add new module for conifer (nf-core#3763)

* add new module for conifer * fixing CI * fix test * Update main.nf --------- Co-authored-by: Robert A. Petit III <[email protected]>
LouisLeNezet · Sep 25, 2023 · f9c512b · f9c512b
1 parent 6a37f9f
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diff --git a/modules/nf-core/conifer/main.nf b/modules/nf-core/conifer/main.nf
@@ -0,0 +1,47 @@
+process CONIFER {
+    tag "$meta.id"
+    label 'process_single'
+
+    conda "bioconda::conifer=1.0.2"
+    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+        'https://depot.galaxyproject.org/singularity/conifer%3A1.0.2--he4a0461_0':
+        'biocontainers/conifer:1.0.2--he4a0461_0' }"
+
+    input:
+    tuple val(meta), path(kraken_result)
+    path kraken_taxon_db
+
+    output:
+    tuple val(meta), path("*.score"), emit: score
+    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}"
+    """
+    conifer \\
+        $args \\
+        --input $kraken_result \\
+        --db $kraken_taxon_db > ${prefix}.score
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        conifer: \$(echo \$(conifer --version 2>&1) | sed 's/^.*Conifer //')
+    END_VERSIONS
+    """
+
+    stub:
+    def args = task.ext.args ?: ''
+    def prefix = task.ext.prefix ?: "${meta.id}"
+    """
+    touch ${prefix}.score
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        conifer: \$(echo \$(conifer --version 2>&1) | sed 's/^.*Conifer //')
+    END_VERSIONS
+    """
+}
diff --git a/modules/nf-core/conifer/meta.yml b/modules/nf-core/conifer/meta.yml
@@ -0,0 +1,46 @@
+name: conifer
+description: Calculate confidence scores from Kraken2 output
+keywords:
+  - classify
+  - metagenomics
+  - kraken2
+  - confidence
+tools:
+  - conifer:
+      description: "Calculate confidence scores from Kraken2 output"
+      homepage: "https://github.com/Ivarz/Conifer"
+      documentation: "https://github.com/Ivarz/Conifer"
+      tool_dev_url: "https://github.com/Ivarz/Conifer"
+      licence: ["BSD / BSD-2-Clause"]
+input:
+  - meta:
+      type: map
+      description: |
+        Groovy Map containing sample information
+        e.g. [ id:'test', single_end:false ]
+  - kraken_result:
+      type: file
+      description: |
+        Raw Kraken2 standard output file
+  - kraken_taxon_db:
+      type: file
+      description: Kraken2 taxo.k2d database file
+
+output:
+  - meta:
+      type: map
+      description: |
+        Groovy Map containing sample information
+        e.g. [ id:'test', single_end:false ]
+  - score:
+      type: file
+      description: |
+        Conifer report file containing confidence scores of Kraken2 classified reads.
+      pattern: "*.score"
+  - versions:
+      type: file
+      description: File containing software versions
+      pattern: "versions.yml"
+authors:
+  - "@icaromsc"
+  - "@rpetit3"
diff --git a/tests/config/pytest_modules.yml b/tests/config/pytest_modules.yml
@@ -802,6 +802,10 @@ concoct/mergecutupclustering:
   - modules/nf-core/concoct/mergecutupclustering/**
   - tests/modules/nf-core/concoct/mergecutupclustering/**
 
+conifer:
+  - modules/nf-core/conifer/**
+  - tests/modules/nf-core/conifer/**
+
 controlfreec/assesssignificance:
   - modules/nf-core/controlfreec/assesssignificance/**
   - tests/modules/nf-core/controlfreec/assesssignificance/**

diff --git a/tests/modules/nf-core/conifer/main.nf b/tests/modules/nf-core/conifer/main.nf
@@ -0,0 +1,15 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { CONIFER } from '../../../../modules/nf-core/conifer/main.nf'
+
+workflow test_conifer {
+
+    input = [
+        [ id:'test', single_end:false ], // meta map
+        file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
+    ]
+
+    CONIFER ( input, [] )
+}
diff --git a/tests/modules/nf-core/conifer/nextflow.config b/tests/modules/nf-core/conifer/nextflow.config
@@ -0,0 +1,5 @@
+process {
+
+    publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
+
+}
diff --git a/tests/modules/nf-core/conifer/test.yml b/tests/modules/nf-core/conifer/test.yml
@@ -0,0 +1,6 @@
+- name: conifer test_conifer
+  command: nextflow run ./tests/modules/nf-core/conifer -entry test_conifer -c ./tests/config/nextflow.config -stub-run
+  tags:
+    - conifer
+  files:
+    - path: output/conifer/test.score