An nf-core module for the OATK
meta:map
Groovy Map containing sample information e.g. [ id:‘Cladonia_norvegica’ ]
reads:file
HiFi reads in FASTA format
*.{fasta,fasta.gz,fa,fa.gz}
mito_hmm:file
mitochondria gene annotation HMM profile database
*.{fa,fam}
mito_hmm_h3f:file
mitochondria gene annotation HMM profile binary auxfile
*.{h3f}
mito_hmm_h3i:file
*.{h3i}
mito_hmm_h3m:file
*.{h3m}
mito_hmm_h3p:file
*.{h3p}
pltd_hmm:file
plastid gene annotation HMM profile database
pltd_hmm_h3f:file
plastid gene annotation HMM profile binary auxfile
pltd_hmm_h3i:file
pltd_hmm_h3m:file
pltd_hmm_h3p:file
mito_fasta
Groovy Map containing sample information e.g. [ id:‘test’, single_end
*mito.ctg.fasta:file
the structure-solved MT contigs
*mito.ctg.fasta
pltd_fasta
*pltd.ctg.fasta:file
the structure-solved PT contigs
*pltd.ctg.fasta
mito_bed
*mito.ctg.bed:file
the gene annotation for the MT sequences
*mito.ctg.bed
pltd_bed
*pltd.ctg.bed:file
the gene annotation for the PT sequences
*pltd.ctg.bed
mito_gfa
*mito.gfa:file
the subgraph for the MT genome
*mito.gfa
pltd_gfa
*pltd.gfa:file
the subgraph for the PT genome
*pltd.gfa
annot_mito_txt
*annot_mito.txt:file
the MT gene annotation file over all assembled sequences
*annot_mito.txt
annot_pltd_txt
*annot_pltd.txt:file
the PT gene annotation file over all assembled sequences
*annot_pltd.txt
clean_gfa
*utg.clean.gfa:file
the GFA file for the clean genome assembly
*utg.clean.gfa
final_gfa
*utg.final.gfa:file
the GFA file for the final genome assembly
*utg.final.gfa
initial_gfa
*utg.gfa:file
the GFA file for the initial genome assembly
*utg.gfa
multiplex_gfa
*utg.multiplex.gfa:file
the mutliplexed GFA file
*utg.multiplex.gfa
unzip_gfa
*utg.unzip.gfa:file
the unzipped GFA file
*utg.unzip.gfa
versions
versions.yml:file
File containing software versions
versions.yml
An organelle genome assembly toolkit
