nf-core · Vedanth-Ramji · Jul 25, 2024 · Jul 15, 2024 · Jul 15, 2024 · Jul 16, 2024
diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -18,6 +18,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 - [#382](https://github.com/nf-core/funcscan/pull/382) Optimised BGC screening run time and prevent crashes due to too-short contigs by adding contig length filtering for BGC workflow only. (by @jfy133, @darcy220606)
 - [#366](https://github.com/nf-core/funcscan/pull/366) Added nf-test on pipeline level. (by @jfy133, @Darcy220606, @jasmezz)
 - [#403](https://github.com/nf-core/funcscan/pull/403) Added antiSMASH parameters `--pfam2go`, `--rre`, and `--tfbs`. (reported by @Darcy220606, added by @jasmezz)
+- [#405](https://github.com/nf-core/funcscan/pull/405) Added argNorm to ARG subworkflow. (by @Vedanth-Ramji)
 
 ### `Fixed`
 
@@ -44,6 +45,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 | AMPlify       | 1.1.0            | 2.0.0       |
 | AMRFinderPlus | 3.11.18          | 3.12.8      |
 | antiSMASH     | 6.1.1            | 7.1.0       |
+| argNorm       | NA               | 0.5.0       |
 | bioawk        | 1.0              | NA          |
 | comBGC        | 1.6.1            | 1.6.2       |
 | DeepARG       | 1.0.2            | 1.0.4       |

diff --git a/CITATIONS.md b/CITATIONS.md
@@ -30,6 +30,10 @@
 
   > Blin, K., Shaw, S., Kloosterman, A. M., Charlop-Powers, Z., van Wezel, G. P., Medema, M. H., & Weber, T. (2021). antiSMASH 6.0: improving cluster detection and comparison capabilities. Nucleic acids research, 49(W1), W29–W35. [DOI: 10.1093/nar/gkab335](https://doi.org/10.1093/nar/gkab335)
 
+- [argNorm](https://github.com/BigDataBiology/argNorm)
+
+  > Svetlana Ugarcina Perovic, Vedanth Ramji, Hui Chong, Yiqian Duan, Finlay Maguire, Luis Pedro Coelho (2024). BigDataBiology/argNorm: Version 0.5.0 (v0.5.0). GitHub. https://github.com/BigDataBiology/argNorm. Zenodo. [DOI:10.5281/zenodo.10963591](https://zenodo.org/doi/10.5281/zenodo.10963591)
+
 - [Bakta](https://doi.org/10.1099/mgen.0.000685)
 
   > Schwengers, O., Jelonek, L., Dieckmann, M. A., Beyvers, S., Blom, J., & Goesmann, A. (2021). Bakta: rapid and standardized annotation of bacterial genomes via alignment-free sequence identification. Microbial Genomics, 7(11). [DOI: 10.1099/mgen.0.000685](https://doi.org/10.1099/mgen.0.000685)

diff --git a/README.md b/README.md
@@ -34,7 +34,7 @@ The nf-core/funcscan AWS full test dataset are contigs generated by the MGnify s
 2. Taxonomic classification of contigs of **prokaryotic origin** with [`MMseqs2`](https://github.com/soedinglab/MMseqs2)
 3. Annotation of assembled prokaryotic contigs with [`Prodigal`](https://github.com/hyattpd/Prodigal), [`Pyrodigal`](https://github.com/althonos/pyrodigal), [`Prokka`](https://github.com/tseemann/prokka), or [`Bakta`](https://github.com/oschwengers/bakta)
 4. Screening contigs for antimicrobial peptide-like sequences with [`ampir`](https://cran.r-project.org/web/packages/ampir/index.html), [`Macrel`](https://github.com/BigDataBiology/macrel), [`HMMER`](http://hmmer.org/), [`AMPlify`](https://github.com/bcgsc/AMPlify)
-5. Screening contigs for antibiotic resistant gene-like sequences with [`ABRicate`](https://github.com/tseemann/abricate), [`AMRFinderPlus`](https://github.com/ncbi/amr), [`fARGene`](https://github.com/fannyhb/fargene), [`RGI`](https://card.mcmaster.ca/analyze/rgi), [`DeepARG`](https://bench.cs.vt.edu/deeparg)
+5. Screening contigs for antibiotic resistant gene-like sequences with [`ABRicate`](https://github.com/tseemann/abricate), [`AMRFinderPlus`](https://github.com/ncbi/amr), [`fARGene`](https://github.com/fannyhb/fargene), [`RGI`](https://card.mcmaster.ca/analyze/rgi), [`DeepARG`](https://bench.cs.vt.edu/deeparg). [`argNorm`](https://github.com/BigDataBiology/argNorm) is used to map the outputs of `DeepARG`, `AMRFinderPlus`, and `ABRicate` to the [`Antibiotic Resistance Ontology`](https://www.ebi.ac.uk/ols4/ontologies/aro) for consistent ARG classification terms.
 6. Screening contigs for biosynthetic gene cluster-like sequences with [`antiSMASH`](https://antismash.secondarymetabolites.org), [`DeepBGC`](https://github.com/Merck/deepbgc), [`GECCO`](https://gecco.embl.de/), [`HMMER`](http://hmmer.org/)
 7. Creating aggregated reports for all samples across the workflows with [`AMPcombi`](https://github.com/Darcy220606/AMPcombi) for AMPs, [`hAMRonization`](https://github.com/pha4ge/hAMRonization) for ARGs, and [`comBGC`](https://raw.githubusercontent.com/nf-core/funcscan/master/bin/comBGC.py) for BGCs
 8. Software version and methods text reporting with [`MultiQC`](http://multiqc.info/)

