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MultiQC skips assembly metadata table for co-assemblies (comma in quoted Runs field)

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Evaluación

Dificultad
3/5
Tiempo estimado
Medio día
Aptitud para principiantes
70/100
Tipo de issue
Error
Claridad
Bien especificado
Estado de actividad
Activo
Área
data

Línea de trabajo

Start with the CONCAT_METADATA output, assemblies_metadata.csv, where a co-assembly row has a quoted Runs field containing commas, and with assets/multiqc_config.yml, which configures the assembly_metadata custom content. Reproduce with tests/assembly_coassembly_with_coverage.nf.test and check multiqc.log for the column-count warning. Done when that warning is gone, the assembly_metadata files appear in the co-assembly snapshots, and the single-run tests still pass.

Escrito por el modelo de indexación a partir del texto del issue.

Descripción

bug
Description of the bug

Description

For co-assemblies, the "Assembly metadata" section is missing from the MultiQC report. multiqc_assembly_metadata.txt and the assembly_metadata.{png,svg,pdf} plots are not produced. Single-run assemblies are not affected.

Cause

assemblies_metadata.csv (from CONCAT_METADATA) stores multiple run accessions as one quoted CSV field:

Runs,Coverage,Assembler,Version,Filepath,Sample
"SRR3183850,SRR3183951",45.5,SPAdes,3.15,genome.fna.gz,ERS32616275

This is valid CSV. However, MultiQC custom content splits rows on every delimiter and ignores quoting. It reads 7 columns in the data row against 6 in the header, and drops the file:

[WARNING] Inconsistent number of columns found in assemblies_metadata.csv. Skipping..
[WARNING] Not able to parse custom data in assemblies_metadata.csv

To reproduce

nf-test test tests/assembly_coassembly_with_coverage.nf.test --profile +docker --verbose

Then check multiqc.log in the MULTIQC work dir. The current tests/assembly_coassembly_*.nf.test.snap snapshots were recorded with this bug, so they don't contain the assembly_metadata files.

Expected behaviour

The co-assembly metadata table appears in the MultiQC report, with all source runs listed in the Runs column.

Possible fix

Give MultiQC its own copy of the metadata without changing the CSV used for manifest generation. Either:

  • convert the MultiQC copy to TSV and set file_format: tsv for assembly_metadata in assets/multiqc_config.yml, or
  • join run accessions with ; in the MultiQC copy only.

After the fix, regenerate the co-assembly snapshots.

Command used and terminal output
Relevant files

No response

System information

No response

Lenguaje dominante
Nextflow
Estrellas
22
Forks
11
Merge medio
1 d 4 h
PR fusionados (30 d)
8

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