custom_countfastq

Count reads in a fastq file

nf-core modules \
  --git-remote https://github.com/CCBR/nf-modules \
  install custom/countfastq

https://github.com/CCBR/nf-modules/…/modules/CCBR/custom/countfastq/

Input

group	name	type	description	pattern
NA	meta	map	Groovy Map containing sample information
e.g. [ id:‘test’, single_end:false ]	NA
NA	fastq	file	fastq file	*.{fastq.gz}

Output

group	name	type	description	pattern
NA	meta	map	Groovy Map containing sample information
e.g. [ id:‘test’, single_end:false ]	NA
NA	count	file	Plain text file containing the number of reads in the fastq files	NA
NA	versions	file	File containing software versions	versions.yml

Tools

Biopython

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Python tools for computational molecular biology