diff --git a/conf/base.config b/conf/base.config
@@ -204,6 +204,21 @@ process {
         cpus   = 1
     }
 
+    withName: ARGNORM_DEEPARG {
+        memory = { check_max( 4.GB * task.attempt, 'memory'  ) }
+        cpus   = 1
+    }
+
+    withName: ARGNORM_ABRICATE {
+        memory = { check_max( 4.GB * task.attempt, 'memory'  ) }
+        cpus   = 1
+    }
+
+    withName: ARGNORM_AMRFINDERPLUS {
+        memory = { check_max( 4.GB * task.attempt, 'memory'  ) }
+        cpus   = 1
+    }
+
     withName: AMPCOMBI2_PARSETABLES {
         memory = { check_max( 8.GB * task.attempt, 'memory'  ) }
         time   = { check_max( 2.h   * task.attempt, 'time'   ) }

diff --git a/conf/modules.config b/conf/modules.config
@@ -629,6 +629,36 @@ process {
         ]
     }
 
+    withName: ARGNORM_ABRICATE {
+        publishDir = [
+            path: {"${params.outdir}/arg/argnorm/abricate/"},
+            mode: params.publish_dir_mode,
+            saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
+        ]
+        ext.prefix = { "${meta.id}.normalized.tsv" }
+        ext.args = "--hamronized"
+    }
+
+    withName: ARGNORM_AMRFINDERPLUS {
+        publishDir = [
+            path: {"${params.outdir}/arg/argnorm/amrfinderplus/"},
+            mode: params.publish_dir_mode,
+            saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
+        ]
+        ext.prefix = { "${meta.id}.normalized.tsv" }
+        ext.args = "--hamronized"
+    }
+
+    withName: ARGNORM_DEEPARG {
+        publishDir = [
+            path: {"${params.outdir}/arg/argnorm/deeparg/"},
+            mode: params.publish_dir_mode,
+            saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
+        ]
+        ext.prefix = { "${meta.id}.normalized.tsv" }
+        ext.args = "--hamronized"
+    }
+
     withName: MERGE_TAXONOMY_COMBGC {
         publishDir = [
             path: { "${params.outdir}/reports/combgc" },

diff --git a/docs/output.md b/docs/output.md
@@ -4,7 +4,7 @@
 
 The output of nf-core/funcscan provides reports for each of the functional groups:
 
-- antibiotic resistance genes (tools: [ABRicate](https://github.com/tseemann/abricate), [AMRFinderPlus](https://www.ncbi.nlm.nih.gov/pathogens/antimicrobial-resistance/AMRFinder), [DeepARG](https://bitbucket.org/gusphdproj/deeparg-ss/src/master), [fARGene](https://github.com/fannyhb/fargene), [RGI](https://card.mcmaster.ca/analyze/rgi) – summarised by [hAMRonization](https://github.com/pha4ge/hAMRonization))
+- antibiotic resistance genes (tools: [ABRicate](https://github.com/tseemann/abricate), [AMRFinderPlus](https://www.ncbi.nlm.nih.gov/pathogens/antimicrobial-resistance/AMRFinder), [DeepARG](https://bitbucket.org/gusphdproj/deeparg-ss/src/master), [fARGene](https://github.com/fannyhb/fargene), [RGI](https://card.mcmaster.ca/analyze/rgi) – summarised by [hAMRonization](https://github.com/pha4ge/hAMRonization) and ABRicate/AMRFinderPlus/DeepARG are normalised to ARO by [argNorm](https://github.com/BigDataBiology/argNorm))
 - antimicrobial peptides (tools: [Macrel](https://github.com/BigDataBiology/macrel), [AMPlify](https://github.com/bcgsc/AMPlify), [ampir](https://ampir.marine-omics.net), [hmmsearch](http://hmmer.org) – summarised by [AMPcombi](https://github.com/Darcy220606/AMPcombi))
 - biosynthetic gene clusters (tools: [antiSMASH](https://docs.antismash.secondarymetabolites.org), [DeepBGC](https://github.com/Merck/deepbgc), [GECCO](https://gecco.embl.de), [hmmsearch](http://hmmer.org) – summarised by [comBGC](#combgc))
 
