updated output

docs/output.md

@@ -37,16 +37,15 @@ The pipeline is built using [Nextflow](https://www.nextflow.io/) and processes d
 <summary>Output files</summary>
 
 - `kraken2/`
-  - `<db_name>_combined_reports.txt`: A combined profile of all samples aligned to a given database (as generated by `krakentools`)
+  - `<sample>.kraken2.report.txt`: A report containing information on the phylogenetic assignment of reads in a given sample.
   - `<db_name>/`
     - `<sample_id>_<db_name>.classified.fastq.gz`: FASTQ file containing all reads that had a hit against a reference in the database for a given sample
     - `<sample_id>_<db_name>.unclassified.fastq.gz`: FASTQ file containing all reads that did not have a hit in the database for a given sample
     - `<sample_id>_<db_name>.classifiedreads.txt`: A list of read IDs and the hits each read had against each database for a given sample
 
 </details>
 
-The main taxonomic classification file from Kraken2 is the `_combined_reports.txt` or `*report.txt` file. The former provides you the broadest over view of the taxonomic classification results across all samples against a single database, where you get two columns for each sample e.g. `2_all` and `2_lvl`, as well as a summarised column summing up across all samples `tot_all` and `tot_lvl`. The latter gives you the most information for a single sample. The report file is also used for the taxpasta step.
-
+The main taxonomic classification file from Kraken2 is the `*report.txt` file. It gives you the most information for a single sample.
 You will only receive the `.fastq` and `*classifiedreads.txt` file if you supply `--kraken2_save_reads` and/or `--kraken2_save_readclassifications` parameters to the pipeline.
 
 ### Krona