Add HAMRONIZATION/FARGENE and updates all HARMONIZATION tools to 1.1.1 (#2107)

* Update main.nf

* Update meta.yml

* Re-add logos as not staged in a way that works with MultiQC config files

* Update main.nf

* Remove now unnecessary input channel

* Remove unused channel from tests

* Update hAMRonization to 1.1.1 and add hAMRonization farGene

* Fix hamronizatio ntests

* Prettier

* Fix fargene linting

* Correct file

* Fix fargene output

* Apply suggestions from code review

Co-authored-by: Jasmin F <73216762+jasmezz@users.noreply.github.com>

* Fix summarise tests

* Prettier

Co-authored-by: Jasmin F <73216762+jasmezz@users.noreply.github.com>

modules/fargene/main.nf

@@ -14,8 +14,8 @@ process FARGENE {
     val hmm_model
 
     output:
-    path "*.log"                                                                                 , emit: log
-    path "${prefix}/results_summary.txt"                                                         , emit: txt
+    tuple val(meta), path("*.log")                                                                               , emit: log
+    tuple val(meta), path("${prefix}/results_summary.txt")                                                       , emit: txt
     tuple val(meta), path("${prefix}/hmmsearchresults/*.out")                                    , optional: true, emit: hmm
     tuple val(meta), path("${prefix}/predictedGenes/predicted-orfs.fasta")                       , optional: true, emit: orfs
     tuple val(meta), path("${prefix}/predictedGenes/predicted-orfs-amino.fasta")                 , optional: true, emit: orfs_amino

modules/hamronization/abricate/main.nf

@@ -2,10 +2,10 @@ process HAMRONIZATION_ABRICATE {
     tag "$meta.id"
     label 'process_single'
 
-    conda (params.enable_conda ? "bioconda::hamronization=1.0.3" : null)
+    conda (params.enable_conda ? "bioconda::hamronization=1.1.1" : null)
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/hamronization:1.0.3--py_0':
-        'quay.io/biocontainers/hamronization:1.0.3--py_0' }"
+        'https://depot.galaxyproject.org/singularity/hamronization:1.1.1--pyhdfd78af_0':
+        'quay.io/biocontainers/hamronization:1.1.1--pyhdfd78af_0' }"
 
     input:
     tuple val(meta), path(report)

modules/hamronization/abricate/meta.yml

@@ -8,8 +8,8 @@ keywords:
 tools:
   - "hamronization":
       description: "Tool to convert and summarize AMR gene detection outputs using the hAMRonization specification"
-      homepage: "https://github.com/pha4ge/hAMRonization/blob/master/README.md"
-      documentation: "https://github.com/pha4ge/hAMRonization/blob/master/README.md"
+      homepage: "https://github.com/pha4ge/hAMRonization/"
+      documentation: "https://github.com/pha4ge/hAMRonization/"
       tool_dev_url: "https://github.com/pha4ge/hAMRonization"
       doi: ""
       licence: "['GNU Lesser General Public v3 (LGPL v3)']"

modules/hamronization/amrfinderplus/main.nf

@@ -1,12 +1,11 @@
-
 process HAMRONIZATION_AMRFINDERPLUS {
     tag "$meta.id"
     label 'process_single'
 
-    conda (params.enable_conda ? "bioconda::hamronization=1.0.3" : null)
+    conda (params.enable_conda ? "bioconda::hamronization=1.1.1" : null)
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/hamronization:1.0.3--py_0':
-        'quay.io/biocontainers/hamronization:1.0.3--py_0' }"
+        'https://depot.galaxyproject.org/singularity/hamronization:1.1.1--pyhdfd78af_0':
+        'quay.io/biocontainers/hamronization:1.1.1--pyhdfd78af_0' }"
 
     input:
     tuple val(meta), path(report)

