Select sequences from a large file based on name/ID
meta{:bash}
:map
Groovy Map containing sample information e.g. [ id:‘test’, single_end:false ]
sequence{:bash}
:file
Fasta or fastq file containing sequences to be filtered
*.{fa,fna,faa,fasta,fq,fastq}[.gz]
pattern{:bash}
pattern file (one record per line). If no pattern is given, a string can be specified within the args using ‘-p pattern_string’
*.{txt,tsv}
filter{:bash}
*.{fa,fq,fa.gz,fq.gz}{:bash}
Fasta or fastq file containing the filtered sequences. Will be gzipped if the input file was gzipped.
versions_seqkit{:bash}
${task.process}{:bash}
:string
The name of the process
seqkit{:bash}
The name of the tool
seqkit version | sed "s/seqkit v//"{:bash}
:eval
The expression to obtain the version of the tool
versions{:bash}
Cross-platform and ultrafast toolkit for FASTA/Q file manipulation, written by Wei Shen.
