Add homopolish for nanopore-only assembly#229
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Daniel-VM
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Daniel-VM
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Good job, Check the review comments, please.
| task.ext.when == null || task.ext.when | ||
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| script: | ||
| def prefix = task.ext.prefix ?: "${meta.id}" |
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We can follow here nf-core structure to get both prefix and potential args:
def args = task.ext.args ?: ''
def prefix = task.ext.prefix ?: "${meta.id}"
Additionally, you'll need to add the $args variable to the Homoplasy bash run.
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I think I copied that from another module with something else, but I don´t think I'm using it.
I don´t know the nf-core structure for that. Do you think we need it?
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If args isnt used there is no need for the def args line imho.
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| process HOMOPOLISH { | |||
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We can follow nf-core convention here: modules/local//
Could you place the main.nf file (and its related files) within homopolish/homopolish/ folder? And also the module would need to be renamed to HOMOPLISH_HOMOPILISH.
| homopolish polish \ | ||
| -a $medaka_genome \ | ||
| -s $bacteria_sketch \ | ||
| -m $params.homopolish_model \ |
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It's okay, but to make the script easier to read, we can use params.homopolish_model as an input channel for this process.
| // Assembly polishing | ||
| polish_method = 'medaka' // Allowed: ['medaka', 'nanopolish'] | ||
| polish_method = 'medaka' // Allowed: ['medaka', 'nanopolish', 'medaka_homopolish'] | ||
| homopolish_bacteria_sketch_url = 'https://bioinfo.cs.ccu.edu.tw/bioinfo/downloads/Homopolish_Sketch/bacteria.msh.gz' |
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It would be great to allow users to define a local sketch database via CLI . Lets say: --homopolish_sketchdb_path ?.
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On second thought, we can replace homopolish_bacteria_sketch_url with homopolish_sketchdb_path. The Nextflow engine can distinguish between a local path and a URL—if a URL is provided, it will fetch it automatically.
| GUNZIP_HOMOPOLISH( ch_sketch ) | ||
| } else { | ||
| // MODULE: Download bacteria sketch | ||
| HOMOPOLISH_SKETCH_PREPARATION( |
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I think this process can be removed, since the Nextflow engine can download and stage a file automatically when a URL is provided via params.
d4straub
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d4straub
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I agree a little work could be done as @Daniel-VM suggested.
Are you up to that @Gilbaja ?
| homopolish polish \ | ||
| -a $medaka_genome \ | ||
| -s $bacteria_sketch \ | ||
| -m $params.homopolish_model \ |
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| homopolish polish \ | |
| -a $medaka_genome \ | |
| -s $bacteria_sketch \ | |
| -m $params.homopolish_model \ | |
| homopolish polish \\ | |
| -a $medaka_genome \\ | |
| -s $bacteria_sketch \\ | |
| -m $homopolish_model \\ |
double slashes to keep formatting in the .command.sh in the work folder.
also, -m $params.homopolish_model \ is bad practice, it should be solved with a val input
| input: | ||
| tuple val(meta), path(medaka_genome) | ||
| tuple val(meta_gunzip), path(bacteria_sketch) | ||
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| val homopolish_model | |
| -s $bacteria_sketch \ | ||
| -m $params.homopolish_model \ | ||
| -o . | ||
| cat <<-END_VERSIONS > versions.yml |
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| cat <<-END_VERSIONS > versions.yml | |
| cat <<-END_VERSIONS > versions.yml |
I like here an empty line for clarity
| GUNZIP_HOMOPOLISH ( HOMOPOLISH_SKETCH_PREPARATION.out.sketch ) | ||
| } | ||
| // MODULE: Homopolish, polishes MEDAKA assembly | ||
| HOMOPOLISH ( ch_assembly, GUNZIP_HOMOPOLISH.out.gunzip ) |
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| HOMOPOLISH ( ch_assembly, GUNZIP_HOMOPOLISH.out.gunzip ) | |
| HOMOPOLISH ( ch_assembly, GUNZIP_HOMOPOLISH.out.gunzip, params.homopolish_model ) |
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PR checklist
nf-core pipelines lint).nextflow run . -profile test,docker --outdir <OUTDIR>).nextflow run . -profile debug,test,docker --outdir <OUTDIR>).docs/usage.mdis updated.docs/output.mdis updated.CHANGELOG.mdis updated.README.mdis updated (including new tool citations and authors/contributors).Issue #66
Adds homopolish as a tool for polishing after polished by medaka.
Before executing homopolish it needs a bacteria sketch to be downloaded (3.3GB) and unzipped.
To do so, an additional module is created, and the workflow includes a condition for checking if it has been already downloaded in the output folder. It also includes a new parameter for forcing the download.
Test cmd
nextflow run . -profile test_long,conda --polish_method medaka_homopolish --outdir results
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