modules/hamronization/amrfinderplus/meta.yml

@@ -10,8 +10,8 @@ keywords:
 tools:
   - "hamronization":
       description: "Tool to convert and summarize AMR gene detection outputs using the hAMRonization specification"
-      homepage: "https://github.com/pha4ge/hAMRonization/blob/master/README.md"
-      documentation: "https://github.com/pha4ge/hAMRonization/blob/master/README.md"
+      homepage: "https://github.com/pha4ge/hAMRonization/"
+      documentation: "https://github.com/pha4ge/hAMRonization/"
       tool_dev_url: "https://github.com/pha4ge/hAMRonization"
       licence: "['GNU Lesser General Public v3 (LGPL v3)']"
 

modules/hamronization/deeparg/main.nf

@@ -2,10 +2,10 @@ process HAMRONIZATION_DEEPARG {
     tag "$meta.id"
     label 'process_single'
 
-    conda (params.enable_conda ? "bioconda::hamronization=1.0.3" : null)
+    conda (params.enable_conda ? "bioconda::hamronization=1.1.1" : null)
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/hamronization:1.0.3--py_0':
-        'quay.io/biocontainers/hamronization:1.0.3--py_0' }"
+        'https://depot.galaxyproject.org/singularity/hamronization:1.1.1--pyhdfd78af_0':
+        'quay.io/biocontainers/hamronization:1.1.1--pyhdfd78af_0' }"
 
     input:
     tuple val(meta), path(report)

modules/hamronization/deeparg/meta.yml

@@ -8,8 +8,8 @@ keywords:
 tools:
   - hamronization:
       description: Tool to convert and summarize AMR gene detection outputs using the hAMRonization specification
-      homepage: https://github.com/pha4ge/hAMRonization/blob/master/README.md
-      documentation: https://github.com/pha4ge/hAMRonization/blob/master/README.md
+      homepage: https://github.com/pha4ge/hAMRonization/
+      documentation: https://github.com/pha4ge/hAMRonization/
       tool_dev_url: https://github.com/pha4ge/hAMRonization
       doi: ""
       licence: ["GNU Lesser General Public v3 (LGPL v3)"]

modules/hamronization/fargene/main.nf

@@ -0,0 +1,43 @@
+process HAMRONIZATION_FARGENE {
+    tag "$meta.id"
+    label 'process_single'
+
+    conda (params.enable_conda ? "bioconda::hamronization=1.1.1" : null)
+    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+        'https://depot.galaxyproject.org/singularity/hamronization:1.1.1--pyhdfd78af_0':
+        'quay.io/biocontainers/hamronization:1.1.1--pyhdfd78af_0' }"
+
+    input:
+    tuple val(meta), path(report)
+    val(format)
+    val(software_version)
+    val(reference_db_version)
+
+    output:
+    tuple val(meta), path("*.json") , optional: true, emit: json
+    tuple val(meta), path("*.tsv")  , optional: true, emit: tsv
+    path "versions.yml"                             , emit: versions
+
+    when:
+    task.ext.when == null || task.ext.when
+
+    script:
+    def args = task.ext.args ?: ''
+    def prefix = task.ext.prefix ?: "${meta.id}"
+    """
+    hamronize \\
+        fargene \\
+        ${report} \\
+        $args \\
+        --format ${format} \\
+        --analysis_software_version ${software_version} \\
+        --reference_database_version ${reference_db_version} \\
+        --input_file_name ${prefix} \\
+        > ${prefix}.${format}
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        hamronization: \$(echo \$(hamronize --version 2>&1) | cut -f 2 -d ' ' )
+    END_VERSIONS
+    """
+}

