diff --git a/CHANGELOG.md b/CHANGELOG.md index 24c37bbb..9230a2d4 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -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` diff --git a/docs/output.md b/docs/output.md index 12e4e603..e42a08c2 100644 --- a/docs/output.md +++ b/docs/output.md @@ -455,11 +455,9 @@ Absolute abundance tables produced by the previous steps contain count data, but Output files - `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. diff --git a/subworkflows/local/dada2_preprocessing.nf b/subworkflows/local/dada2_preprocessing.nf index 0e4889d0..dc5bceb8 100644 --- a/subworkflows/local/dada2_preprocessing.nf +++ b/subworkflows/local/dada2_preprocessing.nf @@ -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`.") } }