Initial release#72
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Co-authored-by: Sofia Ochkalova <61541445+ochkalova@users.noreply.github.com>
Feature/fix tests
add nf-core style module for assembly_manifest
* Create VALIDATE_ASSEMBLY * Pach fastavalidator * Pach fastavalidator test * add nf-core fastavalidator with an extra flag for metagenomes * update gitignore * fix spaces * linter fix * reuse file from nf-test dataset rather than local file * revert changes to nf-test config * linter fix * add secretes to env variables for GI * aaaaaaaaaaaa * (╯°□°)╯( ┻━┻) --------- Co-authored-by: Victoria Cepeda <vickycees@gmail.com>
* Module to register study for assembly uploads * Module to register study for assembly uploads * Module to register study for assembly uploads * Module to register study for assembly uploads * Module to register study for assembly uploads * Module to register study for assembly uploads * Module to register study for assembly uploads * apply linting * temporary disable failing test * update container --------- Co-authored-by: Sofia Ochkalova <61541445+ochkalova@users.noreply.github.com>
Important! Template update for nf-core/tools v3.5.1
Fix download action
fixes after review
| and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html). | ||
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| ## v1.0.0dev - [date] | ||
| ## v1.0.0 - [date] |
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dont forget to add date before release :D
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I just need to check nextflow_Schema.json but I have to run to a train now and don'tw ant to lose this review!
| }, | ||
| "assembly_software": { | ||
| "type": "string", | ||
| "description": "Tool name and version that was used to assemble data" |
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Do you have a preference for formatting of this on the ENA to reduce differences in : MEGAHIT, MEGAhit, megaHIT, megahit, MeGaHiT??
| }, | ||
| "binning_software": { | ||
| "type": "string", | ||
| "description": "Tool name and version that was used to bin data" |
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Do you have a preference for formatting of this on the ENA to reduce differences in : MEGAHIT, MEGAhit, megaHIT, megahit, MeGaHiT??
| SEQSUBMIT ( | ||
| samplesheet | ||
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| // Depending on the input type (mags/bins, metagenomic_assemblies, or reads), one or another workflow will be triggered |
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Not a blocker at this stage, but unless you have a very strong reason to, I would suggest resurrecting seqsubmit.nf and putting this logic there, and hav this main.nf just be an entry into that.
I expect you are going to have horrible template merges in the future because of this... so I won't block this release and it is ultimately up to you, but just wanted to give a warning
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| Make sure you update commands above with your authorised credentials. | ||
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| ## Input samplesheets |
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I think the ## input samplesheets section is rather redundant with usage.md maybe consider removing this and asking users t ogo and refer to the relevaqnt section there instead? This would make the README simpler and you don't have to maintain the same info twice
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Thanks for the suggestion, James!
I checked other nf-core pipelines and usually this section contains small example with links to usage doc.
I agree that our README is bigger than needed, so I decreased this section to only show examples.
Changes were made in #83
From the other side, in the PR above I added 2 new sections to README: lImitations and scalability, which maybe belong to other doc as well. What do you think?
| ```csv | ||
| sample,fastq_1,fastq_2 | ||
| CONTROL_REP1,AEG588A1_S1_L002_R1_001.fastq.gz,AEG588A1_S1_L002_R2_001.fastq.gz | ||
| ### Data privacy |
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This is again too detailed for README< I would move this to usage.md
| | Bins generated from private reads and assemblies. Bins should remain private for 2 years after submission. User **has access** via Webin account | private | private | `--is_private`, `--release_date YYYY-MM-DD` (+2 years) | SUCCESS | | ||
| | MAGs generated from private reads and assemblies. MAGs should be public after submission. User **does not have access** to the reads and assemblies via Webin account | private | public | – | ERROR (submission can only reference accessible data) | | ||
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| ### Database setup (`CheckM2` and `CAT_pack`) |
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This one is already quite slim and doesn't contain much infomation... I would keep it in here to highlight the need for additional DBs
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And last comment :)
OVerall looks very good and very clean! Main things overall are just a few inconsistencies and docs/interface suggeostions, but nothing that will delay the release majorly :)
| "type": "string", | ||
| "description": "CAT_pack database ID for download", | ||
| "help": "There are two options available: nr (default) NCBI non-redundant protein database and gtdb (Genome Taxonomy Database (GTDB) proteins). We use NCBI proteins because ENA supports only NCBI format of taxonomy for submission", | ||
| "fa_icon": "fas fa-users-cog", |
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If you use the schema builder, you should be able to press the cog at the end of the row of the parameter, and can specify a drop down list of valud options using a pipe separated list.
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Note if ENA only supports nr I would maybe just remove this parameter for now
| "default": null, | ||
| "description": "Type of upload", | ||
| "help_text": "Different types of data require specific upload steps. That mode controls what upload workflow to run depending on type of data (mags/bins/metagenomic_assemblies/reads)", | ||
| "enum": ["mags", "bins", "metagenomic_assemblies", "reads"] |
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OK you do know about this, then I would suggest remove the catpack ID option entirely if you can't change it
| "type": "boolean", | ||
| "description": "Use that flag if you are referring to private data in ENA", | ||
| "default": false, | ||
| "help": "This flag is used during metadata fetch steps. If you are referring to private data (project/reads/assembly) set to True. That flag does NOT regulate privacy of your submission data (check --release_date)" |
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| "help": "This flag is used during metadata fetch steps. If you are referring to private data (project/reads/assembly) set to True. That flag does NOT regulate privacy of your submission data (check --release_date)" | |
| "help": "This flag is used during metadata fetch steps. Specify if you are referring to private data (project/reads/assembly). That flag does NOT regulate privacy of your submission data (check --release_date)" |
I wouldn't say to 'set to true' as the default use of a boolean parameter is that by providing it is implicity true (as in you don't normally go --is_private=true you would just give --is_private
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nf-core/seqsubmit v1.0.0 — Initial Release
This is the first release of nf-core/seqsubmit, a Nextflow pipeline for submitting sequence data to the European Nucleotide Archive (ENA).
What it does:
The pipeline supports four submission modes via dedicated workflows:
Key features:
Workflows and modules