seqkit_grep

Description¶

Select sequences from a large file based on name/ID

Keywords: filter, seqkit, subseq, grep

nf-core modules -g https://www.github.com/ebi-metagenomics/nf-modules install seqkit/grep

Cross-platform and ultrafast toolkit for FASTA/Q file manipulation, written by Wei Shen.

Name	Type	Description	Pattern
`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`	file	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}`

Name	Type	Description	Pattern
`filter`	file		-
`versions`	file		-

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