Sylph profile command for taxonoming profiling
meta
:map
Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
[ id:'test', single_end:false ]
reads
:file
List of input FastQ/FASTA files of size 1 and 2 for single-end and paired-end data, respectively. They are automatically sketched to .sylsp/.syldb
*.{fasta,fastq,fna,fa,fq,fas,fasta.gz,fastq.gz,fna,fa.gz,fq,fas.gz}
database
Pre-sketched .syldb/.sylsp files. Raw single-end fastq/fasta are allowed and will be automatically sketched to .sylsp/.syldb.
*.{syldb,sylsp}
profile_out
Groovy Map containing sample information
*.tsv
Output file of species-level taxonomic profiling with abundances and ANIs.
*tsv
versions_sylph
${task.process}
:string
The process the versions were collected from
sylph
The tool name
sylph -V | sed "s/sylph //g"
:eval
The expression to obtain the version of the tool
versions
Sylph quickly enables querying of genomes against even low-coverage shotgun metagenomes to find nearest neighbour ANI.
