Start adding framework for altenrative host-removal tools

CITATIONS.md

@@ -69,6 +69,10 @@
 
   > Danecek, P., Bonfield, J. K., Liddle, J., Marshall, J., Ohan, V., Pollard, M. O., Whitwham, A., Keane, T., McCarthy, S. A., Davies, R. M., & Li, H. (2021). Twelve years of SAMtools and BCFtools. GigaScience, 10(2). https://doi.org/10.1093/gigascience/giab008
 
+- [Hostile](https://doi.org/10.1093/bioinformatics/btad728)
+
+  > Constantinides, B., Hunt, M., Crook, D.W., 2023. Hostile: accurate decontamination of microbial host sequences. Bioinformatics 39. https://doi.org/10.1093/bioinformatics/btad728
+
 - [Bracken](https://doi.org/10.7717/peerj-cs.104)
 
   > Lu, J., Breitwieser, F. P., Thielen, P., & Salzberg, S. L. (2017). Bracken: estimating species abundance in metagenomics data. PeerJ. Computer Science, 3(e104), e104. https://doi.org/10.7717/peerj-cs.104

README.md

@@ -32,7 +32,7 @@
 2. Performs optional read pre-processing
    - Adapter clipping and merging (short-read: [fastp](https://github.com/OpenGene/fastp), [AdapterRemoval2](https://github.com/MikkelSchubert/adapterremoval); long-read: [porechop](https://github.com/rrwick/Porechop), [Porechop_ABI](https://github.com/bonsai-team/Porechop_ABI))
    - Low complexity and quality filtering (short-read: [bbduk](https://jgi.doe.gov/data-and-tools/software-tools/bbtools/), [PRINSEQ++](https://github.com/Adrian-Cantu/PRINSEQ-plus-plus); long-read: [Filtlong](https://github.com/rrwick/Filtlong)), [Nanoq](https://github.com/esteinig/nanoq)
-   - Host-read removal (short-read: [BowTie2](http://bowtie-bio.sourceforge.net/bowtie2/); long-read: [Minimap2](https://github.com/lh3/minimap2))
+   - Host-read removal (short-read: [BowTie2](http://bowtie-bio.sourceforge.net/bowtie2/); long-read: [Minimap2](https://github.com/lh3/minimap2), both: [Hostile](https://github.com/bede/hostile)),
    - Run merging
 3. Supports statistics metagenome coverage estimation ([Nonpareil](https://nonpareil.readthedocs.io/en/latest/)) and for host-read removal ([Samtools](http://www.htslib.org/))
 4. Performs taxonomic classification and/or profiling using one or more of:

assets/multiqc_config.yml

@@ -38,6 +38,8 @@ report_section_order:
     order: 200
   samtools:
     order: 100
+  hostile:
+    order: 95
   kraken:
     order: 90
   bracken:
@@ -74,6 +76,7 @@ run_modules:
   - nanoq
   - bowtie2
   - samtools
+  - hostile
   - kraken
   - kaiju
   - diamond
@@ -141,6 +144,8 @@ top_modules:
       name: "bowtie2"
   - "samtools":
       name: "Samtools Stats"
+  - "hostile":
+      name: "Hostile"
   - "kraken":
       name: "Kraken"
       path_filters:

docs/output.md

@@ -295,6 +295,30 @@ The resulting `.fastq` files may _not_ always be the 'final' reads that go into
 While there is a dedicated section in the MultiQC HTML for Bowtie2, these values are not displayed by default in the General Stats table. Rather, alignment statistics to host genome is reported via samtools stats module in MultiQC report for direct comparison with minimap2 (see below).
 :::
 
+### Hostile
+
+[Hostile](https://github.com/bede/hostile) removes host sequences from short and long read (meta)genomes, consuming single or paired FASTQ using specialised reference genomes.
+
+<details markdown="1">
+<summary>Output files</summary>
+
+- `hostile/`
+  - `fetch/`
+    - `*.{bt2,fa.gz}`: bowtie2 indices of downloaded reference genome, only if `--save_hostremoval_index` supplied.
+  - `clean/`  
+    -`<sample_id>_<accession_id>.clean_{1,2}.fastq.gz`: FASTQ file(s) with host reads removed.  
+    -`<sample_id>_<accession_id>.json`: host removal statistics in JSON format.
+
+</details>
+
+By default nf-core/taxprofiler will only provide the `.json` file if host removal is turned on.
+You will only get FASTQ files if you specify to save `--save_hostremoval_unmapped` - these contain only unmapped reads.
+Alternatively, if you wish only to have the 'final' reads that go into classification/profiling (i.e., that may have additional processing), do not specify this flag but rather specify `--save_analysis_ready_fastqs`, in which case the reads will be in the folder `analysis_ready_reads`.
+
+:::info
+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..
+:::
+
 ### minimap2
 
 [minimap2](https://github.com/lh3/minimap2) is an alignment tool suited to mapping long reads to reference sequences.

modules.json

@@ -95,6 +95,16 @@
                         "git_sha": "41dfa3f7c0ffabb96a6a813fe321c6d1cc5b6e46",
                         "installed_by": ["modules"]
                     },
+                    "hostile/clean": {
+                        "branch": "master",
+                        "git_sha": "cbe28fbf71fd3eddd868140ccd9c3456fa1df363",
+                        "installed_by": ["modules"]
+                    },
+                    "hostile/fetch": {
+                        "branch": "master",
+                        "git_sha": "f9e0c7508d84c6bbb6aef566bb1f23cf44c2b5bf",
+                        "installed_by": ["modules"]
+                    },
                     "kaiju/kaiju": {
                         "branch": "master",
                         "git_sha": "41dfa3f7c0ffabb96a6a813fe321c6d1cc5b6e46",