Add module for Circlator (all)#11013
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famosab
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famosab
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I realized that the any2fasta is actually in a separate PR (right??) can you use this PR to only add the cirlator one please?
| { assert snapshot( | ||
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| ).match() } |
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You can use
{ assert snapshot(sanitizeOutput(process.out)).match() }
to clean up the snapshot using nft-utils. It is used to clean process and workflow outputs by removing the numbered keys. This will create snapshots that are more easy to read by humans.
| { assert snapshot( | |
| process.out | |
| ).match() } | |
| { assert snapshot(sanitizeOutput(process.out)).match() } |
| { assert snapshot( | ||
| process.out | ||
| ).match() } |
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| { assert snapshot( | |
| process.out | |
| ).match() } | |
| { assert snapshot(sanitizeOutput(process.out)).match() } |
| { assert snapshot( | ||
| process.out | ||
| ).match() } |
There was a problem hiding this comment.
| { assert snapshot( | |
| process.out | |
| ).match() } | |
| { assert snapshot(sanitizeOutput(process.out)).match() } |
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You can run
nextflow lint -format -sort-declarations -spaces 4 -harshil-alignmenton this file to clean this up nicely.
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Please just remove the any2fasta files because that was done here: #10994 I'll review the other module directly :) |
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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.
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| output: | ||
| tuple val(meta), path("${prefix}"), emit: results | ||
| tuple val(meta), path("${prefix}/*.fasta"), emit: fasta |
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Can we move the output fasta out of that folder and emit just the fasta?
What are other outputs of this module?
| name: "circlator_all" | ||
| description: > | ||
| Runs the full Circlator pipeline to circularise genome assemblies from long reads. | ||
| Sequentially runs: mapreads, bam2reads, assemble, merge, clean, and fixstart. |
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Is there a possibility to have each of these modules separate? Because that seems like a hard to find failure if something goes wrong
Oh my gosh! I didn't realize that I hadn't switched brands! So sorry, yes I will. |
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PR checklist
Closes #11010
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.