database
pltd_hmm_h3f{:bash}
plastid gene annotation HMM profile binary auxfile
pltd_hmm_h3i{:bash}
pltd_hmm_h3m{:bash}
pltd_hmm_h3p{:bash}
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
clean_gfa{:bash}
*utg.clean.gfa{:bash}
the GFA file for the clean genome assembly
*utg.clean.gfa
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
multiplex_gfa{:bash}
*utg.multiplex.gfa{:bash}
the mutliplexed GFA file
*utg.multiplex.gfa
unzip_gfa{:bash}
*utg.unzip.gfa{:bash}
the unzipped GFA file
*utg.unzip.gfa
versions{:bash}
versions.yml{:bash}
File containing software versions
versions.yml
An organelle genome assembly toolkit
