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