@@ -35,8 +35,9 @@ results/
 |   ├── amrfinderplus/
 |   ├── deeparg/
 |   ├── fargene/
+|   ├── rgi/
 |   ├── hamronization/
-|   └── rgi/
+|   └── argnorm/
 ├── bgc/
 |   ├── antismash/
 |   ├── deepbgc/
@@ -99,6 +100,7 @@ Output Summaries:
 
 - [AMPcombi](#ampcombi) – summary report of antimicrobial peptide gene output from various detection tools.
 - [hAMRonization](#hamronization) – summary of antimicrobial resistance gene output from various detection tools.
+- [argNorm](#argNorm) - Normalize ARG annotations from [ABRicate](#abricate), [AMRFinderPlus](#amrfinderplus), and [DeepARG](#deeparg) to the ARO
 - [comBGC](#combgc) – summary of biosynthetic gene cluster output from various detection tools.
 - [MultiQC](#multiqc) – report of all software and versions used in the pipeline.
 - [Pipeline information](#pipeline-information) – report metrics generated during the workflow execution.
@@ -274,7 +276,7 @@ Output Summaries:
 
 ### ARG detection tools
 
-[ABRicate](#abricate), [AMRFinderPlus](#amrfinderplus), [DeepARG](#deeparg), [fARGene](#fargene), [RGI](#rgi)
+[ABRicate](#abricate), [AMRFinderPlus](#amrfinderplus), [DeepARG](#deeparg), [fARGene](#fargene), [RGI](#rgi).
 
 #### ABRicate
 
@@ -441,7 +443,7 @@ Note that filtered FASTA is only used for BGC workflow for run-time optimisation
 
 ### Summary tools
 
-[AMPcombi](#ampcombi), [hAMRonization](#hamronization), [comBGC](#combgc), [MultiQC](#multiqc), [pipeline information](#pipeline-information)
+[AMPcombi](#ampcombi), [hAMRonization](#hamronization), [comBGC](#combgc), [MultiQC](#multiqc), [pipeline information](#pipeline-information), [argNorm](#argnorm).
 
 #### AMPcombi
 
@@ -566,6 +568,29 @@ Note that filtered FASTA is only used for BGC workflow for run-time optimisation
 
 [hAMRonization](https://github.com/pha4ge/hAMRonization) summarizes the outputs of the **antimicrobial resistance gene** detection tools (ABRicate, AMRFinderPlus, DeepARG, fARGene, RGI) into a single unified tabular format. It supports a variety of summary options including an interactive summary.
 
+#### argNorm
+
+<details markdown="1">
+<summary>Output files</summary>
+
+- `normalized/`
+  - `*.{tsv}`: search results in tabular format
+  </details>
+  <details markdown="1">
+  <summary>ARG summary table headers</summary>
+
+| Table column                 | Description                                                                      |
+| ---------------------------- | -------------------------------------------------------------------------------- |
+| `ARO`                        | ARO accessions of ARG                                                            |
+| `confers_resistance_to`      | ARO accessions of drugs to which ARGs confer resistance to                       |
+| `resistance_to_drug_classes` | ARO accessions of drugs classes to which drugs in `confers_resistance_to` belong |
+
+</details>
+
+[argnorm](https://github.com/BigDataBiology/argNorm) is a tool to normalize antibiotic resistance genes (ARGs) by mapping them to the antibiotic resistance ontology (ARO) created by the CARD database. argNorm also enhances antibiotic resistance gene annotations by providing categorization of the drugs that antibiotic resistance genes confer resistance to.
+
+argNorm takes the outputs of the [hAMRonization](#hamronization) tool of [ABRicate](#abricate), [AMRFinderPlus](#amrfinderplus), and [DeepARG](#deeparg) and normalizes ARGs in the hAMRonization output to the ARO.
+
 #### comBGC
 
 <details markdown="1">

diff --git a/modules.json b/modules.json
@@ -205,6 +205,11 @@
                         "git_sha": "4e5f4687318f24ba944a13609d3ea6ebd890737d",
                         "installed_by": ["modules"],
                         "patch": "modules/nf-core/untar/untar.diff"
+                    },
+                    "argnorm": {
+                        "branch": "master",
+                        "git_sha": "e4fc46af5ec30070e6aef780aba14f89a28caa88",
+                        "installed_by": ["modules"]
                     }
                 }
             },

diff --git a/modules/nf-core/argnorm/environment.yml b/modules/nf-core/argnorm/environment.yml
diff --git a/modules/nf-core/argnorm/main.nf b/modules/nf-core/argnorm/main.nf
diff --git a/modules/nf-core/argnorm/meta.yml b/modules/nf-core/argnorm/meta.yml
diff --git a/modules/nf-core/argnorm/tests/argnorm_hamronized.config b/modules/nf-core/argnorm/tests/argnorm_hamronized.config
diff --git a/modules/nf-core/argnorm/tests/argnorm_raw.config b/modules/nf-core/argnorm/tests/argnorm_raw.config