nf-core · jfy133 · Jul 3, 2024 · Jul 2, 2024 · Jul 2, 2024 · Jul 3, 2024
diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -8,7 +8,8 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 ### `Added`
 
 - [#417](https://github.com/nf-core/taxprofiler/pull/417) - Added reference-free metagenome estimation with Nonpareil (added by @jfy133)
-- [#466](https://github.com/nf-core/taxprofiler/pull/466) - Input database sheets now require a `db_type` column to distinguish between short- and long-read databases
+- [#466](https://github.com/nf-core/taxprofiler/pull/466) - Input database sheets now require a `db_type` column to distinguish between short- and long-read databases (added by @LilyAnderssonLee)
+- [#505](https://github.com/nf-core/taxprofiler/pull/505) - Add small files to the file `tower.yml` (added by @LilyAnderssonLee)
 
 ## v1.1.8dev - Augmented Akita Patch []
 

diff --git a/docs/output.md b/docs/output.md
@@ -227,7 +227,7 @@ The resulting `.fastq` files may _not_ always be the 'final' reads that go into
 <summary>Output files</summary>
 
 - `filtlong/`
-  - `<sample_id>_filtered.fastq.gz`: Quality or short read data filtered file
+  - `<sample_id>_filtered.fastq.gz`: Quality or long read data filtered file
   - `<sample_id>_filtered.log`: log file containing summary statistics
 
 </details>

diff --git a/tower.yml b/tower.yml
@@ -1,5 +1,59 @@
 reports:
   multiqc_report.html:
     display: "MultiQC HTML report"
-  samplesheet.csv:
-    display: "Auto-created samplesheet with collated metadata and FASTQ paths"
+  "**/fastqc/raw/*.html":
+    display: "A FastQC report containing quality metrics of raw reads in HTML format."
+  "**/fastqc/raw/*.txt":
+    display: "A FastQC report containing quality metrics of raw reads in TXT format."
+  "**/fastqc/preprocessed/*.html":
+    display: "A FastQC report containing quality metrics of processed reads in HTML format."
+  "**/fastqc/preprocessed/*.txt":
+    display: "A FastQC report containing quality metrics of processed reads in TXT format."
+  "**/falco/raw/*.html":
+    display: "A Falco report containing quality metrics of raw reads in HTML format."
+  "**/falco/raw/*.txt":
+    display: "A Falco report containing quality metrics of raw reads in TXT format."
+  "**/falco/preprocessed/*.html":
+    display: "A Falco report containing quality metrics of processed reads in HTML format."
+  "**/falco/preprocessed/*.txt":
+    display: "A Falco report containing quality metrics of processed reads in TXT format."
+  "**/fastp/*.html":
+    display: "A Log file in HTML format."
+  "**/bracken/*_combined_reports.txt":
+    display: "Combined bracken results as output from Bracken's combine_bracken_outputs.py script."
+  "**/bracken/*/*.tsv":
+    display: "A TSV file containing per-sample summary of Bracken results with abundance information."
+  "**/bracken/*/*report_bracken_species.txt":
+    display: "A Kraken2 style report with Bracken abundance information."
+  "**/kraken2/kraken2_*_combined_reports.txt":
+    display: "A combined profile of all samples aligned to a given database (as generated by krakentools)."
+  "**/kraken2/*/*.kraken2.report.txt":
+    display: "A Kraken2 report that summarises the fraction abundance, taxonomic ID, number of Kmers, taxonomic path of all the hits in the Kraken2 run for a given sample. Will be 6 column rather than 8 if --save_minimizers specified."
+  "**/krakenuniq/*.krakenuniq.report.txt":
+    display: "A Kraken2-style report that summarises the fraction abundance, taxonomic ID, number of Kmers, taxonomic path of all the hits, with an additional column for k-mer coverage, that allows for more accurate distinguishing between false-positive/true-postitive hits."
+  "**/krakenuniq/*.krakenuniq.classified.txt":
+    display: "An optional list of read IDs and the hits each read had against each database for a given sample."
+  "**/centrifuge/*_combined_reports.txt":
+    display: "A combined profile of all samples aligned to a given database (as generated by centrifuge-kreport)."
+  "**/centrifuge/*/*.centrifuge.report.txt":
+    display: "A classification report that summarises the taxonomic ID, the taxonomic rank, length of genome sequence, number of classified and uniquely classified reads."
+  "**/centrifuge/*/*.centrifuge.txt":
+    display: "A Kraken2-style report that summarises the fraction abundance, taxonomic ID, number of k-mers, taxonomic path of all the hits in the centrifuge run for a given sample."
+  "**/ganon/*_combined_reports.txt":
+    display: "A combined profile of all samples aligned to a given database (as generated by ganon table)."
+  "**/kaiju/*_combined_reports.txt":
+    display: "A combined profile of all samples aligned to a given database (as generated by kaiju2table)"
+  "**/kaiju/*/*.kaijutable.txt":
+    display: "Summarised Kaiju output with fraction abundance, taxonomic ID, number of reads, and taxonomic names (as generated by kaiju2table)"
+  "**/krona/*.html":
+    display: "Per-tool/per-database interactive HTML file containing hierarchical piecharts."
+  "**/metaphlan/*/*_combined_reports.txt":
+    display: "A combined profile of all samples aligned to a given database (as generated by metaphlan_merge_tables)."
+  "**/metaphlan/*/*.bowtie2out.txt":
+    display: "Bowtie2 alignment information (can be re-used for skipping alignment when re-running MetaPhlAn with different parameters)."
+  "**/metaphlan/*/*_profile.txt":
+    display: "A MetaPhlAn taxonomic profile including abundance estimates."
+  "**/motus/*/*_combined_reports.txt":
+    display: "A combined profile of all samples aligned to a given database (as generated by motus_merge)."
+  "**/taxpasta/*tsv":
+    display: "Standardised taxon table containing multiple samples. The first column describes the taxonomy ID and the rest of the columns describe the read counts for each sample."