From d83deb097a671bef2f947b1f8e73e6a17ae4471f Mon Sep 17 00:00:00 2001 From: Dan Clayton Date: Wed, 6 Dec 2023 15:23:11 +0000 Subject: [PATCH 1/3] update output docs for collapsed abundance tables --- docs/output.md | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/docs/output.md b/docs/output.md index f12fc41f..62433cea 100644 --- a/docs/output.md +++ b/docs/output.md @@ -407,7 +407,7 @@ All following analysis is based on these filtered tables. - `seven_number_summary.tsv`: Length of ASV sequences in different quantiles. - `filtered-sequences.qza`: QIIME2 fragment. - `qiime2/abundance_tables/` - - `abs-abund-table-*.tsv`: Tab-separated absolute abundance table at taxa level `*`, where `*` ranges by default from 2 to 6 or 7, depending on the used reference taxonomy database. + - `abs-abund-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. - `count_table_filter_stats.tsv`: Tab-separated table with information on how much counts were filtered for each sample. - `feature-table.biom`: Abundance table in biom format for importing into downstream analysis tools. - `feature-table.tsv`: Tab-separated abundance table for each ASV and each sample. @@ -423,7 +423,7 @@ 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 or 7, depending on the used reference taxonomy database. + - `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-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. From d8ea1f03225d237161a95f420416056407f558aa Mon Sep 17 00:00:00 2001 From: Dan Clayton Date: Thu, 7 Dec 2023 09:20:58 +0000 Subject: [PATCH 2/3] update changelog --- CHANGELOG.md | 1 + 1 file changed, 1 insertion(+) diff --git a/CHANGELOG.md b/CHANGELOG.md index 620c9716..e51badb3 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -10,6 +10,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 ### `Changed` ### `Fixed` +- [#672](https://github.com/nf-core/ampliseq/pull/672) - Update output docs for collapsed abundance tables ### `Dependencies` From feacdd59242c8af026a4ded19447c6c3b724d19e Mon Sep 17 00:00:00 2001 From: Dan Clayton Date: Thu, 7 Dec 2023 11:42:31 +0000 Subject: [PATCH 3/3] run prettier --- CHANGELOG.md | 1 + 1 file changed, 1 insertion(+) diff --git a/CHANGELOG.md b/CHANGELOG.md index e51badb3..b0879526 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -10,6 +10,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 ### `Changed` ### `Fixed` + - [#672](https://github.com/nf-core/ampliseq/pull/672) - Update output docs for collapsed abundance tables ### `Dependencies`