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I added a few comments to this updated PR :) looks good already
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You can run
nextflow lint -format -sort-declarations -spaces 4 -harshil-alignmenton this file to clean this up nicely.
| tuple val(meta), path(assembly) | ||
| tuple val(meta2), path(reads) |
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Can we put all these inputs into one tuple? That will make sure you're sure that EVERY time everything comes together in the right combination.
Not 100% sure on this but if these things should match per sample I would do one input but if for example the reads stay consistent and only the assembly changes we can leave it as is :)
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| output: | ||
| tuple val(meta), path("${prefix}"), emit: results | ||
| tuple val(meta), path("${prefix}/*.fasta"), emit: fasta |
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I would copy the fasta files into the base dir with
mv ${prefix}/*.fasta *.fasta
and emit them directly that makes downstream easier I think
| prefix = task.ext.prefix ?: "${meta.id}" | ||
| """ | ||
| mkdir -p ${prefix} | ||
| touch ${prefix}/06.fixstart.fasta |
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how many fasta files are actually being created?
| tag "circlator" | ||
| tag "circlator/all" | ||
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| test("sarscov2 - fasta reads - stub") { |
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Why do we only have the stub test here? :)
Has that been reported to the developers? |
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General remark on this PR: I would rather / also have the singular steps of this "pipeline" which would make this more compatible with all the Nextflow capabilities (I think) |
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PR checklist
Closes #11010 #11010
Fixed/Updated PR from #11013
topic: versions- See version_topicslabelnf-core modules test <MODULE> --profile dockernf-core modules test <MODULE> --profile singularitynf-core modules test <MODULE> --profile condaDescription
Adds a new module for circlator all, which runs the full Circlator pipeline to circularise genome assemblies from long reads (PacBio/Oxford Nanopore). The module takes an input assembly (FASTA) and long reads (FASTA/FASTQ) and outputs a circularised assembly. A stub test is used as the tool requires substantial real long-read data to run successfully.
Note
Singularity not available on local dev machine. Conda test fails due to a known libcrypto incompatibility with the circlator 1.5.5 conda package on modern systems — this is an upstream issue. Docker test passes successfully.
Also, my previous PR I made for this I accidentally committed any2fasta commits. I created this clean PR to fix it.