Select sequences from a large file based on name/ID
meta
:map
Groovy Map containing sample information e.g. [ id:‘test’, single_end:false ]
sequence
:file
Fasta or fastq file containing sequences to be filtered
*.{fa,fna,faa,fasta,fq,fastq}[.gz]
pattern
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}
out_ext
:string
Output file extension. Leave empty to auto-detect from input (for example fa or fq)
fa
fq
filter
*.{fa,fq,fa.gz,fq.gz}
Fasta or fastq file containing the filtered sequences. Will be gzipped if the input file was gzipped.
versions_seqkit
${task.process}
The name of the process
seqkit
The name of the tool
seqkit version | sed "s/seqkit v//"
:eval
The expression to obtain the version of the tool
versions
Cross-platform and ultrafast toolkit for FASTA/Q file manipulation, written by Wei Shen.
