minimap2_align

Description¶

A versatile pairwise aligner for genomic and spliced nucleotide sequences

This module is used by the following pipelines:

nf-core modules -g https://www.github.com/ebi-metagenomics/nf-modules install minimap2/align

A versatile pairwise aligner for genomic and spliced nucleotide sequences.

Name	Type	Description	Pattern
`meta`	map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]	-
`reads`	file	List of input FASTA or FASTQ files of size 1 and 2 for single-end and paired-end data, respectively.	-
`meta2`	map	Groovy Map containing reference information e.g. [ id:'test_ref']	-
`reference`	file	Reference database in FASTA format.	-
`bam_format`	boolean	Specify that output should be in BAM format	-
`bam_index_extension`	string	BAM alignment index extension (e.g. "bai")	-
`cigar_paf_format`	boolean	Specify that output CIGAR should be in PAF format	-
`cigar_bam`	boolean	Write CIGAR with >65535 ops at the CG tag. This is recommended when doing XYZ (https://github.com/lh3/minimap2#working-with-65535-cigar-operations)	-

Name	Type	Pattern
`paf`	file	-
`bam`	file	-
`index`	file	-
`versions`	file	-