modules/hamronization/fargene/meta.yml

@@ -0,0 +1,62 @@
+name: "hamronization_fargene"
+description: Tool to convert and summarize fARGene outputs using the hAMRonization specification
+keywords:
+  - amr
+  - antimicrobial resistance
+  - arg
+  - antimicrobial resistance genes
+  - reporting
+  - fARGene
+tools:
+  - hamronization:
+      description: "Tool to convert and summarize AMR gene detection outputs using the hAMRonization specification"
+      homepage: "https://github.com/pha4ge/hAMRonization/"
+      documentation: "https://github.com/pha4ge/hAMRonization/"
+      tool_dev_url: "https://github.com/pha4ge/hAMRonization"
+      doi: ""
+      licence: "['GNU Lesser General Public v3 (LGPL v3)']"
+
+input:
+  - meta:
+      type: map
+      description: |
+        Groovy Map containing sample information
+        e.g. [ id:'test', single_end:false ]
+  - report:
+      type: file
+      description: Output .txt file from fARGene
+      pattern: "*.txt"
+  - format:
+      type: value
+      description: Type of report file to be produced
+      pattern: "tsv|json"
+  - software_version:
+      type: value
+      description: Version of fARGene used
+      pattern: "[0-9].[0-9].[0-9]"
+  - reference_db_version:
+      type: value
+      description: Database version of fARGene used
+      pattern: "[0-9].[0-9].[0-9]"
+
+output:
+  - meta:
+      type: map
+      description: |
+        Groovy Map containing sample information
+        e.g. [ id:'test', single_end:false ]
+  - versions:
+      type: file
+      description: File containing software versions
+      pattern: "versions.yml"
+  - json:
+      type: file
+      description: hAMRonised report in JSON format
+      pattern: "*.json"
+  - tsv:
+      type: file
+      description: hAMRonised report in TSV format
+      pattern: "*.json"
+
+authors:
+  - "@jfy133"

modules/hamronization/rgi/main.nf

@@ -1,12 +1,11 @@
-
 process HAMRONIZATION_RGI {
     tag "$meta.id"
     label 'process_single'
 
-    conda (params.enable_conda ? "bioconda::hamronization=1.0.3" : null)
+    conda (params.enable_conda ? "bioconda::hamronization=1.1.1" : null)
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/hamronization:1.0.3--py_0':
-        'quay.io/biocontainers/hamronization:1.0.3--py_0' }"
+        'https://depot.galaxyproject.org/singularity/hamronization:1.1.1--pyhdfd78af_0':
+        'quay.io/biocontainers/hamronization:1.1.1--pyhdfd78af_0' }"
 
     input:
     tuple val(meta), path(report)

modules/hamronization/rgi/meta.yml

@@ -10,8 +10,8 @@ keywords:
 tools:
   - hamronization:
       description: "Tool to convert and summarize AMR gene detection outputs using the hAMRonization specification"
-      homepage: "https://github.com/pha4ge/hAMRonization/blob/master/README.md"
-      documentation: "https://github.com/pha4ge/hAMRonization/blob/master/README.md"
+      homepage: "https://github.com/pha4ge/hAMRonization/"
+      documentation: "https://github.com/pha4ge/hAMRonization/"
       tool_dev_url: "https://github.com/pha4ge/hAMRonization"
       doi: ""
       licence: "['GNU Lesser General Public v3 (LGPL v3)']"

modules/hamronization/summarize/main.nf

@@ -1,10 +1,10 @@
 process HAMRONIZATION_SUMMARIZE {
     label 'process_single'
 
-    conda (params.enable_conda ? "bioconda::hamronization=1.0.3" : null)
+    conda (params.enable_conda ? "bioconda::hamronization=1.1.1" : null)
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/hamronization:1.0.3--py_0':
-        'quay.io/biocontainers/hamronization:1.0.3--py_0' }"
+        'https://depot.galaxyproject.org/singularity/hamronization:1.1.1--pyhdfd78af_0':
+        'quay.io/biocontainers/hamronization:1.1.1--pyhdfd78af_0' }"
 
     input:
     path(reports)

modules/hamronization/summarize/meta.yml

@@ -7,8 +7,8 @@ keywords:
 tools:
   - hamronization:
       description: Tool to convert and summarize AMR gene detection outputs using the hAMRonization specification
-      homepage: https://github.com/pha4ge/hAMRonization/blob/master/README.md
-      documentation: https://github.com/pha4ge/hAMRonization/blob/master/README.md
+      homepage: https://github.com/pha4ge/hAMRonization/
+      documentation: https://github.com/pha4ge/hAMRonization/
       tool_dev_url: https://github.com/pha4ge/hAMRonization
       doi: ""
       licence: ["GNU Lesser General Public v3 (LGPL v3)"]

tests/config/pytest_modules.yml

@@ -1159,6 +1159,10 @@ hamronization/deeparg:
   - modules/hamronization/deeparg/**
   - tests/modules/hamronization/deeparg/**
 
