modules/merquryfk_merquryfk

FastK based version of Merqury

Merquryreference-freeassembly evaluation

https://github.com/nf-core/modules/[...]/modules/nf-core/merquryfk/merquryfk

Description

FastK based version of Merqury

Input

name:type

description

pattern

`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`
`:file`

Histogram ktab files from the program FastK (option -t)

*.ktab*

`assembly`
`:file`

Genome (primary) assembly files (fasta format)

.fasta

`haplotigs`
`:file`

Assembly haplotigs (fasta format)

.fasta

`meta2`
`:map`

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

`mathaptab`
`:file`

trio maternal histogram ktab files from the program FastK (option -t)

*.ktab*

`meta3`
`:map`

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

`pathaptab`
`:file`

trio paternal histogram ktab files from the program FastK (option -t)

*.ktab*

Output

name:type

description

pattern

`stats`

`meta`
`:map`

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

`${prefix}.completeness.stats`
`:file`

Assembly statistics file

*.completeness.stats

`bed`

`meta`
`:map`

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

`${prefix}.*_only.bed`
`:file`

Assembly only kmer positions not supported by reads in bed format

*_only.bed

`assembly_qv`

`meta`
`:map`

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

`${prefix}.*.qv`
`:file`

error and qv table for each scaffold of the assembly

*.qv

`spectra_cn_fl`

`meta`
`:map`

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

`${prefix}.*.spectra-cn.fl.{png,pdf}`
`:file`

Unstacked copy number spectra filled plot in PNG or PDF format

*.spectra-cn.fl.{png,pdf}

`spectra_cn_ln`

`meta`
`:map`

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

`${prefix}.*.spectra-cn.ln.{png,pdf}`
`:file`

Unstacked copy number spectra line plot in PNG or PDF format

*.spectra-cn.ln.{png,pdf}

`spectra_cn_st`

`meta`
`:map`

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

`${prefix}.*.spectra-cn.st.{png,pdf}`
`:file`

Stacked copy number spectra line plot in PNG or PDF format

*.spectra-cn.st.{png,pdf}

`qv`

`meta`
`:map`

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

`${prefix}.qv`
`:file`

error and qv of each assembly as a whole

*.qv

`spectra_asm_fl`

`meta`
`:map`

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

`${prefix}.spectra-asm.fl.{png,pdf}`
`:file`

Unstacked assembly spectra filled plot in PNG or PDF format

*.spectra-asm.fl.{png,pdf}

`spectra_asm_ln`

`meta`
`:map`

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

`${prefix}.spectra-asm.ln.{png,pdf}`
`:file`

Unstacked assembly spectra line plot in PNG or PDF format

*.spectra-asm.ln.{png,pdf}

`spectra_asm_st`

`meta`
`:map`

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

`${prefix}.spectra-asm.st.{png,pdf}`
`:file`

Stacked assembly spectra line plot in PNG or PDF format

*.spectra-asm.st.{png,pdf}

`phased_block_bed`

`meta`
`:map`

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

`${prefix}.phased_block.bed`
`:file`

Assembly kmer positions separated by block in bed format

*.phased.block.bed

`phased_block_stats`

`meta`
`:map`

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

`${prefix}.phased_block.stats`
`:file`

phased assembly statistics file

*.phased.block.stats

`continuity_N`

`meta`
`:map`

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

`${prefix}.continuity.N.{pdf,png}`
`:file`

Stacked assembly N continuity plot in PNG or PDF format

*.continuity.N.{png,pdf}

`block_N`

