diff --git a/CHANGELOG.md b/CHANGELOG.md index 680c5047..2bb1ce9c 100644 --- 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 index 59f50cb0..edc90bd2 100644 --- 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 Output files - `filtlong/` - - `_filtered.fastq.gz`: Quality or short read data filtered file + - `_filtered.fastq.gz`: Quality or long read data filtered file - `_filtered.log`: log file containing summary statistics diff --git a/tower.yml b/tower.yml index 787aedfe..1101572e 100644 --- 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."