From ee04fc27377391c39cacd79641301f87af48cc4d Mon Sep 17 00:00:00 2001
From: JIANHONG OU <jianhong@users.noreply.github.com>
Date: Thu, 14 Apr 2022 12:56:42 -0400
Subject: [PATCH] add module motus_downloaddb

---
 modules/motus/downloaddb/main.nf              | 39 +++++++++++++++++++
 modules/motus/downloaddb/meta.yml             | 35 +++++++++++++++++
 tests/config/pytest_modules.yml               |  4 ++
 tests/modules/motus/downloaddb/main.nf        | 12 ++++++
 .../modules/motus/downloaddb/nextflow.config  |  5 +++
 tests/modules/motus/downloaddb/test.yml       |  9 +++++
 6 files changed, 104 insertions(+)
 create mode 100644 modules/motus/downloaddb/main.nf
 create mode 100644 modules/motus/downloaddb/meta.yml
 create mode 100644 tests/modules/motus/downloaddb/main.nf
 create mode 100644 tests/modules/motus/downloaddb/nextflow.config
 create mode 100644 tests/modules/motus/downloaddb/test.yml

diff --git a/modules/motus/downloaddb/main.nf b/modules/motus/downloaddb/main.nf
new file mode 100644
index 00000000..02e5c22d
--- /dev/null
+++ b/modules/motus/downloaddb/main.nf
@@ -0,0 +1,39 @@
+process MOTUS_DOWNLOADDB {
+    label 'process_low'
+
+    conda (params.enable_conda ? "bioconda::motus=3.0.1" : null)
+    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+        'https://depot.galaxyproject.org/singularity/motus:3.0.1--pyhdfd78af_0':
+        'quay.io/biocontainers/motus:3.0.1--pyhdfd78af_0' }"
+
+    input:
+    path motus_downloaddb
+
+    output:
+    path "db_mOTU"                , emit: db
+    path "versions.yml"           , emit: versions
+
+    when:
+    task.ext.when == null || task.ext.when
+
+    script:
+    def args = task.ext.args ?: ''
+    """
+    ## must copy file to working directory,
+    ## otherwise the reference_db will be download to bin folder
+    ## other than current directory
+    cp $motus_downloaddb ${motus_downloaddb.simpleName}_copy.py
+    python ${motus_downloaddb.simpleName}_copy.py \\
+        -t $task.cpus
+    ## clean up
+    rm ${motus_downloaddb.simpleName}_copy.py
+
+    ## mOTUs version number is not available from command line.
+    ## mOTUs save the version number in index database folder.
+    ## mOTUs will check the database version is same version as exec version.
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        mOTUs: \$(grep motus db_mOTU/db_mOTU_versions | sed 's/motus\\t//g')
+    END_VERSIONS
+    """
+}
diff --git a/modules/motus/downloaddb/meta.yml b/modules/motus/downloaddb/meta.yml
new file mode 100644
index 00000000..8557b2ed
--- /dev/null
+++ b/modules/motus/downloaddb/meta.yml
@@ -0,0 +1,35 @@
+name: "motus_downloaddb"
+description: Download the mOTUs database
+keywords:
+  - classify
+  - metagenomics
+  - fastq
+  - taxonomic profiling
+tools:
+  - "motus":
+      description: "The mOTU profiler is a computational tool that estimates relative taxonomic abundance of known and currently unknown microbial community members using metagenomic shotgun sequencing data."
+      homepage: "None"
+      documentation: "https://github.com/motu-tool/mOTUs/wiki"
+      tool_dev_url: "https://github.com/motu-tool/mOTUs"
+      doi: "10.1038/s41467-019-08844-4"
+      licence: "['GPL v3']"
+
+input:
+  - motus_downloaddb:
+      type: file
+      description: |
+        the mOTUs downloadDB source file
+      pattern: "*{.py}"
+
+output:
+  - versions:
+      type: file
+      description: File containing software versions
+      pattern: "versions.yml"
+  - db:
+      type: file
+      description: The mOTUs database
+      pattern: "db_mOTU"
+
+authors:
+  - "@jianhong"
diff --git a/tests/config/pytest_modules.yml b/tests/config/pytest_modules.yml
index cd4913cf..b11f5516 100644
--- a/tests/config/pytest_modules.yml
+++ b/tests/config/pytest_modules.yml
@@ -1194,6 +1194,10 @@ mosdepth:
   - modules/mosdepth/**
   - tests/modules/mosdepth/**
 
+motus/downloaddb:
+  - modules/motus/downloaddb/**
+  - tests/modules/motus/downloaddb/**
+
 msisensor/msi:
   - modules/msisensor/msi/**
   - tests/modules/msisensor/msi/**
diff --git a/tests/modules/motus/downloaddb/main.nf b/tests/modules/motus/downloaddb/main.nf
new file mode 100644
index 00000000..f7680ca9
--- /dev/null
+++ b/tests/modules/motus/downloaddb/main.nf
@@ -0,0 +1,12 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { MOTUS_DOWNLOADDB } from '../../../../modules/motus/downloaddb/main.nf'
+
+workflow test_motus_downloaddb {
+
+    input = file('https://raw.githubusercontent.com/motu-tool/mOTUs/master/motus/downloadDB.py')
+
+    MOTUS_DOWNLOADDB ( input )
+}
diff --git a/tests/modules/motus/downloaddb/nextflow.config b/tests/modules/motus/downloaddb/nextflow.config
new file mode 100644
index 00000000..50f50a7a
--- /dev/null
+++ b/tests/modules/motus/downloaddb/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/motus/downloaddb/test.yml b/tests/modules/motus/downloaddb/test.yml
new file mode 100644
index 00000000..ada5383a
--- /dev/null
+++ b/tests/modules/motus/downloaddb/test.yml
@@ -0,0 +1,9 @@
+- name: motus downloaddb test_motus_downloaddb
+  command: nextflow run tests/modules/motus/downloaddb -entry test_motus_downloaddb -c tests/config/nextflow.config
+  tags:
+    - motus
+    - motus/downloaddb
+  files:
+    - path: output/motus/db_mOTU/db_mOTU_versions
+    - path: output/motus/versions.yml
+      md5sum: b9b843b2435b01bb430ee8780b5c639e