Adding gappa/examineheattree (#2084)

* Adding gappa/examineheattree

* Update modules/gappa/examineheattree/meta.yml

Co-authored-by: Daniel Straub <42973691+d4straub@users.noreply.github.com>

* Check versions.yml for md5 sum instead

Co-authored-by: Daniel Straub <42973691+d4straub@users.noreply.github.com>

modules/gappa/examineheattree/main.nf

@@ -0,0 +1,45 @@
+process GAPPA_EXAMINEHEATTREE {
+    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  , optional: true
+    tuple val(meta), path("*.nexus")      , emit: nexus   , optional: true
+    tuple val(meta), path("*.phyloxml")   , emit: phyloxml, optional: true
+    tuple val(meta), path("*.svg")        , emit: svg     , optional: true
+    tuple val(meta), path("*.colours.txt"), emit: colours
+    tuple val(meta), path("*.log")        , emit: log
+    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 \\
+        heat-tree \\
+        --threads $task.cpus \\
+        --file-prefix ${prefix}. \\
+        --jplace-path $jplace \\
+        $args \\
+        --log-file ${prefix}.log
+
+    grep '^ *At' ${prefix}.log > ${prefix}.colours.txt
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        gappa: \$(echo \$(gappa --version 2>&1 | sed 's/v//' ))
+    END_VERSIONS
+    """
+}

modules/gappa/examineheattree/meta.yml

@@ -0,0 +1,64 @@
+name: "gappa_examineheattree"
+description: colours a phylogeny with placement densities
+keywords:
+  - phylogeny
+  - phylogenetic placement
+  - heattree
+  - visualisation
+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"
+  - nexus:
+      type: file
+      description: coloured phylogenetic tree file in nexus format
+      pattern: "*.nexus"
+  - phyloxml:
+      type: file
+      description: coloured phylogenetic tree file in phyloxml format
+      pattern: "*.phyloxml"
+  - svg:
+      type: file
+      description: coloured phylogenetic tree file in svg format
+      pattern: "*.svg"
+  - colours:
+      type: file
+      description: colours used in plot
+      pattern: "*.colours.txt"
+  - log:
+      type: file
+      description: log file from the run
+      pattern: "*.log"
+
+authors:
+  - "@erikrikarddaniel"

tests/config/pytest_modules.yml

@@ -835,6 +835,10 @@ gappa/examinegraft:
   - modules/gappa/examinegraft/**
   - tests/modules/gappa/examinegraft/**
 
+gappa/examineheattree:
+  - modules/gappa/examineheattree/**
+  - tests/modules/gappa/examineheattree/**
+
 gatk/indelrealigner:
   - modules/gatk/indelrealigner/**
   - tests/modules/gatk/indelrealigner/**

tests/modules/gappa/examineheattree/main.nf

@@ -0,0 +1,15 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { GAPPA_EXAMINEHEATTREE } from '../../../../modules/gappa/examineheattree/main.nf'
+
+workflow test_gappa_examineheattree {
+    
+    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_EXAMINEHEATTREE ( input )
+}

tests/modules/gappa/examineheattree/nextflow.config

@@ -0,0 +1,10 @@
+process {
+
+    publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
+
+    withName: '.*EXAMINEHEATTREE.*' {
+        ext.args = "--write-newick-tree --write-nexus-tree --write-phyloxml-tree --write-svg-tree"
+        prefix   = { "${meta.id}.heat-tree." }
+    }
+    
+}

tests/modules/gappa/examineheattree/test.yml

@@ -0,0 +1,18 @@
+- name: "gappa examineheattree"
+  command: nextflow run ./tests/modules/gappa/examineheattree -entry test_gappa_examineheattree -c ./tests/config/nextflow.config -c ./tests/modules/gappa/examineheattree/nextflow.config
+  tags:
+    - "gappa"
+    - "gappa/examineheattree"
+  files:
+    - path: output/gappa/test.tree.newick
+      md5sum: f055e11c9b44b6d3afb502aba99d9579
+    - path: output/gappa/test.tree.nexus
+      md5sum: e1cfdcb63f3a751677d0e78fb6b9230a
+    - path: output/gappa/test.tree.phyloxml
+      md5sum: ea35b07e4fd8d174fd6b2f204629cc4e
+    - path: output/gappa/test.tree.svg
+    - path: output/gappa/test.colours.txt
+      md5sum: 7704cd341c8693981253ba6d740c1061
+    - path: output/gappa/test.log
+    - path: output/gappa/versions.yml
+      md5sum: 1cfb752399307413b475438ab1997731