From d1a7dd2c7259132d138b4b7b93c48cbc3287641c Mon Sep 17 00:00:00 2001
From: "Thomas A. Christensen II" <25492070+MillironX@users.noreply.github.com>
Date: Thu, 9 Jun 2022 08:54:31 -0500
Subject: [PATCH] Add tests for kreport2krona

---
 tests/config/pytest_modules.yml               |  4 ++++
 .../modules/krakentools/kreport2krona/main.nf | 20 +++++++++++++++++++
 .../krakentools/kreport2krona/nextflow.config |  5 +++++
 .../krakentools/kreport2krona/test.yml        |  8 ++++++++
 4 files changed, 37 insertions(+)
 create mode 100644 tests/modules/krakentools/kreport2krona/main.nf
 create mode 100644 tests/modules/krakentools/kreport2krona/nextflow.config
 create mode 100644 tests/modules/krakentools/kreport2krona/test.yml

diff --git a/tests/config/pytest_modules.yml b/tests/config/pytest_modules.yml
index 578d8252..7999940e 100644
--- a/tests/config/pytest_modules.yml
+++ b/tests/config/pytest_modules.yml
@@ -1146,6 +1146,10 @@ kraken2/kraken2:
   - modules/untar/**
   - tests/modules/kraken2/kraken2/**
 
+krakentools/kreport2krona:
+  - modules/krakentools/kreport2krona/**
+  - tests/modules/krakentools/kreport2krona/**
+
 krona/kronadb:
   - modules/krona/kronadb/**
   - tests/modules/krona/kronadb/**
diff --git a/tests/modules/krakentools/kreport2krona/main.nf b/tests/modules/krakentools/kreport2krona/main.nf
new file mode 100644
index 00000000..c9c626fd
--- /dev/null
+++ b/tests/modules/krakentools/kreport2krona/main.nf
@@ -0,0 +1,20 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { UNTAR } from '../../../../modules/untar/main'
+include { KRAKEN2_KRAKEN2 } from '../../../../modules/kraken2/kraken2/main'
+include { KRAKENTOOLS_KREPORT2KRONA } from '../../../../modules/krakentools/kreport2krona/main'
+
+workflow test_krakentools_kreport2krona {
+
+    input = Channel.of([ [ id:'test', single_end:false ], // meta map
+              [ file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true),
+                file(params.test_data['sarscov2']['illumina']['test_2_fastq_gz'], checkIfExists: true) ]
+            ])
+    db    = [ [], file(params.test_data['sarscov2']['genome']['kraken2_tar_gz'], checkIfExists: true) ]
+
+    UNTAR ( db )
+    KRAKEN2_KRAKEN2 ( input, UNTAR.out.untar.map{ it[1] }, false, false )
+    KRAKENTOOLS_KREPORT2KRONA ( KRAKEN2_KRAKEN2.out.report )
+}
diff --git a/tests/modules/krakentools/kreport2krona/nextflow.config b/tests/modules/krakentools/kreport2krona/nextflow.config
new file mode 100644
index 00000000..50f50a7a
--- /dev/null
+++ b/tests/modules/krakentools/kreport2krona/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/krakentools/kreport2krona/test.yml b/tests/modules/krakentools/kreport2krona/test.yml
new file mode 100644
index 00000000..6525e915
--- /dev/null
+++ b/tests/modules/krakentools/kreport2krona/test.yml
@@ -0,0 +1,8 @@
+- name: krakentools kreport2krona test_krakentools_kreport2krona
+  command: nextflow run ./tests/modules/krakentools/kreport2krona -entry test_krakentools_kreport2krona -c ./tests/config/nextflow.config  -c ./tests/modules/krakentools/kreport2krona/nextflow.config
+  tags:
+    - krakentools/kreport2krona
+    - krakentools
+  files:
+    - path: output/krakentools/test.txt
+      md5sum: c89a9db7acbdba9dea0fe246bcaa85c1