Rapid haploid variant calling
meta{:bash}
:map
Groovy Map containing sample information e.g. [ id:‘test’, single_end:false ]
reads{:bash}
: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{:bash}
Reference genome in FASTA format
*.{fasta,fna,fa}
tab{:bash}
${prefix}/${prefix}.tab{:bash}
A simple tab-separated summary of all the variants
*.tab
csv{:bash}
${prefix}/${prefix}.csv{:bash}
A comma-separated version of the .tab file
*.csv
html{:bash}
${prefix}/${prefix}.html{:bash}
A HTML version of the .tab file
*.html
vcf{:bash}
${prefix}/${prefix}.vcf{:bash}
The final annotated variants in VCF format
*.vcf
bed{:bash}
${prefix}/${prefix}.bed{:bash}
The variants in BED format
*.bed
gff{:bash}
${prefix}/${prefix}.gff{:bash}
The variants in GFF3 format
*.gff
bam{:bash}
${prefix}/${prefix}.bam{:bash}
The alignments in BAM format. Includes unmapped, multimapping reads. Excludes duplicates.
*.bam
bai{:bash}
${prefix}/${prefix}.bam.bai{:bash}
Index for the .bam file
*.bam.bai
log{:bash}
${prefix}/${prefix}.log{:bash}
A log file with the commands run and their outputs
*.log
aligned_fa{:bash}
${prefix}/${prefix}.aligned.fa{:bash}
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{:bash}
${prefix}/${prefix}.consensus.fa{:bash}
A version of the reference genome with all variants instantiated
*.consensus.fa
consensus_subs_fa{:bash}
${prefix}/${prefix}.consensus.subs.fa{:bash}
A version of the reference genome with only substitution variants instantiated
*.consensus.subs.fa
raw_vcf{:bash}
${prefix}/${prefix}.raw.vcf{:bash}
The unfiltered variant calls from Freebayes
*.raw.vcf
filt_vcf{:bash}
${prefix}/${prefix}.filt.vcf{:bash}
The filtered variant calls from Freebayes
*.filt.vcf
vcf_gz{:bash}
${prefix}/${prefix}.vcf.gz{:bash}
Compressed .vcf file via BGZIP
*.vcf.gz
vcf_csi{:bash}
${prefix}/${prefix}.vcf.gz.csi{:bash}
Index for the .vcf.gz via bcftools index
*.vcf.gz.csi
txt{:bash}
${prefix}/${prefix}.txt{:bash}
Tab-separated columnar list of statistics
*.txt
versions{:bash}
versions.yml{:bash}
File containing software versions
versions.yml
Rapid bacterial SNP calling and core genome alignments
