FastK based version of Merqury
meta{:bash}
:map
Groovy Map containing sample information e.g. [ id:‘test’, single_end:false ]
fastk_hist{:bash}
:file
A histogram files from the program FastK
*.hist
fastk_ktab{:bash}
Histogram ktab files from the program FastK (option -t)
*.ktab*
assembly{:bash}
Genome (primary) assembly files (fasta format)
.fasta
haplotigs{:bash}
Assembly haplotigs (fasta format)
meta2{:bash}
Groovy Map containing maternal sample information e.g. [ id:‘test’, single_end:false ]
mathaptab{:bash}
trio maternal histogram ktab files from the program FastK (option -t)
meta3{:bash}
Groovy Map containing paternal sample information e.g. [ id:‘test’, single_end:false ]
pathaptab{:bash}
trio paternal histogram ktab files from the program FastK (option -t)
stats{:bash}
${prefix}.completeness.stats{:bash}
Assembly statistics file
*.completeness.stats
bed{:bash}
${prefix}.*_only.bed{:bash}
Assembly only kmer positions not supported by reads in bed format
*_only.bed
assembly_qv{:bash}
${prefix}.*.qv{:bash}
error and qv table for each scaffold of the assembly
*.qv
qv{:bash}
${prefix}.qv{:bash}
error and qv of each assembly as a whole
phased_block_bed{:bash}
${prefix}.phased_block.bed{:bash}
Assembly kmer positions separated by block in bed format
*.phased.block.bed
phased_block_stats{:bash}
${prefix}.phased_block.stats{:bash}
phased assembly statistics file
*.phased.block.stats
images{:bash}
*.{pdf,png}{:bash}
Output graphs from MerquryFK
*.{pdf,png}
versions_merquryfk{:bash}
${task.process}{:bash}
:string
Name of the process
merquryfk{:bash}
The name of the tool
1.2{:bash}
The expression to obtain the version of the tool
versions_fastk{:bash}
fastk{:bash}
Name of the tool
versions_r{:bash}
R{:bash}
R --version | sed "1!d; s/.*version //; s/ .*//"{:bash}
:eval
versions{:bash}
