mirror of
https://github.com/MillironX/nf-core_modules.git
synced 2024-12-21 10:48:18 +00:00
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>
This commit is contained in:
parent
1780cf9bcf
commit
daab0a77dd
23 changed files with 179 additions and 38 deletions
|
@ -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("${prefix}/predictedGenes/predicted-orfs-amino.fasta") , optional: true, emit: orfs_amino
|
||||
|
|
|
@ -2,10 +2,10 @@ process HAMRONIZATION_ABRICATE {
|
|||
tag "$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 "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
|
||||
'https://depot.galaxyproject.org/singularity/hamronization:1.0.3--py_0':
|
||||
'quay.io/biocontainers/hamronization:1.0.3--py_0' }"
|
||||
'https://depot.galaxyproject.org/singularity/hamronization:1.1.1--pyhdfd78af_0':
|
||||
'quay.io/biocontainers/hamronization:1.1.1--pyhdfd78af_0' }"
|
||||
|
||||
input:
|
||||
tuple val(meta), path(report)
|
||||
|
|
|
@ -8,8 +8,8 @@ keywords:
|
|||
tools:
|
||||
- "hamronization":
|
||||
description: "Tool to convert and summarize AMR gene detection outputs using the hAMRonization specification"
|
||||
homepage: "https://github.com/pha4ge/hAMRonization/blob/master/README.md"
|
||||
documentation: "https://github.com/pha4ge/hAMRonization/blob/master/README.md"
|
||||
homepage: "https://github.com/pha4ge/hAMRonization/"
|
||||
documentation: "https://github.com/pha4ge/hAMRonization/"
|
||||
tool_dev_url: "https://github.com/pha4ge/hAMRonization"
|
||||
doi: ""
|
||||
licence: "['GNU Lesser General Public v3 (LGPL v3)']"
|
||||
|
|
|
@ -1,12 +1,11 @@
|
|||
|
||||
process HAMRONIZATION_AMRFINDERPLUS {
|
||||
tag "$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 "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
|
||||
'https://depot.galaxyproject.org/singularity/hamronization:1.0.3--py_0':
|
||||
'quay.io/biocontainers/hamronization:1.0.3--py_0' }"
|
||||
'https://depot.galaxyproject.org/singularity/hamronization:1.1.1--pyhdfd78af_0':
|
||||
'quay.io/biocontainers/hamronization:1.1.1--pyhdfd78af_0' }"
|
||||
|
||||
input:
|
||||
tuple val(meta), path(report)
|
||||
|
|
|
@ -10,8 +10,8 @@ keywords:
|
|||
tools:
|
||||
- "hamronization":
|
||||
description: "Tool to convert and summarize AMR gene detection outputs using the hAMRonization specification"
|
||||
homepage: "https://github.com/pha4ge/hAMRonization/blob/master/README.md"
|
||||
documentation: "https://github.com/pha4ge/hAMRonization/blob/master/README.md"
|
||||
homepage: "https://github.com/pha4ge/hAMRonization/"
|
||||
documentation: "https://github.com/pha4ge/hAMRonization/"
|
||||
tool_dev_url: "https://github.com/pha4ge/hAMRonization"
|
||||
licence: "['GNU Lesser General Public v3 (LGPL v3)']"
|
||||
|
||||
|
|
|
@ -2,10 +2,10 @@ process HAMRONIZATION_DEEPARG {
|
|||
tag "$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 "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
|
||||
'https://depot.galaxyproject.org/singularity/hamronization:1.0.3--py_0':
|
||||
'quay.io/biocontainers/hamronization:1.0.3--py_0' }"
|
||||
'https://depot.galaxyproject.org/singularity/hamronization:1.1.1--pyhdfd78af_0':
|
||||
'quay.io/biocontainers/hamronization:1.1.1--pyhdfd78af_0' }"
|
||||
|
||||
input:
|
||||
tuple val(meta), path(report)
|
||||
|
|
|
@ -8,8 +8,8 @@ keywords:
|
|||
tools:
|
||||
- hamronization:
|
||||
description: Tool to convert and summarize AMR gene detection outputs using the hAMRonization specification
|
||||
