mirror of
https://github.com/MillironX/nf-core_modules.git
synced 2024-11-10 20:23:10 +00:00
1de4bd46b7
* Add merqury files * Remove md5sum for completeness stats file * update container and test output * Update modules/merqury/meta.yml Co-authored-by: Daniel Straub <42973691+d4straub@users.noreply.github.com> * Explicitly set thread usage for meryl * Remove empty file md5sum Co-authored-by: Daniel Straub <42973691+d4straub@users.noreply.github.com>
101 lines
3 KiB
YAML
101 lines
3 KiB
YAML
name: "merqury"
|
|
description: k-mer based assembly evaluation.
|
|
keywords:
|
|
- "k-mer"
|
|
- "assembly"
|
|
- "evaluation"
|
|
tools:
|
|
- "merqury":
|
|
description: "Evaluate genome assemblies with k-mers and more."
|
|
homepage: "None"
|
|
documentation: "None"
|
|
tool_dev_url: "https://github.com/marbl/merqury"
|
|
doi: "10.1186/s13059-020-02134-9"
|
|
licence: "['PUBLIC DOMAIN']"
|
|
|
|
input:
|
|
- meta:
|
|
type: map
|
|
description: |
|
|
Groovy Map containing sample information
|
|
e.g. [ id:'test', single_end:false ]
|
|
- meryl_db:
|
|
type: file
|
|
description: "Meryl read database"
|
|
- assembly:
|
|
type: file
|
|
description: FASTA assembly file
|
|
|
|
output:
|
|
- meta:
|
|
type: map
|
|
description: |
|
|
Groovy Map containing sample information
|
|
e.g. [ id:'test', single_end:false ]
|
|
- versions:
|
|
type: file
|
|
description: File containing software versions
|
|
pattern: "versions.yml"
|
|
- assembly_only_kmers_bed:
|
|
type: file
|
|
description: "The positions of the k-mers found only in an assembly for further investigation in .bed"
|
|
pattern: "*_only.bed"
|
|
- assembly_only_kmers_wig:
|
|
type: file
|
|
description: "The positions of the k-mers found only in an assembly for further investigation in .wig"
|
|
pattern: "*_only.wig"
|
|
- stats:
|
|
type: file
|
|
description: Assembly statistics file
|
|
pattern: "*.completeness.stats"
|
|
- dist_hist:
|
|
type: file
|
|
description: Histogram
|
|
pattern: "*.dist_only.hist"
|
|
- spectra_cn_fl_png:
|
|
type: file
|
|
description: "Unstacked copy number spectra filled plot in PNG format"
|
|
pattern: "*.spectra-cn.fl.png"
|
|
- spectra_cn_ln_png:
|
|
type: file
|
|
description: "Unstacked copy number spectra line plot in PNG format"
|
|
pattern: "*.spectra-cn.ln.png"
|
|
- spectra_cn_st_png:
|
|
type: file
|
|
description: "Stacked copy number spectra line plot in PNG format"
|
|
pattern: "*.spectra-cn.st.png"
|
|
- spectra_cn_hist:
|
|
type: file
|
|
description: "Copy number spectra histogram"
|
|
pattern: "*.spectra-cn.hist"
|
|
- spectra_asm_fl_png:
|
|
type: file
|
|
description: "Unstacked assembly spectra filled plot in PNG format"
|
|
pattern: "*.spectra-asm.fl.png"
|
|
- spectra_asm_ln_png:
|
|
type: file
|
|
description: "Unstacked assembly spectra line plot in PNG format"
|
|
pattern: "*.spectra-asm.ln.png"
|
|
- spectra_asm_st_png:
|
|
type: file
|
|
description: "Stacked assembly spectra line plot in PNG format"
|
|
pattern: "*.spectra-asm.st.png"
|
|
- spectra_asm_hist:
|
|
type: file
|
|
description: "Assembly spectra histogram"
|
|
pattern: "*.spectra-asm.hist"
|
|
- assembly_qv:
|
|
type: file
|
|
description: "Assembly consensus quality estimation"
|
|
pattern: "*.qv"
|
|
- scaffold_qv:
|
|
type: file
|
|
description: "Scaffold consensus quality estimation"
|
|
pattern: "*.qv"
|
|
- read_ploidy:
|
|
type: file
|
|
description: "Ploidy estimate from read k-mer database"
|
|
pattern: "*.hist.ploidy"
|
|
|
|
authors:
|
|
- "@mahesh-panchal"
|