feat: Replace VIBRANT with PhiSpy (#116)

* feat: Add PhiSpy to annotation subworkflow

* refactor: Remove VIBRANT from the workflow

* chore: Patch phispy image

* refactor: Add param to skip phispy

* feat: Add some optional outputs to phispy

* feat: Concatenate PhiSpy output

* feat: Add PhiSpy info to report

* fix: Change to correct phispy columns

* fix: Change merge order for phispy

* Revert "fix: Change merge order for phispy"

This reverts commit 15993c7.

* Revert "fix: Change to correct phispy columns"

This reverts commit 336f5dd.

* Revert "feat: Add PhiSpy info to report"

This reverts commit 8c88c73.

* docs: Fix integron finder name in yml

CITATIONS.md

@@ -81,8 +81,8 @@
 
   > Claire Bertelli, Fiona S L Brinkman, Improved genomic island predictions with IslandPath-DIMOB, Bioinformatics, Volume 34, Issue 13, 01 July 2018, Pages 2161–2167, https://doi.org/10.1093/bioinformatics/bty095
 
-- [VIBRANT](https://doi.org/10.1186/s40168-020-00867-0)
-  > Kieft, K., Zhou, Z. & Anantharaman, K. VIBRANT: automated recovery, annotation and curation of microbial viruses, and evaluation of viral community function from genomic sequences. Microbiome 8, 90 (2020). https://doi.org/10.1186/s40168-020-00867-0
+- [PhiSpy](https://doi.org/10.1093/nar/gks406)
+  > Sajia Akhter, Ramy K. Aziz, Robert A. Edwards; PhiSpy: a novel algorithm for finding prophages in bacterial genomes that combines similarity- and composition-based strategies. Nucl Acids Res 2012; 40 (16): e126. doi: 10.1093/nar/gks406
 
 ## Software packaging/containerisation tools
 

README.md

@@ -38,14 +38,14 @@ Annotation:
 - AMR ([`RGI`](https://github.com/arpcard/rgi))
 - Plasmids ([`mob_suite`](https://github.com/phac-nml/mob-suite))
 - Genomic Islands ([`IslandPath`](https://github.com/brinkmanlab/islandpath))
-- Virus identification ([`VIBRANT`](https://github.com/AnantharamanLab/VIBRANT))
+- Phage identification ([`PhiSpy`](https://github.com/linsalrob/PhiSpy))
 - CAZY, VFDB, and BacMet query using DIAMOND ([`diamond`](https://github.com/bbuchfink/diamond))
 
 Phylogeny:
 
 - Panaroo ([`panaroo`](https://github.com/gtonkinhill/panaroo))
 - FastTree ([`fasttree`](http://www.microbesonline.org/fasttree/))
-- (_optionally_) SNP-sites([`SNPsites`](https://github.com/sanger-pathogens/snp-sites))
+- (_optionally_) SNP-sites ([`SNPsites`](https://github.com/sanger-pathogens/snp-sites))
 - (_optionally_) IQTree ([`iqtree`](http://www.iqtree.org/))
 
 Other:
@@ -92,11 +92,10 @@ To test the worklow on a minimal dataset you can use the test configuration (wit
     ```
 
 Due to download speed of the Kraken2, Bakta and CAZY databases this will take ~35 minutes.
-However to accelerate it you can download/cache the database files to a folder (e.g., `test/db_cache`) and provide a database cache parameter. As well as set `--bakta_db` to the directory containing the Bakta database and `--vibrant_db`
-to the directory containing the VIBRANT database.
+However to accelerate it you can download/cache the database files to a folder (e.g., `test/db_cache`) and provide a database cache parameter. As well as set `--bakta_db` to the directory containing the Bakta database.
 