+hamronization/fargene:
+  - modules/hamronization/fargene/**
+  - tests/modules/hamronization/fargene/**
+
 hamronization/rgi:
   - modules/hamronization/rgi/**
   - tests/modules/hamronization/rgi/**

tests/modules/fargene/test.yml

@@ -8,7 +8,6 @@
     - path: output/fargene/test/results_summary.txt
       md5sum: 690d351cfc52577263ef4cfab1c81f50
     - path: output/fargene/test/tmpdir/test1.contigs-positives.out
-      md5sum: d41d8cd98f00b204e9800998ecf8427e
     - path: output/fargene/test/tmpdir/tmp.out
     - path: output/gunzip/test1.contigs.fa
       md5sum: 80c4d78f2810f6d9e90fa6da9bb9c4f9

tests/modules/hamronization/abricate/test.yml

@@ -5,4 +5,5 @@
     - hamronization
   files:
     - path: output/hamronization/test.tsv
-      md5sum: 1c774f024872da954126d0ff77b77ea7
+      contains:
+        - "input_file_name	gene_symbol	gene_name	reference_database_name	reference_database_version	reference_accession	analysis_software_name	analysis_software_version	genetic_variation_type	antimicrobial_agent	coverage_percentage	coverage_depth	coverage_ratio	drug_class	input_gene_length	input_gene_start	input_gene_stop	input_protein_length	input_protein_start	input_protein_stop	input_sequence_id	nucleotide_mutation	nucleotide_mutation_interpretation	predicted_phenotype	predicted_phenotype_confidence_level	amino_acid_mutation	amino_acid_mutation_interpretation	reference_gene_length	reference_gene_start	reference_gene_stop	reference_protein_length	reference_protein_start	reference_protein_stop	resistance_mechanism	strand_orientation	sequence_identity"

tests/modules/hamronization/amrfinderplus/test.yml

@@ -5,4 +5,5 @@
     - hamronization/amrfinderplus
   files:
     - path: output/hamronization/test.tsv
-      md5sum: 6ed7f74659df7bce285ca80fd531e138
+      contains:
+        - "input_file_name	gene_symbol	gene_name	reference_database_name	reference_database_version	reference_accession	analysis_software_name	analysis_software_version	genetic_variation_type	antimicrobial_agent	coverage_percentage	coverage_depth	coverage_ratio	drug_class	input_gene_length	input_gene_start	input_gene_stop	input_protein_length	input_protein_start	input_protein_stop	input_sequence_id	nucleotide_mutation	nucleotide_mutation_interpretation	predicted_phenotype	predicted_phenotype_confidence_level	amino_acid_mutation	amino_acid_mutation_interpretation	reference_gene_length	reference_gene_start	reference_gene_stop	reference_protein_length	reference_protein_start	reference_protein_stop	resistance_mechanism	strand_orientation	sequence_identity"

tests/modules/hamronization/deeparg/test.yml

@@ -5,4 +5,5 @@
     - hamronization/deeparg
   files:
     - path: output/hamronization/test.tsv
-      md5sum: 3c315605aca0c5964796bb5fd4cdd522
+      contains:
+        - "input_file_name	gene_symbol	gene_name	reference_database_name	reference_database_version	reference_accession	analysis_software_name	analysis_software_version	genetic_variation_type	antimicrobial_agent	coverage_percentage	coverage_depth	coverage_ratio	drug_class	input_gene_length	input_gene_start	input_gene_stop	input_protein_length	input_protein_start	input_protein_stop	input_sequence_id	nucleotide_mutation	nucleotide_mutation_interpretation	predicted_phenotype	predicted_phenotype_confidence_level	amino_acid_mutation	amino_acid_mutation_interpretation	reference_gene_length	reference_gene_start	reference_gene_stop	reference_protein_length	reference_protein_start	reference_protein_stop	resistance_mechanism	strand_orientation	sequence_identity"

