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KateSakharovaKateSakharova
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wip fixing tests
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‎.nf-core.yml‎

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- params.input
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files_unchanged:
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- .github/PULL_REQUEST_TEMPLATE.md
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- docs/images/nf-core-seqsubmit_logo_light.png
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- docs/images/nf-core-seqsubmit_logo_light_old.png
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- docs/images/nf-core-seqsubmit_logo_dark.png
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- assets/nf-core-seqsubmit_logo_light.png
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- assets/nf-core-seqsubmit_logo_light_old.png
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nf_core_version: 4.0.2
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repository_type: pipeline
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template:

‎README.md‎

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@@ -176,13 +176,13 @@ You can also control the privacy of your submitted data:
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- If you provide an existing study via `--submission_study`, your submission will inherit the same privacy status as that study.
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- If no study is provided, the pipeline will register a new one for you. To keep this new study private, you must specify a release date using `--hold_data_private YYYY-MM-DD` (up to 2 years from the current date).
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| Example | Source Data | Submission Visibility | Required Arguments | Result |
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| -------------------------------------------------------------------------------------------------------------------------------------------------------------------- | ----------- | --------------------- | -------------------------------------------------------- | ------------------------------------------------------- |
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| Assemblies generated from public reads. Assemblies should be public immediately after submission | public | public | – | SUCCESS |
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| Assemblies generated from public reads. Assemblies should remain private for 1 year after submission | public | private | `--hold_data_private today(YYYY-MM-DD)+1Y | SUCCESS |
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| Bins generated from private reads and assemblies. Bins should be public after submission. User **has access** to the reads and assemblies via Webin account | private | public | `--is_private` | SUCCESS |
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| 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`, `--hold_data_private YYYY-MM-DD` (+2 years) | SUCCESS |
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| 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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| Example | Source Data | Submission Visibility | Required Arguments | Result |
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| --------------------------------------------------------------------------------------------------------------------------------------------------------------------- | ----------- | --------------------- | ----------------------------------------------------------- | ----------------------------------------------------- |
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| Assemblies generated from public reads. Assemblies should be public immediately after submission | public | public | – | SUCCESS |
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| Assemblies generated from public reads. Assemblies should remain private for 1 year after submission | public | private | `--hold_data_private today(YYYY-MM-DD)+1Y | SUCCESS |
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| Bins generated from private reads and assemblies. Bins should be public after submission. User **has access** to the reads and assemblies via Webin account | private | public | `--is_private` | SUCCESS |
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| 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`, `--hold_data_private YYYY-MM-DD` (+2 years) | SUCCESS |
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| 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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‎assets/nf-core-seqsubmit_logo_light.png‎

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‎assets/nf-core-seqsubmit_logo_light_old.png‎

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‎assets/seqsubmit_logo.png‎

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‎main.nf‎

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@@ -61,7 +61,7 @@ workflow NFCORE_SEQSUBMIT {
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params.test_upload,
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params.webincli_mode,
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params.is_private,
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params.hold_data_private
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params.release_date ? channel.value(params.release_date): channel.value(false)
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)
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ch_multiqc_report = GENOMESUBMIT.out.multiqc_report
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} else if (params.mode == "metagenomic_assemblies") {
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params.test_upload,
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params.webincli_mode,
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params.is_private,
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params.hold_data_private
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params.release_date ? channel.value(params.release_date): channel.value(false)
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)
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ch_multiqc_report = ASSEMBLYSUBMIT.out.multiqc_report
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} else if (params.mode == "reads") {
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params.study_metadata,
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params.test_upload,
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params.webincli_mode,
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params.hold_data_private
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params.release_date ? channel.value(params.release_date): channel.value(false)
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)
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ch_multiqc_report = READSUBMIT.out.multiqc_report
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}

‎modules/local/count_rna/environment.yml‎

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- bioconda
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- defaults
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dependencies:
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- python=3.9
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- python=3.8.13

‎modules/local/create_reads_manifest/environment.yml‎

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---
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# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json
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channels:
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- conda-forge
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- bioconda
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dependencies:
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- "bioconda::mgnify-pipelines-toolkit=1.5.1"

‎modules/local/create_reads_manifest/meta.yml‎

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# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/meta-schema.json
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name: "create_reads_manifest"
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description: |
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Create a manifest file for submitting raw reads to ENA via webin-cli.
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Reads metadata (platform, instrument, library information) from the sample
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map and generates a manifest file for each sample.
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keywords:
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- ena
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- manifest
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- reads
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- submission
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- webin
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tools:
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- mgnify-pipelines-toolkit:
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description: |
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A toolkit of utilities used in MGnify metagenomics pipelines,
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including click, requests, and other dependencies required by
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the ENA submission scripts.
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homepage: https://github.com/EBI-Metagenomics/mgnify-pipelines-toolkit
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documentation: https://github.com/EBI-Metagenomics/mgnify-pipelines-toolkit
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tool_dev_url: https://github.com/EBI-Metagenomics/mgnify-pipelines-toolkit
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doi: ""
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licence: ["Apache-2.0"]
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identifier: null
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input:
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- - meta:
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type: map
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description: |
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Groovy Map containing sample information, including platform,
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instrument, library_source, library_selection, library_strategy,
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sample_accession, and optionally insert_size, library_name,
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description.
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e.g. `[ id:'sample1', platform:'ILLUMINA', instrument:'Illumina HiSeq 2500' ]`
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- fastq_files:
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type: file
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description: One or two FASTQ files (single-end or paired-end reads).
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pattern: "*.{fastq,fastq.gz,fq,fq.gz}"
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- - study_accession:
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type: value
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description: ENA study accession to submit reads to.
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output:
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- manifest:
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- meta:
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type: map
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description: |
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Groovy Map containing sample information.
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e.g. `[ id:'sample1' ]`
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- "*.manifest":
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type: file
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description: Manifest file required for reads submission with webin-cli.
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pattern: "*.manifest"
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authors:
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- "@ochkalova"
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- "@timrozday-mgnify"
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- "@KateSakharova"
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maintainers:
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- "@ochkalova"
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- "@timrozday-mgnify"
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- "@KateSakharova"

‎modules/local/generate_assembly_manifest/meta.yml‎

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- test_upload:
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type: value
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description: Whether generated manifests are going to be submitted in test mode.
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- is_private:
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type: value
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description: Referring to private data in ENA.
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output:
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- meta:

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