Description

Rapid haploid variant calling

Input

name:type
description
pattern

meta:map

Groovy Map containing sample information e.g. [ id:‘test’, single_end

]

reads:file

List of input FastQ files of size 1 and 2 for single-end and paired-end data, respectively.

*.{fq,fastq,fq.gz,fastq.gz}

reference:file

Reference genome in FASTA format

*.{fasta,fna,fa}

Output

name:type
description
pattern

tab

meta:map

Groovy Map containing sample information e.g. [ id:‘test’, single_end

]

${prefix}/${prefix}.tab:file

A simple tab-separated summary of all the variants

*.tab

csv

meta:map

Groovy Map containing sample information e.g. [ id:‘test’, single_end

]

${prefix}/${prefix}.csv:file

A comma-separated version of the .tab file

*.csv

html

meta:map

Groovy Map containing sample information e.g. [ id:‘test’, single_end

]

${prefix}/${prefix}.html:file

A HTML version of the .tab file

*.html

vcf

meta:map

Groovy Map containing sample information e.g. [ id:‘test’, single_end

]

${prefix}/${prefix}.vcf:file

The final annotated variants in VCF format

*.vcf

bed

meta:map

Groovy Map containing sample information e.g. [ id:‘test’, single_end

]

${prefix}/${prefix}.bed:file

The variants in BED format

*.bed

gff

meta:map

Groovy Map containing sample information e.g. [ id:‘test’, single_end

]

${prefix}/${prefix}.gff:file

The variants in GFF3 format

*.gff

bam

meta:map

Groovy Map containing sample information e.g. [ id:‘test’, single_end

]

${prefix}/${prefix}.bam:file

The alignments in BAM format. Includes unmapped, multimapping reads. Excludes duplicates.

*.bam

bai

meta:map

Groovy Map containing sample information e.g. [ id:‘test’, single_end

]

${prefix}/${prefix}.bam.bai:file

Index for the .bam file

*.bam.bai

log

meta:map

Groovy Map containing sample information e.g. [ id:‘test’, single_end

]

${prefix}/${prefix}.log:file

A log file with the commands run and their outputs

*.log

aligned_fa

meta:map

Groovy Map containing sample information e.g. [ id:‘test’, single_end

]

${prefix}/${prefix}.aligned.fa:file

A version of the reference but with - at position with depth=0 and N for 0 < depth < —mincov (does not have variants)

*.aligned.fa

consensus_fa

meta:map

Groovy Map containing sample information e.g. [ id:‘test’, single_end

]

${prefix}/${prefix}.consensus.fa:file

A version of the reference genome with all variants instantiated

*.consensus.fa

consensus_subs_fa

meta:map

Groovy Map containing sample information e.g. [ id:‘test’, single_end

]

${prefix}/${prefix}.consensus.subs.fa:file

A version of the reference genome with only substitution variants instantiated

*.consensus.subs.fa

raw_vcf

meta:map

Groovy Map containing sample information e.g. [ id:‘test’, single_end

]

${prefix}/${prefix}.raw.vcf:file

The unfiltered variant calls from Freebayes

*.raw.vcf

filt_vcf

meta:map

Groovy Map containing sample information e.g. [ id:‘test’, single_end

]

${prefix}/${prefix}.filt.vcf:file

The filtered variant calls from Freebayes

*.filt.vcf

vcf_gz

meta:map

Groovy Map containing sample information e.g. [ id:‘test’, single_end

]

${prefix}/${prefix}.vcf.gz:file

Compressed .vcf file via BGZIP

*.vcf.gz

vcf_csi

meta:map

Groovy Map containing sample information e.g. [ id:‘test’, single_end

]

${prefix}/${prefix}.vcf.gz.csi:file

Index for the .vcf.gz via bcftools index

*.vcf.gz.csi

txt

meta:map

Groovy Map containing sample information e.g. [ id:‘test’, single_end

]

${prefix}/${prefix}.txt:file

Tab-separated columnar list of statistics

*.txt

versions

versions.yml:file

File containing software versions

versions.yml

Tools

snippy
GPL v2

Rapid bacterial SNP calling and core genome alignments