`meta`
`:map`

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

`${prefix}.block.N.{pdf,png}`
`:file`

Stacked assembly N continuity by block plot in PNG or PDF format

*.block.N.{png,pdf}

`block_blob`

`meta`
`:map`

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

`${prefix}.block.blob.{pdf,png}`
`:file`

Stacked assembly block plot in PNG or PDF format

*.block.blob.{png,pdf}

`hapmers_blob`

`meta`
`:map`

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

`${prefix}.hapmers.blob.{pdf,png}`
`:file`

Stacked assembly hapmers block plot in PNG or PDF format

*.hapmers.blob.{png,pdf}

`versions`

`versions.yml`
`:file`

File containing software versions

versions.yml

Tools

merquryfk
https://github.com/thegenemyers/MERQURY.FK/blob/main/LICENSE

FastK based version of Merqury

github.com/thegenemyers/MERQURY.FK https://github.com/thegenemyers/MERQURY.FK

modules/merquryfk_merquryfk

Description

Input

meta:map

fastk_hist:file

fastk_ktab:file

assembly:file

haplotigs:file

meta2:map

mathaptab:file

meta3:map

pathaptab:file

Output

stats

meta:map

${prefix}.completeness.stats:file

bed

meta:map

${prefix}.*_only.bed:file

assembly_qv

meta:map

${prefix}.*.qv:file

spectra_cn_fl

meta:map

${prefix}.*.spectra-cn.fl.{png,pdf}:file

spectra_cn_ln

meta:map

${prefix}.*.spectra-cn.ln.{png,pdf}:file

spectra_cn_st

meta:map

${prefix}.*.spectra-cn.st.{png,pdf}:file

qv

meta:map

${prefix}.qv:file

spectra_asm_fl

meta:map

${prefix}.spectra-asm.fl.{png,pdf}:file

spectra_asm_ln

meta:map

${prefix}.spectra-asm.ln.{png,pdf}:file

spectra_asm_st

meta:map

${prefix}.spectra-asm.st.{png,pdf}:file

phased_block_bed

meta:map

${prefix}.phased_block.bed:file

phased_block_stats

meta:map

${prefix}.phased_block.stats:file

continuity_N

meta:map

${prefix}.continuity.N.{pdf,png}:file

block_N

meta:map

${prefix}.block.N.{pdf,png}:file

block_blob

meta:map

${prefix}.block.blob.{pdf,png}:file

hapmers_blob

meta:map

${prefix}.hapmers.blob.{pdf,png}:file

versions

versions.yml:file

Tools

merquryfk https://github.com/thegenemyers/MERQURY.FK/blob/main/LICENSE

maintainers

get in touch

`meta`
`:map`

`fastk_hist`
`:file`

`fastk_ktab`
`:file`

`assembly`
`:file`

`haplotigs`
`:file`

`meta2`
`:map`

`mathaptab`
`:file`

`meta3`
`:map`

`pathaptab`
`:file`

`stats`

`meta`
`:map`

`${prefix}.completeness.stats`
`:file`

`bed`

`meta`
`:map`

`${prefix}.*_only.bed`
`:file`

`assembly_qv`

`meta`
`:map`

`${prefix}.*.qv`
`:file`

`spectra_cn_fl`

`meta`
`:map`

`${prefix}.*.spectra-cn.fl.{png,pdf}`
`:file`

`spectra_cn_ln`

`meta`
`:map`

`${prefix}.*.spectra-cn.ln.{png,pdf}`
`:file`

`spectra_cn_st`

`meta`
`:map`

`${prefix}.*.spectra-cn.st.{png,pdf}`
`:file`

`qv`

`meta`
`:map`

`${prefix}.qv`
`:file`

`spectra_asm_fl`

`meta`
`:map`

`${prefix}.spectra-asm.fl.{png,pdf}`
`:file`

`spectra_asm_ln`

`meta`
`:map`

`${prefix}.spectra-asm.ln.{png,pdf}`
`:file`

`spectra_asm_st`

`meta`
`:map`

`${prefix}.spectra-asm.st.{png,pdf}`
`:file`

`phased_block_bed`

`meta`
`:map`

`${prefix}.phased_block.bed`
`:file`

`phased_block_stats`

`meta`
`:map`

`${prefix}.phased_block.stats`
`:file`

`continuity_N`

`meta`
`:map`

`${prefix}.continuity.N.{pdf,png}`
`:file`

`block_N`

`meta`
`:map`

`${prefix}.block.N.{pdf,png}`
`:file`

`block_blob`

`meta`
`:map`

`${prefix}.block.blob.{pdf,png}`
`:file`

`hapmers_blob`

`meta`
`:map`

`${prefix}.hapmers.blob.{pdf,png}`
`:file`

`versions`

`versions.yml`
`:file`

merquryfk
https://github.com/thegenemyers/MERQURY.FK/blob/main/LICENSE