From 538dbac98ba9c8f799536cd5a617195501439457 Mon Sep 17 00:00:00 2001
From: Sofia Stamouli <91951607+sofstam@users.noreply.github.com>
Date: Fri, 22 Apr 2022 11:26:30 +0200
Subject: [PATCH] Kaiju2table module (#1545)

* Add kaiju2table module
---
 modules/kaiju/kaiju2table/main.nf             | 40 +++++++++++++++
 modules/kaiju/kaiju2table/meta.yml            | 50 +++++++++++++++++++
 tests/config/pytest_modules.yml               |  4 ++
 tests/modules/kaiju/kaiju2table/main.nf       | 21 ++++++++
 .../modules/kaiju/kaiju2table/nextflow.config |  5 ++
 tests/modules/kaiju/kaiju2table/test.yml      |  9 ++++
 6 files changed, 129 insertions(+)
 create mode 100644 modules/kaiju/kaiju2table/main.nf
 create mode 100644 modules/kaiju/kaiju2table/meta.yml
 create mode 100644 tests/modules/kaiju/kaiju2table/main.nf
 create mode 100644 tests/modules/kaiju/kaiju2table/nextflow.config
 create mode 100644 tests/modules/kaiju/kaiju2table/test.yml

diff --git a/modules/kaiju/kaiju2table/main.nf b/modules/kaiju/kaiju2table/main.nf
new file mode 100644
index 00000000..00739d1e
--- /dev/null
+++ b/modules/kaiju/kaiju2table/main.nf
@@ -0,0 +1,40 @@
+process KAIJU_KAIJU2TABLE {
+    tag "$meta.id"
+    label 'process_low'
+
+    conda (params.enable_conda ? "bioconda::kaiju=1.8.2" : null)
+    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+        'https://depot.galaxyproject.org/singularity/kaiju:1.8.2--h5b5514e_1':
+        'quay.io/biocontainers/kaiju:1.8.2--h2e03b76_0' }"
+
+    input:
+    tuple val(meta), path(results)
+    path db
+    val taxon_rank
+
+    output:
+    tuple val(meta), path('*.txt'), emit: summary
+    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}"
+    """
+    dbnodes=`find -L ${db} -name "*nodes.dmp"`
+    dbname=`find -L ${db} -name "*.fmi" -not -name "._*"`
+    kaiju2table   $args \\
+        -t \$dbnodes \\
+        -n \$dbname \\
+        -r ${taxon_rank} \\
+        -o ${prefix}.txt \\
+        ${results}
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        kaiju: \$(echo \$( kaiju -h 2>&1 | sed -n 1p | sed 's/^.*Kaiju //' ))
+    END_VERSIONS
+    """
+}
diff --git a/modules/kaiju/kaiju2table/meta.yml b/modules/kaiju/kaiju2table/meta.yml
new file mode 100644
index 00000000..bc3e85d7
--- /dev/null
+++ b/modules/kaiju/kaiju2table/meta.yml
@@ -0,0 +1,50 @@
+name: "kaiju_kaiju2table"
+description: write your description here
+keywords:
+  - classify
+  - metagenomics
+tools:
+  - kaiju:
+      description: Fast and sensitive taxonomic classification for metagenomics
+      homepage: https://kaiju.binf.ku.dk/
+      documentation: https://github.com/bioinformatics-centre/kaiju/blob/master/README.md
+      tool_dev_url: https://github.com/bioinformatics-centre/kaiju
+      doi: "10.1038/ncomms11257"
+      licence: ["GNU GPL v3"]
+
+input:
+  - meta:
+      type: map
+      description: |
+        Groovy Map containing sample information
+        e.g. [ id:'test', single_end:false ]
+  - results:
+      type: file
+      description: File containing the kaiju classification results
+      pattern: "*.{txt}"
+  - taxon_rank:
+      type: string
+      description: |
+        Taxonomic rank to display in report
+        pattern: "phylum|class|order|family|genus|species"
+
+output:
+  - meta:
+      type: map
+      description: |
+        Groovy Map containing sample information
+        e.g. [ id:'test', single_end:false ]
+  - versions:
+      type: file
+      description: File containing software versions
+      pattern: "versions.yml"
+  - results:
+      type: file
+      description: |
+        Summary table for a given taxonomic rank
+      pattern: "*.{tsv}"
+
+authors:
+  - "@sofstam"
+  - "@talnor"
+  - "@jfy133"
diff --git a/tests/config/pytest_modules.yml b/tests/config/pytest_modules.yml
index c3bf04aa..a1a969e7 100644
--- a/tests/config/pytest_modules.yml
+++ b/tests/config/pytest_modules.yml
@@ -1009,6 +1009,10 @@ kaiju/kaiju:
   - modules/kaiju/kaiju/**
   - tests/modules/kaiju/kaiju/**
 
+kaiju/kaiju2table:
+  - modules/kaiju/kaiju2table/**
+  - tests/modules/kaiju/kaiju2table/**
+
 kallisto/index:
   - modules/kallisto/index/**
   - tests/modules/kallisto/index/**
diff --git a/tests/modules/kaiju/kaiju2table/main.nf b/tests/modules/kaiju/kaiju2table/main.nf
new file mode 100644
index 00000000..b7169ba5
--- /dev/null
+++ b/tests/modules/kaiju/kaiju2table/main.nf
@@ -0,0 +1,21 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { UNTAR             } from '../../../../modules/untar/main.nf'
+include { KAIJU_KAIJU       } from '../../../../modules/kaiju/kaiju/main.nf'
+include { KAIJU_KAIJU2TABLE } from '../../../../modules/kaiju/kaiju2table/main.nf'
+
+workflow test_kaiju_kaiju_single_end {
+
+    input = [
+        [ id:'test', single_end:true ], // meta map
+        file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true)
+    ]
+    db    = [ [], file(params.test_data['sarscov2']['genome']['kaiju_tar_gz'], checkIfExists: true) ]
+    taxon_rank = "species"
+
+    ch_db = UNTAR ( db )
+    KAIJU_KAIJU ( input, ch_db.untar.map{ it[1] } )
+    KAIJU_KAIJU2TABLE ( KAIJU_KAIJU.out.results, ch_db.untar.map{ it[1] }, taxon_rank )
+}
diff --git a/tests/modules/kaiju/kaiju2table/nextflow.config b/tests/modules/kaiju/kaiju2table/nextflow.config
new file mode 100644
index 00000000..50f50a7a
--- /dev/null
+++ b/tests/modules/kaiju/kaiju2table/nextflow.config
@@ -0,0 +1,5 @@
+process {
+
+    publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
+    
+}
\ No newline at end of file
diff --git a/tests/modules/kaiju/kaiju2table/test.yml b/tests/modules/kaiju/kaiju2table/test.yml
new file mode 100644
index 00000000..47d99c89
--- /dev/null
+++ b/tests/modules/kaiju/kaiju2table/test.yml
@@ -0,0 +1,9 @@
+- name: kaiju kaiju2table test_kaiju_kaiju_single_end
+  command: nextflow run tests/modules/kaiju/kaiju2table -entry test_kaiju_kaiju_single_end -c tests/config/nextflow.config
+  tags:
+    - kaiju
+    - kaiju/kaiju2table
+  files:
+    - path: output/kaiju/test.txt
+      md5sum: 0d9f8fd36fcf2888296ae12632c5f0a8
+    - path: output/kaiju/versions.yml