Add tests for kreport2krona

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/**

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 )
+}

tests/modules/krakentools/kreport2krona/nextflow.config

@@ -0,0 +1,5 @@
+process {
+
+    publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
+    
+}

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