homepage: https://github.com/pha4ge/hAMRonization/blob/master/README.md
|
||||
documentation: https://github.com/pha4ge/hAMRonization/blob/master/README.md
|
||||
homepage: https://github.com/pha4ge/hAMRonization/
|
||||
documentation: https://github.com/pha4ge/hAMRonization/
|
||||
tool_dev_url: https://github.com/pha4ge/hAMRonization
|
||||
doi: ""
|
||||
licence: ["GNU Lesser General Public v3 (LGPL v3)"]
|
||||
|
|
43
modules/hamronization/fargene/main.nf
Normal file
43
modules/hamronization/fargene/main.nf
Normal file
|
@ -0,0 +1,43 @@
|
|||
process HAMRONIZATION_FARGENE {
|
||||
tag "$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
|
||||
"""
|
||||
}
|
62
modules/hamronization/fargene/meta.yml
Normal file
62
modules/hamronization/fargene/meta.yml
Normal file
|
@ -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"
|
|
@ -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 "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
|
||||
'https://depot.galaxyproject.org/singularity/hamronization:1.0.3--py_0':
|
||||
'quay.io/biocontainers/hamronization:1.0.3--py_0' }"
|
||||
'https://depot.galaxyproject.org/singularity/hamronization:1.1.1--pyhdfd78af_0':
|
||||
'quay.io/biocontainers/hamronization:1.1.1--pyhdfd78af_0' }"
|
||||
|
||||
input:
|
||||
tuple val(meta), path(report)
|
||||
|
|
|
@ -10,8 +10,8 @@ keywords:
|
|||
tools:
|
||||
- hamronization:
|
||||
description: "Tool to convert and summarize AMR gene detection outputs using the hAMRonization specification"
|
||||
homepage: "https://github.com/pha4ge/hAMRonization/blob/master/README.md"
|
||||
documentation: "https://github.com/pha4ge/hAMRonization/blob/master/README.md"
|
||||
homepage: "https://github.com/pha4ge/hAMRonization/"
|
||||
documentation: "https://github.com/pha4ge/hAMRonization/"
|
||||
tool_dev_url: "https://github.com/pha4ge/hAMRonization"
|
||||
doi: ""
|
||||
licence: "['GNU Lesser General Public v3 (LGPL v3)']"
|
||||
|
|
|
@ -1,10 +1,10 @@
|
|||
process HAMRONIZATION_SUMMARIZE {
|
||||
label 'process_single'
|
||||
|
||||
conda (params.enable_conda ? "bioconda::hamronization=1.0.3" : null)
|
||||
conda (params.enable_conda ? "bioconda::hamronization=1.1.1" : null)
|
||||
container "${ 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)
|
||||
|
|
|
@ -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)"]
|
||||
|
|
|
@ -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/**
|
||||
|
|
|
@ -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
|
||||
|
|
|
@ -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"
|
||||
|
|
|
@ -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"
|
||||
|
|
|
@ -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"
|
||||
|
|
19
tests/modules/hamronization/fargene/main.nf
Normal file
19
tests/modules/hamronization/fargene/main.nf
Normal file
|
@ -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' )
|
||||
}
|
5
tests/modules/hamronization/fargene/nextflow.config
Normal file
5
tests/modules/hamronization/fargene/nextflow.config
Normal file
|
@ -0,0 +1,5 @@
|
|||
process {
|
||||
|
||||
publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
|
||||
|
||||
}
|
7
tests/modules/hamronization/fargene/test.yml
Normal file
7
tests/modules/hamronization/fargene/test.yml
Normal file
|
@ -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
|
|
@ -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"
|
||||
|
|
|
@ -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
|
||||
|
|
Loading…
Reference in a new issue