Merge pull request #748 from d4straub/fix-docu-2.10dev

Fix misleading error message and documentation

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`
 

docs/output.md

@@ -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>
 

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`.")
             }
         }