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docs/output.md

@@ -23,8 +23,7 @@ The pipeline is built using [Nextflow](https://www.nextflow.io/) and processes d
 - [Bowtie2](#bowtie2) - Host removal for Illumina reads
 - [minimap2](#minimap2) - Host removal for Nanopore reads
 - [SAMtools stats](#samtoolsstats) - Statistics from host removal
-- [SAMtools view](#samtoolsview) - Views and converts the alignment file
-- [SAMtools bam2fq](#samtoolsbam2fq) - Converts the alignment file in fastq format
+- [SAMtools fastq](#samtoolsfastq) - Converts the alignment file in fastq format
 - [Bracken](#bracken) - Taxonomic classifier using k-mers and abundance estimations
 - [Kraken2](#kraken2) - Taxonomic classifier using exact k-mer matches
 - [KrakenUniq](#krakenuniq) - Taxonomic classifier that combines the k-mer-based classification and the number of unique k-mers found in each species
@@ -194,7 +193,7 @@ It is used with nf-core/taxprofiler to allow removal of 'host' (e.g. human) and/
 
 </details>
 
-By default nf-core/taxprofiler will only provide the `.log` file if host removal is turned on. You will only see the mapped (host) reads `.bam` file or the off-target reads in `.fastq` format in your results directory if you provide `--save_hostremoval_mapped` and ` --save_hostremoval_unmapped` respectively.
+By default nf-core/taxprofiler will only provide the `.log` file if host removal is turned on. You will only see the mapped (host) and unmapped reads in `.bam` format or the off-target reads in .fastq format in your results directory if you provide `--save_hostremoval_mapped` and ` --save_hostremoval_unmapped` respectively.
 
 > ⚠️ The resulting `.fastq` files may _not_ always be the 'final' reads that go into taxprofiling, if you also run other steps such as run merging etc..
 
@@ -214,33 +213,23 @@ It is used with nf-core/taxprofiler to allow removal of 'host' (e.g. human) or o
 
 </details>
 
-By default, nf-core taxprofiler will only provide the `.bam` file if host removal for long reads is turned on (i.e., `--save_hostremoval_mapped` and ` --save_hostremoval_unmapped`).
+By default, nf-core taxprofiler will only provide the `.bam` file containing mapped and unmapped if host removal for long reads is turned on (i.e., `--save_hostremoval_mapped` and ` --save_hostremoval_unmapped`).
 
 > ℹ️ minimap2 is not yet supported as a module in MultiQC and therefore there is no dedicated section in the MultiQC HTML. Rather, alignment statistics to host genome is reported via samtools stats module in MultiQC report.
 
-### SAMtools view
+### SAMtools fastq
 
-[SAMtools view](http://www.htslib.org/doc/samtools-view.html) views and comverts a `.sam`, `.bam`, or `.cram` alignment file.
+[SAMtools fastq](http://www.htslib.org/doc/1.1/samtools.html) converts a `.sam`, `.bam`, or `.cram` alignment file to FASTQ format
 
 <details markdown="1">
 <summary>Output files</summary>
 
 - `samtoolsstats`
-  - `<sample_id>.bam`: Alignment file in BAM format
+  - `<sample_id>.fq.gz`: Alignment file in FASTQ gzip format.
 
 </details>
 
-### SAMtools bam2fq
-
-[SAMtools bam2fq](http://www.htslib.org/doc/1.1/samtools.html) converts a `.sam`, `.bam`, or `.cram` alignment file to FASTQ format
-
-<details markdown="1">
-<summary>Output files</summary>
-
-- `samtoolsstats`
-  - `<sample_id>.fq.zg`: Alignment file in FASTQ gzip format.
-
-</details>
+This directory will be present and contain the unmapped reads from the FASTQ format from long-read minimap2 host removal (for short-read unmapped reads, see [bowtie2](#bowtie2), if `--save_hostremoval_unmapped` is supplied.
 
 ### SAMtools stats
 
@@ -359,7 +348,7 @@ The most summary file is the `*combined_reports.txt` file which summarises resul
 
 - `diamond`
   - `<sample_id>.log`: A log file containing stdout information
-  - `<sample_id>*.{blast,xml,txt,daa,sam,tsv,paf,log}`: A file containing alignment information in various formats, or taxonomic information in a text-based format. Exact output depends on user choice.
+  - `<sample_id>*.{blast,xml,txt,daa,sam,tsv,paf}`: A file containing alignment information in various formats, or taxonomic information in a text-based format. Exact output depends on user choice.
 
 </details>
 

nextflow_schema.json

@@ -296,8 +296,8 @@
                 "save_hostremoval_mapped": {
                     "type": "boolean",
                     "fa_icon": "fas fa-save",
-                    "description": "Save mapped reads in BAM format from host removal",
-                    "help_text": "Save the reads mapped to the reference genome in BAM format as output by the respective hostremoval alignment tool.\n\nThis can be useful if you wish to perform other analyses on the host organism (such as host-microbe interaction), however, you should consider whether the default mapping parameters of Bowtie2 (short-read) or minimap2 (long-read) are optimised to your context. "
+                    "description": "Saved mapped and unmapped reads in BAM format from host removal",
+                    "help_text": "Save the reads mapped to the reference genome and offtarget reads in BAM format as output by the respective hostremoval alignment tool.\n\nThis can be useful if you wish to perform other analyses on the host organism (such as host-microbe interaction), however, you should consider whether the default mapping parameters of Bowtie2 (short-read) or minimap2 (long-read) are optimised to your context. "
                 },
                 "save_hostremoval_unmapped": {
                     "type": "boolean",