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{: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}`
`:file`

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

*.ktab*

`assembly{:bash}`
`:file`

Genome (primary) assembly files (fasta format)

.fasta

`haplotigs{:bash}`
`:file`

Assembly haplotigs (fasta format)

.fasta

`meta2{:bash}`
`:map`

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

`mathaptab{:bash}`
`:file`

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

*.ktab*

`meta3{:bash}`
`:map`

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

`pathaptab{:bash}`
`:file`

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

*.ktab*

Output

name:type

description

pattern

`stats{:bash}`

`meta{:bash}`
`:map`

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

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

Assembly statistics file

*.completeness.stats

`bed{:bash}`

`meta{:bash}`
`:map`

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

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

Assembly only kmer positions not supported by reads in bed format

*_only.bed

`assembly_qv{:bash}`

`meta{:bash}`
`:map`

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

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

error and qv table for each scaffold of the assembly

*.qv

`spectra_cn_fl{:bash}`

`meta{:bash}`
`:map`

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

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

Unstacked copy number spectra filled plot in PNG or PDF format

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

`spectra_cn_ln{:bash}`

`meta{:bash}`
`:map`

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

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

Unstacked copy number spectra line plot in PNG or PDF format

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

`spectra_cn_st{:bash}`

`meta{:bash}`
`:map`

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

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

Stacked copy number spectra line plot in PNG or PDF format

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

`qv{:bash}`

`meta{:bash}`
`:map`

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

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

error and qv of each assembly as a whole

*.qv

`spectra_asm_fl{:bash}`

`meta{:bash}`
`:map`

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

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

Unstacked assembly spectra filled plot in PNG or PDF format

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

`spectra_asm_ln{:bash}`

`meta{:bash}`
`:map`

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

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

Unstacked assembly spectra line plot in PNG or PDF format

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

`spectra_asm_st{:bash}`

`meta{:bash}`
`:map`

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

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

Stacked assembly spectra line plot in PNG or PDF format

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

`phased_block_bed{:bash}`

`meta{:bash}`
`:map`

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

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

Assembly kmer positions separated by block in bed format

*.phased.block.bed

`phased_block_stats{:bash}`

`meta{:bash}`
`:map`

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

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

phased assembly statistics file

*.phased.block.stats

`continuity_N{:bash}`

`meta{:bash}`
`:map`

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

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

Stacked assembly N continuity plot in PNG or PDF format

*.continuity.N.{png,pdf}

`block_N{:bash}`

`meta{:bash}`
`:map`

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

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

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

*.block.N.{png,pdf}

`block_blob{:bash}`

`meta{:bash}`
`:map`

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

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

Stacked assembly block plot in PNG or PDF format

*.block.blob.{png,pdf}

`hapmers_blob{:bash}`

`meta{:bash}`
`:map`

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

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

Stacked assembly hapmers block plot in PNG or PDF format

*.hapmers.blob.{png,pdf}

`versions{:bash}`

`versions.yml{:bash}`
`: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{:bash}:map

fastk_hist{:bash}:file

fastk_ktab{:bash}:file

assembly{:bash}:file

haplotigs{:bash}:file

meta2{:bash}:map

mathaptab{:bash}:file

meta3{:bash}:map

pathaptab{:bash}:file

Output

stats{:bash}

meta{:bash}:map

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

bed{:bash}

meta{:bash}:map

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

assembly_qv{:bash}

meta{:bash}:map

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

spectra_cn_fl{:bash}

meta{:bash}:map

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

spectra_cn_ln{:bash}

meta{:bash}:map

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

spectra_cn_st{:bash}

meta{:bash}:map

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

qv{:bash}

meta{:bash}:map

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

spectra_asm_fl{:bash}

meta{:bash}:map

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

spectra_asm_ln{:bash}

meta{:bash}:map

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

spectra_asm_st{:bash}

meta{:bash}:map

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

phased_block_bed{:bash}

meta{:bash}:map

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

phased_block_stats{:bash}

meta{:bash}:map

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

continuity_N{:bash}

meta{:bash}:map

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

block_N{:bash}

meta{:bash}:map

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

block_blob{:bash}

meta{:bash}:map

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

hapmers_blob{:bash}

meta{:bash}:map

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

versions{:bash}

versions.yml{:bash}:file

Tools

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

maintainers

get in touch

`meta{:bash}`
`:map`

`fastk_hist{:bash}`
`:file`

`fastk_ktab{:bash}`
`:file`

`assembly{:bash}`
`:file`

`haplotigs{:bash}`
`:file`

`meta2{:bash}`
`:map`

`mathaptab{:bash}`
`:file`

`meta3{:bash}`
`:map`

`pathaptab{:bash}`
`:file`

`stats{:bash}`

`meta{:bash}`
`:map`

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

`bed{:bash}`

`meta{:bash}`
`:map`

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

`assembly_qv{:bash}`

`meta{:bash}`
`:map`

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

`spectra_cn_fl{:bash}`

`meta{:bash}`
`:map`

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

`spectra_cn_ln{:bash}`

`meta{:bash}`
`:map`

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

`spectra_cn_st{:bash}`

`meta{:bash}`
`:map`

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

`qv{:bash}`

`meta{:bash}`
`:map`

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

`spectra_asm_fl{:bash}`

`meta{:bash}`
`:map`

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

`spectra_asm_ln{:bash}`

`meta{:bash}`
`:map`

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

`spectra_asm_st{:bash}`

`meta{:bash}`
`:map`

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

`phased_block_bed{:bash}`

`meta{:bash}`
`:map`

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

`phased_block_stats{:bash}`

`meta{:bash}`
`:map`

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

`continuity_N{:bash}`

`meta{:bash}`
`:map`

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

`block_N{:bash}`

`meta{:bash}`
`:map`

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

`block_blob{:bash}`

`meta{:bash}`
`:map`

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

`hapmers_blob{:bash}`

`meta{:bash}`
`:map`

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

`versions{:bash}`

`versions.yml{:bash}`
`:file`

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