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Fix misleading error message and documentation #748

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Jun 17, 2024
Merged

Fix misleading error message and documentation #748

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0db031a
fix docu and misleading error message
d4straub Jun 17, 2024
9d26084
fix linting
d4straub Jun 17, 2024
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1 change: 1 addition & 0 deletions CHANGELOG.md
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Expand Up @@ -12,6 +12,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
### `Fixed`

- [#747](https://github.com/nf-core/ampliseq/pull/747) - Template update for nf-core/tools version 2.14.1
- [#748](https://github.com/nf-core/ampliseq/pull/748) - Updating misleading error message and documentation

### `Dependencies`

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6 changes: 2 additions & 4 deletions docs/output.md
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Expand Up @@ -455,11 +455,9 @@ Absolute abundance tables produced by the previous steps contain count data, but
<summary>Output files</summary>

- `qiime2/rel_abundance_tables/`
- `rel-table-*.tsv`: Tab-separated absolute abundance table at taxa level `*`, where `*` ranges by default from 2 to 6, specified by the `--tax_agglom_min` and `--tax_agglom_max` parameters.
- `rel-table-*.tsv`: Tab-separated relative abundance table at taxa level `*`, where `*` ranges by default from 2 to 6, specified by the `--tax_agglom_min` and `--tax_agglom_max` parameters.
- `rel-table-ASV.tsv`: Tab-separated relative abundance table for all ASVs.
- `rel-table-ASV_with-DADA2-tax.tsv`: Tab-separated table for all ASVs with DADA2 taxonomic classification, sequence and relative abundance.
- `rel-table-ASV_with-QIIME2-tax.tsv`: Tab-separated table for all ASVs with QIIME2 taxonomic classification, sequence and relative abundance.
- `rel-table-ASV_with-PPLACE-tax.tsv`: Tab-separated table for all ASVs with EPA-NG - Gappa taxonomic classification, sequence and relative abundance.
- `rel-table-ASV_with-*-tax.tsv`: Tab-separated table for all ASVs with taxonomic classification, sequence and relative abundance. The star (\*) is replaced by the taxonomic classification method.

</details>

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2 changes: 1 addition & 1 deletion subworkflows/local/dada2_preprocessing.nf
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Expand Up @@ -90,7 +90,7 @@ workflow DADA2_PREPROCESSING {
if (params.ignore_failed_filtering) {
log.warn "The following samples had too few reads (<$params.min_read_counts) after quality filtering with DADA2:\n$samples\nIgnoring failed samples and continue!\n"
} else {
error("The following samples had too few reads (<$params.min_read_counts) after quality filtering with DADA2:\n$samples\nPlease check whether the correct primer sequences for trimming were supplied. Ignore that samples using `--ignore_failed_filtering` or adjust the threshold with `--min_read_counts`.")
error("The following samples had too few reads (<$params.min_read_counts) after quality filtering with DADA2:\n$samples\nPlease check settings related to quality filtering such as `--max_ee` (increase), `--trunc_qmin` (increase) or `--trunclenf`/`--trunclenr` (decrease). Ignore that samples using `--ignore_failed_filtering` or adjust the threshold with `--min_read_counts`.")
}
}

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