Subworkflow for organelles

ksenia-krasheninnikova commented 1 year ago

Implements assembling mito from raw reads and from assembly

PR checklist

[ ] This comment contains a description of changes (with reason).
[ ] If you've fixed a bug or added code that should be tested, add tests!
[ ] If you've added a new tool - have you followed the pipeline conventions in the contribution docs
[ ] If necessary, also make a PR on the sanger-tol/genomeassembly branch on the nf-core/test-datasets repository.
[ ] Make sure your code lints (nf-core lint).
[ ] Ensure the test suite passes (nextflow run . -profile test,docker --outdir <OUTDIR>).
[ ] Usage Documentation in docs/usage.md is updated.
[ ] Output Documentation in docs/output.md is updated.
[ ] CHANGELOG.md is updated.
[ ] README.md is updated (including new tool citations and authors/contributors).

github-actions[bot] commented 1 year ago

`nf-core lint` overall result: Passed :white_check_mark: :warning:

Posted for pipeline commit 10093d9

+| ✅ 131 tests passed       |+
#| ❔  18 tests were ignored |#
!| ❗  14 tests had warnings |!

### :heavy_exclamation_mark: Test warnings: * [files_exist](https://nf-co.re/tools-docs/lint_tests/files_exist.html) - File not found: `conf/igenomes.config` * [readme](https://nf-co.re/tools-docs/lint_tests/readme.html) - README contains the placeholder `zenodo.XXXXXXX`. 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For general topics, please point to (and add to) the main nf-core website._ * [pipeline_todos](https://nf-co.re/tools-docs/lint_tests/pipeline_todos.html) - TODO string in `genomeassembly.nf`: _Add all file path parameters for the pipeline to the list below_ * [system_exit](https://nf-co.re/tools-docs/lint_tests/system_exit.html) - `System.exit` in WorkflowSanger-tol-genomeassembly.groovy: _System.exit(1)_ [line 51] * [schema_description](https://nf-co.re/tools-docs/lint_tests/schema_description.html) - No description provided in schema for parameter: `timestamp` * [schema_description](https://nf-co.re/tools-docs/lint_tests/schema_description.html) - No description provided in schema for parameter: `hifiasm` * [schema_description](https://nf-co.re/tools-docs/lint_tests/schema_description.html) - No description provided in schema for parameter: `hifiasmhic` ### :grey_question: Tests ignored: * [files_exist](https://nf-co.re/tools-docs/lint_tests/files_exist.html) - File is ignored: `assets/nf-core-genomeassembly_logo_light.png` * [files_exist](https://nf-co.re/tools-docs/lint_tests/files_exist.html) - 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ksenia-krasheninnikova commented 10 months ago

Removed all redundant files from the emit section. I think it can be merged in now. Thanks @priyanka-surana

muffato commented 10 months ago

I find this emit section confusing and difficult to navigate. Could be just me since I am not familiar with MitoHifi. Looking for a more informed view @muffato since you are familiar with the tool.

I'm not that familiar with MitoHifi :) !

I can see you cleaned up the entire emit section. It simplifies things a lot ! For the record, I had some questions about that structure:

Could you make the MitoHifi module take a single input like this:
1. Define it as tuple val(meta), path(input) rather than the mutually-exclusive reads and contigs
2. Use $args $input in the MitoHifi command-line rather than ${run_type}
3. First check that $args does contain either -c or -r (one of them is mandatory)
Then, do you need this one subworkflow to choose between the assembly and read mode and duplicate the input and output channels ? Could you imagine having a single subworkflow that is agnostic of the mode (just one input channel and one et of output channels), and in the parent workflow you would import it twice: once as ORGANELLES_READS and once as ORGANELLES_ASM

ksenia-krasheninnikova commented 10 months ago

Could you make the MitoHifi module take a single input like this:

Define it as tuple val(meta), path(input) rather than the mutually-exclusive reads and contigs

Use $args $input in the MitoHifi command-line rather than ${run_type}

First check that $args does contain either -c or -r (one of them is mandatory)

Then, do you need this one subworkflow to choose between the assembly and read mode and duplicate the input and output channels ? Could you imagine having a single subworkflow that is agnostic of the mode (just one input channel and one et of output channels), and in the parent workflow you would import it twice: once as ORGANELLES_READS and once as ORGANELLES_ASM

Thank you @muffato for suggestions. I've updated the code, could you have a look if it's what you mean please? I had to put -r/-c into ext.args2 because the input file should follow the corresponding option immediately:

usage: MitoHiFi [-h] (-r <reads>.fasta | -c <contigs>.fasta) -f
                <relatedMito>.fasta -g <relatedMito>.gbk -t <THREADS> [-d]
                [-a {animal,plant,fungi}] [-p <PERC>] [-m <BLOOM FILTER>]
                [--max-read-len MAX_READ_LEN] [--mitos]
                [--circular-size CIRCULAR_SIZE]
                [--circular-offset CIRCULAR_OFFSET] [-winSize WINSIZE]
                [-covMap COVMAP] [-v] [-o <GENETIC CODE>]

The purpose of the original implementation of the organelles workflow was to separate the whole organelles logic into the separate workflow to lighten up the main workflow. My concern though is that the main workflow getting rather long. Is it a standard practice to keep it that way? It will become more readable when I add documentation.

ksenia-krasheninnikova commented 10 months ago

@muffato Merged it updated mitohifi module from nf-core. All the review items must have been addressed for now! PR ready for the final review. Thanks!

sanger-tol / genomeassembly