Nextflow Registry | nf-core/nanocomp@0.0.0-6c4ed3a

nf-core/nanocomp @ 0.0.0-6c4ed3a

Compare multiple runs of long read sequencing data and alignments

bam fasta fastq qc nanopore

Latest version: 0.0.0-6c4ed3a

Total downloads: 11

Source: nf-core/modules

Authors: @paulwolk

Maintainers: @paulwolk

Compare multiple runs of long read sequencing data and alignments

Add the following snippet to your workflow script to include this module.

include { NANOCOMP } from 'nf-core/nanocomp'

MIT License

Process

`Name`	`NANOCOMP`

Input 1 channel

#1 tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test', single_end:false]
`filelist` file	List of all the files you want to compare, they have to be all the same filetype (either fastq, fasta, bam or Nanopore sequencing summary) `*.{fastq,fq,fna,ffn,faa,frn,fa,fasta,txt,bam}`

Output 19 channels

#1 n50_html tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test', single_end:false]
`*NanoComp_N50.html` file	Bar plot of N50 sequence length per sample `*NanoComp_N50.html`

#2 versions

`versions.yml` file	File containing software versions `versions.yml`

#3 stats_txt tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test', single_end:false]
`*NanoStats.txt` file	txt file with basic statistics `*NanoStats.txt`

#4 report_html tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test', single_end:false]
`*NanoComp-report.html` file	Summary of all collected statistics `*NanoComp-report.html`

#5 quals_violin_html tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test', single_end:false]
`*NanoComp_quals_violin.html` file	Violin plot of base qualities, only for bam, fastq and sequencing summary input `*NanoComp_quals_violin.html`

#6 lengths_violin_html tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test', single_end:false]
`*NanoComp_lengths_violin.html` file	Violin plot of the sequence lengths `*NanoComp_lengths_violin.html`

#7 number_of_reads_html tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test', single_end:false]
`*NanoComp_number_of_reads.html` file	Bar plot of number of reads per sample `*NanoComp_number_of_reads.html`

#8 total_throughput_html tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test', single_end:false]
`*NanoComp_total_throughput.html` file	Barplot comparing throughput in bases `*NanoComp_total_throughput.html`

#9 log_length_violin_html tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test', single_end:false]
`*NanoComp_log_length_violin.html` file	Violin plot of the sequence lengths, log function applied `*NanoComp_log_length_violin.html`

#10 overlay_histogram_html tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test', single_end:false]
`*NanoComp_OverlayHistogram.html` file	Histogram of all read lengths per sample `*NanoComp_OverlayHistogram.html`

#11 overlay_log_histogram_html tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test', single_end:false]
`*NanoComp_OverlayLogHistogram.html` file	Histogram of all read lengths per sample, log function applied `*NanoComp_OverlayLogHistogram.html`

#12 active_pores_over_time_html tuple

`meta`