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Co-authored-by: Copilot <copilot@github.com>
Co-authored-by: Copilot <copilot@github.com>
Co-authored-by: Copilot <copilot@github.com>
Co-authored-by: Copilot <copilot@github.com>
Co-authored-by: Copilot <copilot@github.com>
ochkalova
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Warning Newer version of the nf-core template is available. Your pipeline is using an old version of the nf-core template: 4.1.0. For more documentation on how to update your pipeline, please see the Synchronisation documentation. |
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This was referenced Aug 27, 2026
Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
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KateSakharova
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Oct 20, 2026
| id,fasta,fastq_1,fastq_2,coverage,run_accession,assembler,assembler_version,assembly_type | ||
| assembly_001,data/assembly_001.fasta.gz,data/assembly_001_R1.fastq.gz,data/assembly_001_R2.fastq.gz,,ERR011322,SPAdes,3.15.5,metagenome | ||
| assembly_002,data/assembly_002.fasta.gz,,,42.7,ERR011323,MEGAHIT,1.2.9,metatranscriptome | ||
| coassembly_001,data/coassembly_001.fasta.gz,data/run1_R1.fastq.gz;data/run2_R1.fastq.gz,data/run1_R2.fastq.gz;data/run2_R2.fastq.gz,,ERR011324;ERR011325,MEGAHIT,1.2.9, |
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is it possible to have PE and SE in co-assembly?
like
...,data/run1_R1.fastq.gz;data/run2_SE.fastq.gz,data/run1_R2.fastq.gz;,...
if yes - maybe add it as example. If not - we should think can we support it or not
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add those to Limitations
| @@ -0,0 +1,11 @@ | |||
| Runs,Coverage,Assembler,Version,Filepath | |||
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do you have example here pointing to one sample somewhere? if not - I think it might worth adding and check in test that no new sample created 🤔
- Move ERC000011 checklist and ENA Portal field lists to global constants - Validate secondary sample accessions with a regex - Report tax_id/scientific_name of all source samples in one error - Reword virtual sample description Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
| | `fastq_1` | Conditional | Path to single-end/paired-end forward reads in FASTQ format (optionally gzipped). Required if `coverage` is not provided. | | ||
| | `fastq_2` | No | Path to the second read file in FASTQ format for paired-end data used to generate the source metagenomic assembly. Leave empty for single-end reads. | | ||
| | `coverage` | Conditional | Estimated sequencing depth of the assembly. If this value is missing, it is computed automatically during pipeline execution when reads are provided. | | ||
| | `run_accession` | Yes | ENA run accession for the reads used to generate the metagenomic assembly. Reads must already be submitted to ENA. | |
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could you add a note about runs for co-assembly in here as well?
…ause name is defined by the tax_id
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Resolves #61
What this PR does
--mode metagenomic_assembliescan now submit co-assemblies: assemblies built from the reads of several runs.Bins and MAGs made from co-assemblies are not supported yet.
How to use it
A co-assembly is one row in the samplesheet. List all its runs in
run_accession, and their read files infastq_1/fastq_2, separated by;:Read files must be in the same order as the run accessions. If coverage is given in the samplesheet, read files can be left empty, as before.
Changes
Samplesheet
fastq_1,fastq_2andrun_accessionaccept semicolon-separated values.;-separated list exists, so"format": "file-path"and"exists": truewere removed fromfastq_1/fastq_2. Instead, the workflow now checks each read file withfile(..., checkIfExists: true), so missing files still fail early, before any process runs.run_accessionare removed.Coverage
coverm contig --methods mean length).calculateCoassemblyCoveragefunction turns the CoverM table into one number:docs/methods.md.Virtual sample for co-assemblies
ENA lets an assembly point to only one sample. The new
REGISTER_COASSEMBLY_SAMPLEmodule (bin/register_coassembly_sample.py) handles this:ERC000011) with acomposed ofattribute that lists the source samples. The assembly is then submitted against this sample.collection dateandcountryare kept if all source samples agree, otherwise they're set tonot provided. Countries not allowed byERC000011are also set tonot provided.--private): ENA is queried with your Webin credentials.--test_upload, the sample is registered on the ENA test server. A random suffix is added to its alias so repeated test runs don't clash.Other changes
CREATE_ASSEMBLY_METADATA_CSVwrites a list of run accessions in theRunscolumn for co-assemblies.Tests
test_assembly_coassembly_with_coverageandtest_assembly_coassembly_no_coverage. Their samplesheets are in nf-core/test-datasets.REGISTER_COASSEMBLY_SAMPLEmodule.calculateCoassemblyCoverage: one run, three runs, header only, missingLengthcolumn, zero depth.Docs
README.mdanddocs/usage.md: how to describe a co-assembly in the samplesheet, and how the virtual sample is made. Co-assemblies are removed from the list of unsupported features.docs/methods.md: the new coverage formula.PR checklist
nf-core pipelines lint).nextflow run . -profile test,docker --outdir <OUTDIR>).nextflow run . -profile debug,test,docker --outdir <OUTDIR>).docs/usage.mdis updated.docs/output.mdis updated.CHANGELOG.mdis updated.README.mdis updated (including new tool citations and authors/contributors).🤖 Generated with Claude Code