tests/modules/hamronization/fargene/main.nf

@@ -0,0 +1,19 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { GUNZIP                } from '../../../modules/gunzip/main.nf'
+include { FARGENE               } from '../../../modules/fargene/main.nf'
+include { HAMRONIZATION_FARGENE } from '../../../../modules/hamronization/fargene/main.nf'
+
+workflow test_hamronization_fargene {
+
+    input = [ [ id:'test', single_end:false ], // meta map
+              file(params.test_data['bacteroides_fragilis']['illumina']['test1_contigs_fa_gz'], checkIfExists: true) ]
+    hmm_model = 'class_a'
+
+    GUNZIP ( input )
+    FARGENE ( GUNZIP.out.gunzip, hmm_model )
+
+    HAMRONIZATION_FARGENE ( FARGENE.out.hmm, 'tsv', '0.1', '0.1' )
+}

tests/modules/hamronization/fargene/nextflow.config

@@ -0,0 +1,5 @@
+process {
+
+    publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
+    
+}

tests/modules/hamronization/fargene/test.yml

@@ -0,0 +1,7 @@
+- name: hamronization fargene test_hamronization_fargene
+  command: nextflow run ./tests/modules/hamronization/fargene -entry test_hamronization_fargene -c ./tests/config/nextflow.config  -c ./tests/modules/hamronization/fargene/nextflow.config
+  tags:
+    - hamronization
+    - hamronization/fargene
+  files:
+    - path: output/hamronization/test.tsv

tests/modules/hamronization/rgi/test.yml

@@ -5,4 +5,5 @@
     - hamronization/rgi
   files:
     - path: output/hamronization/test.tsv
-      md5sum: 3e0f7e9321afbc947dd1ea32ce9c0559
+      contains:
+        - "input_file_name	gene_symbol	gene_name	reference_database_name	reference_database_version	reference_accession	analysis_software_name	analysis_software_version	genetic_variation_type	antimicrobial_agent	coverage_percentage	coverage_depth	coverage_ratio	drug_class	input_gene_length	input_gene_start	input_gene_stop	input_protein_length	input_protein_start	input_protein_stop	input_sequence_id	nucleotide_mutation	nucleotide_mutation_interpretation	predicted_phenotype	predicted_phenotype_confidence_level	amino_acid_mutation	amino_acid_mutation_interpretation	reference_gene_length	reference_gene_start	reference_gene_stop	reference_protein_length	reference_protein_start	reference_protein_stop	resistance_mechanism	strand_orientation	sequence_identity"

tests/modules/hamronization/summarize/test.yml

@@ -1,12 +1,12 @@
 - name: hamronization summarize test_hamronization_summarize
   command: nextflow run ./tests/modules/hamronization/summarize -entry test_hamronization_summarize -c ./tests/config/nextflow.config  -c ./tests/modules/hamronization/summarize/nextflow.config
   tags:
-    - hamronization/summarize
     - hamronization
+    - hamronization/summarize
   files:
     - path: output/hamronization/hamronization_combined_report.json
-      md5sum: 1623b6cc3b213208a425e023edd94691
+      md5sum: ab0c899664398193a25a699b92f960b9
     - path: output/hamronization/test.tsv
-      md5sum: 3c315605aca0c5964796bb5fd4cdd522
+      md5sum: e886d665bf9fc266be8193859863d2f4
     - path: output/hamronization/test2.tsv
-      md5sum: 453f38502e35261a50a0849dca34f05b
+      md5sum: 2d94ecb8be8d9036877e47a81ae92a41