ADD MODULE: Famsa guidetree (nf-core#3691)

* famsa_guidetree module: add * famsa_guidetree module: add * Modify meta.yaml -> family to id * Remove white space * Fix report of famsa version * Remove trailing whitespace
FriederikeHanssen · Aug 4, 2023 · 2fe424b · 2fe424b
1 parent 8aa36d4
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diff --git a/modules/nf-core/famsa/guidetree/main.nf b/modules/nf-core/famsa/guidetree/main.nf
@@ -0,0 +1,49 @@
+
+process FAMSA_GUIDETREE {
+    tag "$meta.id"
+    label 'process_medium'
+
+    conda "bioconda::famsa=2.2.2"
+    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+        'https://depot.galaxyproject.org/singularity/famsa:2.2.2--h9f5acd7_0':
+        'biocontainers/famsa:2.2.2--h9f5acd7_0' }"
+
+    input:
+    tuple val(meta), path(fasta)
+
+    output:
+    tuple val(meta), path("*.dnd"), emit: tree
+    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}"
+    """
+    famsa -gt_export \\
+        $args \\
+        -t ${task.cpus} \\
+        ${fasta} \\
+        ${prefix}.dnd
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        famsa: \$( famsa -help 2>&1 | head -n 2 | tail -n 1 | sed 's/ version //g' )
+    END_VERSIONS
+    """
+
+    stub:
+    def args = task.ext.args ?: ''
+    def prefix = task.ext.prefix ?: "${meta.id}"
+    """
+    touch ${prefix}.dnd
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        famsa: \$( famsa -help 2>&1 | head -n 2 | tail -n 1 | sed 's/ version //g' )
+    END_VERSIONS
+    """
+}
+
diff --git a/modules/nf-core/famsa/guidetree/meta.yml b/modules/nf-core/famsa/guidetree/meta.yml
@@ -0,0 +1,48 @@
+---
+# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/yaml-schema.json
+name: "famsa_guidetree"
+description: Renders a guidetree in famsa
+keywords:
+  - guide tree
+  - msa
+  - newick
+tools:
+  - "famsa":
+      description: "Algorithm for large-scale multiple sequence alignments"
+      homepage: "https://github.com/refresh-bio/FAMSA"
+      documentation: "https://github.com/refresh-bio/FAMSA"
+      tool_dev_url: "https://github.com/refresh-bio/FAMSA"
+      doi: "10.1038/srep33964"
+      licence: "['GPL v3']"
+
+input:
+  - meta:
+      type: map
+      description: |
+        Groovy Map containing sample information
+        e.g. `[ id:'test']`
+
+  - fasta:
+      type: file
+      description: Input sequences in FASTA format
+      pattern: "*.{fa,fasta}"
+
+output:
+  - meta:
+      type: map
+      description: |
+        Groovy Map containing sample information
+        e.g. `[ id:'test']`
+
+  - tree:
+      type: file
+      description: Guide tree file in Newick format
+      pattern: "*.{dnd}"
+
+  - versions:
+      type: file
+      description: File containing software versions
+      pattern: "versions.yml"
+
+authors:
+  - "@luisas"
diff --git a/tests/config/pytest_modules.yml b/tests/config/pytest_modules.yml
@@ -1110,6 +1110,10 @@ falco:
   - modules/nf-core/falco/**
   - tests/modules/nf-core/falco/**
 
+famsa/guidetree:
+  - modules/nf-core/famsa/guidetree/**
+  - tests/modules/nf-core/famsa/guidetree/**
+
 faqcs:
   - modules/nf-core/faqcs/**
   - tests/modules/nf-core/faqcs/**

diff --git a/tests/modules/nf-core/famsa/guidetree/main.nf b/tests/modules/nf-core/famsa/guidetree/main.nf
@@ -0,0 +1,15 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { FAMSA_GUIDETREE } from '../../../../../modules/nf-core/famsa/guidetree/main.nf'
+
+workflow test_famsa_guidetree {
+
+    input = [
+        [ id:'test' ], // meta map
+        file(params.test_data['sarscov2']['illumina']['contigs_fasta'], checkIfExists: true)
+    ]
+
+    FAMSA_GUIDETREE ( input )
+}
diff --git a/tests/modules/nf-core/famsa/guidetree/nextflow.config b/tests/modules/nf-core/famsa/guidetree/nextflow.config
@@ -0,0 +1,6 @@
+process {
+
+    publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
+
+
+}
diff --git a/tests/modules/nf-core/famsa/guidetree/test.yml b/tests/modules/nf-core/famsa/guidetree/test.yml
@@ -0,0 +1,9 @@
+- name: famsa guidetree test_famsa_guidetree
+  command: nextflow run ./tests/modules/nf-core/famsa/guidetree -entry test_famsa_guidetree -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/famsa/guidetree/nextflow.config
+  tags:
+    - famsa/guidetree
+    - famsa
+  files:
+    - path: output/famsa/test.dnd
+      md5sum: f3ef8b16a7a16cb4548942ebf2e7bad6
+    - path: output/famsa/versions.yml