Add gappa/examinegraft (#2035)

modules/gappa/examinegraft/main.nf

@@ -0,0 +1,37 @@
+process GAPPA_EXAMINEGRAFT {
+    tag "$meta.id"
+    label 'process_low'
+
+    conda (params.enable_conda ? "bioconda::gappa=0.8.0" : null)
+    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+        'https://depot.galaxyproject.org/singularity/gappa:0.8.0--h9a82719_0':
+        'quay.io/biocontainers/gappa:0.8.0--h9a82719_0' }"
+
+    input:
+    tuple val(meta), path(jplace)
+
+    output:
+    tuple val(meta), path("*.newick"), emit: newick
+    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}"
+    """
+    gappa \\
+        examine \\
+        graft \\
+        $args \\
+        --threads $task.cpus \\
+        --file-prefix ${prefix}. \\
+        --jplace-path $jplace
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        gappa: \$(echo \$(gappa --version 2>&1 | sed 's/v//' ))
+    END_VERSIONS
+    """
+}

modules/gappa/examinegraft/meta.yml

@@ -0,0 +1,41 @@
+name: "gappa_examinegraft"
+description: grafts query sequences from phylogenetic placement on the reference tree
+keywords:
+  - sort
+tools:
+  - "gappa":
+      description: "Genesis Applications for Phylogenetic Placement Analysis"
+      homepage: "https://github.com/lczech/gappa"
+      documentation: "https://github.com/lczech/gappa/wiki"
+      tool_dev_url: "https://github.com/lczech/gappa"
+      doi: "https://doi.org/10.1093/bioinformatics/btaa070"
+      licence: "['GPL v3']"
+
+input:
+  - meta:
+      type: map
+      description: |
+        Groovy Map containing sample information
+        e.g. [ id:'test' ]
+  - jplace:
+      type: file
+      description: jplace file output from phylogenetic placement, e.g. EPA-NG, gzipped or not
+      pattern: "*.{jplace,jplace.gz}"
+
+output:
+  - meta:
+      type: map
+      description: |
+        Groovy Map containing sample information
+        e.g. [ id:'test' ]
+  - versions:
+      type: file
+      description: File containing software versions
+      pattern: "versions.yml"
+  - newick:
+      type: file
+      description: phylogenetic tree file in newick format
+      pattern: "*.newick"
+
+authors:
+  - "@erikrikarddaniel"

tests/config/pytest_modules.yml

@@ -811,6 +811,10 @@ gamma/gamma:
   - modules/gamma/gamma/**
   - tests/modules/gamma/gamma/**
 
+gappa/examinegraft:
+  - modules/gappa/examinegraft/**
+  - tests/modules/gappa/examinegraft/**
+
 gatk/indelrealigner:
   - modules/gatk/indelrealigner/**
   - tests/modules/gatk/indelrealigner/**

tests/modules/gappa/examinegraft/main.nf

@@ -0,0 +1,15 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { GAPPA_EXAMINEGRAFT } from '../../../../modules/gappa/examinegraft/main.nf'
+
+workflow test_gappa_examinegraft {
+    
+    input = [
+        [ id:'test' ], // meta map
+        file('https://github.com/nf-core/test-datasets/raw/modules/data/delete_me/gappa/epa_result.jplace.gz', checkIfExists: true)
+    ]
+
+    GAPPA_EXAMINEGRAFT ( input )
+}

tests/modules/gappa/examinegraft/nextflow.config

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

tests/modules/gappa/examinegraft/test.yml

@@ -0,0 +1,11 @@
+- name: gappa examinegraft test_gappa_examinegraft
+  command: nextflow run ./tests/modules/gappa/examinegraft -entry test_gappa_examinegraft -c ./tests/config/nextflow.config  -c ./tests/modules/gappa/examinegraft/nextflow.config
+  tags:
+    - gappa
+    - gappa/examinegraft
+  files:
+    - path: output/gappa/test.epa_result.newick
+      md5sum: 97e54b6a9576a78b774fd63a050e5474
+    - path: output/gappa/versions.yml
+      contains:
+        - "0.8.0"