     ```bash
-    nextflow run beiko-lab/ARETE -profile test,docker --db_cache $PWD/test/db_cache --bakta_db $PWD/baktadb/db-light --vibrant_db $PWD/vibrant/
+    nextflow run beiko-lab/ARETE -profile test,docker --db_cache $PWD/test/db_cache --bakta_db $PWD/baktadb/db-light
     ```
 
 ## Documentation

conf/modules.config

@@ -255,15 +255,24 @@ process {
         ]
     }
 
-    withName: VIBRANT_VIBRANTRUN {
-        ext.args = '-no_plot'
+    withName: PHISPY {
+        ext.args = '--output_choice 27'
+        ext.prefix = { "${meta.id}_phispy" }
         publishDir = [
-            path: { "${params.outdir}/annotation/vibrant/" },
+            path: { "${params.outdir}/annotation/phispy/${meta.id}" },
             mode: params.publish_dir_mode,
             saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
         ]
     }
 
+    withName: CONCAT_PHISPY {
+        publishDir = [
+            path: { "${params.outdir}/annotation/phispy/" },
+            mode: params.publish_dir_mode,
+            saveAs: { filename -> filename.equals('PHISPY.txt') ? filename : null }
+        ]
+    }
+
     withName: INTEGRON_FINDER {
         ext.args = '--gbk'
         publishDir = [

conf/test.config

@@ -24,7 +24,7 @@ params {
     use_prokka = true
     skip_kraken = true
     skip_poppunk = true
-    skip_vibrant = true
+    skip_phispy  = true
     light = true
 }
 

docs/output.md

@@ -18,7 +18,7 @@ The pipeline is built using [Nextflow](https://www.nextflow.io/) and processes d
 - [MobRecon](#mobrecon) - Reconstruction and typing of plasmids
 - [RGI](#rgi) - Detection and annotation of AMR determinants
 - [IslandPath](#islandpath) - Predicts genomic islands in bacterial and archaeal genomes.
-- [VIBRANT](#vibrant) - Automated recovery and annotation of bacterial and archaeal viruses
+- [PhiSpy](#phispy) - Prediction of prophages from bacterial genomes
 - [IntegronFinder](#integronfinder) - Finds integrons in DNA sequences
 - [Diamond](#diamond) - Detection and annotation of genes using external databases.
   - [CAZy](#cazy): Carbohydrate metabolism
@@ -220,19 +220,19 @@ Disabled by default. Enable by adding `--run_integronfinder` to your command.
 
 [Integron Finder](https://github.com/gem-pasteur/Integron_Finder) is a bioinformatics tool to find integrons in bacterial genomes.
 
-### VIBRANT
+### PhiSpy
 
 <details markdown="1">
 <summary>Output files</summary>
 
-- `annotation/vibrant/`
-  - `${sample_id}/` : VIBRANT results will be in one directory per genome.
+- `annotation/phispy/`
+  - `${sample_id}/` : PhiSpy results will be in one directory per genome.
 
-See the [VIBRANT documentation](https://github.com/AnantharamanLab/VIBRANT/blob/master/output_explanations.pdf) for an extensive description of the output.
+See the [PhiSpy documentation](https://github.com/linsalrob/PhiSpy#output-files) for an extensive description of the output.
 
 </details>
 
-[VIBRANT](https://github.com/AnantharamanLab/VIBRANT) is a tool for automated recovery and annotation of bacterial and archaeal viruses, determination of genome completeness, and characterization of viral community function from metagenomic assemblies.
+[PhiSpy](https://github.com/linsalrob/PhiSpy) is a tool for identification of prophages in Bacterial (and probably Archaeal) genomes. Given an annotated genome it will use several approaches to identify the most likely prophage regions.
 
