Add gappa/examineassign (#2079)

* Created gappa/examineassign from template

* Test passing

* Run only when taxonomy is set

* Revert adding taxonomy to when

* Add period after prefix

* Fix test

* Add some keywords

* Add one more keyword

modules/gappa/examineassign/main.nf

@@ -0,0 +1,41 @@
+process GAPPA_EXAMINEASSIGN {
+    tag "$meta.id"
+    label 'process_medium'
+
+    conda (params.enable_conda ? "bioconda::gappa=0.8.0" : null)
+    container "${ 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)
+    path  taxonomy
+
+    output:
+    tuple val(meta), path("./.")                  , emit: examineassign
+    tuple val(meta), path("*profile.tsv")         , emit: profile
+    tuple val(meta), path("*labelled_tree.newick"), emit: labelled_tree
+    tuple val(meta), path("*per_query.tsv")       , emit: per_query, optional: true
+    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 assign \\
+        $args \\
+        --threads $task.cpus \\
+        --jplace-path $jplace \\
+        --taxon-file $taxonomy \\
+        --file-prefix ${prefix}.
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        gappa: \$(echo \$(gappa --version 2>&1 | sed 's/v//' ))
+    END_VERSIONS
+    """
+}

modules/gappa/examineassign/meta.yml

@@ -0,0 +1,55 @@
+name: "gappa_examineassign"
+description: assigns taxonomy to query sequences in phylogenetic placement output
+keywords:
+  - phylogeny
+  - phylogenetic placement
+  - classification
+  - taxonomy
+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' ]
+  - examineassign:
+      type: directory
+      description: Execution directory
+  - profile:
+      type: file
+      description: profile tsv file
+      pattern: "*profile.tsv"
+  - labelled_tree:
+      type: file
+      description: labelled tree in newick format
+      pattern: "*labelled_tree.newick"
+  - per_query:
+      type: file
+      description: per query taxonomy assignments in tsv format
+      pattern: "*per_query.tsv"
+  - versions:
+      type: file
+      description: File containing software versions
+      pattern: "versions.yml"
+
+authors:
+  - "@erikrikarddaniel"

tests/config/pytest_modules.yml

@@ -827,6 +827,10 @@ gamma/gamma:
   - modules/gamma/gamma/**
   - tests/modules/gamma/gamma/**
 
+gappa/examineassign:
+  - modules/gappa/examineassign/**
+  - tests/modules/gappa/examineassign/**
+
 gappa/examinegraft:
   - modules/gappa/examinegraft/**
   - tests/modules/gappa/examinegraft/**

tests/modules/gappa/examineassign/main.nf

@@ -0,0 +1,16 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { GAPPA_EXAMINEASSIGN } from '../../../../modules/gappa/examineassign/main.nf'
+
+workflow test_gappa_examineassign {
+    
+    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)
+    ]
+    taxonomy = file('https://github.com/nf-core/test-datasets/raw/modules/data/delete_me/gappa/gappa_taxonomy.tsv', checkIfExists: true)
+
+    GAPPA_EXAMINEASSIGN ( input, taxonomy )
+}

tests/modules/gappa/examineassign/nextflow.config

@@ -0,0 +1,9 @@
+process {
+
+    publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
+
+    ext.args   = "--per-query-results"
+
+    ext.when   = { taxonomy }
+    
+}

tests/modules/gappa/examineassign/test.yml

@@ -0,0 +1,15 @@
+- name: gappa examineassign test_gappa_examineassign
+  command: nextflow run ./tests/modules/gappa/examineassign -entry test_gappa_examineassign -c ./tests/config/nextflow.config  -c ./tests/modules/gappa/examineassign/nextflow.config
+  tags:
+    - gappa
+    - gappa/examineassign
+  files:
+    - path: output/gappa/test.labelled_tree.newick
+      md5sum: 39de8a46303ea757f6eb94478db1ffe0
+    - path: output/gappa/test.per_query.tsv
+      md5sum: 16e1fbcc5f79588a0ed21e495cdd91ee
+    - path: output/gappa/test.profile.tsv
+      md5sum: ce604fa03604462358b69cfbff7c1593
+    - path: output/gappa/versions.yml
+      contains:
+        - "0.8.0"