 ### Panaroo
 

modules.json

@@ -105,6 +105,12 @@
                         "installed_by": ["modules"],
                         "patch": "modules/nf-core/panaroo/run/panaroo-run.diff"
                     },
+                    "phispy": {
+                        "branch": "master",
+                        "git_sha": "a60792caf1782dd570ad7a091b61806c592734d7",
+                        "installed_by": ["modules"],
+                        "patch": "modules/nf-core/phispy/phispy.diff"
+                    },
                     "prokka": {
                         "branch": "master",
                         "git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",

modules/local/integronfinder/meta.yml

@@ -5,7 +5,7 @@ keywords:
   - integron
   - annotation
 tools:
-  - vibrant:
+  - integron_finder:
     description: Bioinformatics tool to find integrons in bacterial genomes
     homepage: https://github.com/gem-pasteur/Integron_Finder
     documentation: https://integronfinder.readthedocs.io/en/latest/

modules/nf-core/phispy/main.nf

@@ -0,0 +1,80 @@
+process PHISPY {
+    tag "$meta.id"
+    label 'process_medium'
+
+    conda "bioconda::phispy=4.2.21"
+    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+        'https://depot.galaxyproject.org/singularity/phispy:4.2.21--py310h30d9df9_1':
+        'quay.io/biocontainers/phispy:4.2.21--py310h30d9df9_1' }"
+
+    input:
+    tuple val(meta), path(gbk)
+
+    output:
+    tuple val(meta), path("${prefix}.tsv")                     , emit: coordinates
+    tuple val(meta), path("${prefix}.gb*")                     , emit: gbk
+    tuple val(meta), path("${prefix}.log")                     , emit: log
+    tuple val(meta), path("${prefix}_prophage_information.tsv"), optional:true, emit: information
+    tuple val(meta), path("${prefix}_bacteria.fasta")          , optional:true, emit: bacteria_fasta
+    tuple val(meta), path("${prefix}_bacteria.gbk")            , optional:true, emit: bacteria_gbk
+    tuple val(meta), path("${prefix}_phage.fasta")             , optional:true, emit: phage_fasta
+    tuple val(meta), path("${prefix}_phage.gbk")               , optional:true, emit: phage_gbk
+    tuple val(meta), path("${prefix}_prophage.gff3")           , optional:true, emit: prophage_gff
+    tuple val(meta), path("${prefix}_prophage.tbl")            , optional:true, emit: prophage_tbl
+    tuple val(meta), path("${prefix}_prophage.tsv")            , optional:true, emit: prophage_tsv
+    path "versions.yml"                                        , emit: versions
+
+    when:
+    task.ext.when == null || task.ext.when
+
+    script:
+    def args = task.ext.args ?: ''
+    prefix = task.ext.prefix ?: "${meta.id}"
+    // Extract GBK file extension, i.e. .gbff, .gbk.gz
+    gbk_extension = gbk.getName() - gbk.getSimpleName()
+
+    if ("$gbk" == "${prefix}${gbk_extension}") error "Input and output names are the same, set prefix in module configuration to disambiguate!"
+
+    """
+    PhiSpy.py \\
+        $args \\
+        --threads $task.cpus \\
+        -p $prefix \\
+        -o . \\
+        $gbk
+
+    mv ${prefix}_prophage_coordinates.tsv ${prefix}.tsv
+    mv ${prefix}_${gbk} ${prefix}${gbk_extension}
+    mv ${prefix}_phispy.log ${prefix}.log
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        PhiSpy: \$(echo \$(PhiSpy.py --version 2>&1))
+    END_VERSIONS
+    """
+
+    stub:
+    prefix = task.ext.prefix ?: "${meta.id}"
+    gbk_extension = gbk.getName() - gbk.getSimpleName()
+
+    if ("$gbk" == "${prefix}${gbk_extension}") error "Input and output names are the same, set prefix in module configuration to disambiguate!"
+
+    """
+    touch ${prefix}.tsv
+    touch ${prefix}${gbk_extension}
+    touch ${prefix}.log
+    touch ${prefix}_prophage_information.tsv
+    touch ${prefix}_bacteria.fasta
+    touch ${prefix}_bacteria.gbk
+    touch ${prefix}_phage.fasta
+    touch ${prefix}_phage.gbk
+    touch ${prefix}_prophage.gff3
+    touch ${prefix}_prophage.tbl
+    touch ${prefix}_prophage.tsv
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        PhiSpy: \$(echo \$(PhiSpy.py --version 2>&1))
+    END_VERSIONS
+    """
+}