Merge pull request #1601 from carpanz/firstbranch

Non-breaking changes to krona modules: update kronadb module name, inclusion of ext.args, legacy module maintained

modules/krona/kronadb/main.nf

@@ -18,7 +18,9 @@ process KRONA_KRONADB {
     script:
     def args = task.ext.args ?: ''
     """
-    ktUpdateTaxonomy.sh taxonomy
+    ktUpdateTaxonomy.sh \\
+        $args \\
+        taxonomy/
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":

modules/krona/ktimporttaxonomy/main.nf

@@ -23,7 +23,10 @@ process KRONA_KTIMPORTTAXONOMY {
     script:
     def args = task.ext.args ?: ''
     """
-    ktImportTaxonomy "$report" -tax taxonomy
+    ktImportTaxonomy \\
+        $args \\
+        -tax taxonomy/ \\
+        "$report"
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":

modules/krona/ktimporttaxonomy/meta.yml

@@ -23,8 +23,11 @@ input:
         Groovy Map containing sample information
         e.g. [ id:'test']
   - database:
-      type: path
+      type: file
-      description: "Path to the taxonomy database downloaded by krona/kronadb"
+      description: |
+        Path to the taxonomy database .tab file downloaded by krona/ktUpdateTaxonomy
+        The file will be saved under a folder named "taxonomy" as "taxonomy/taxonomy.tab".
+        The parent folder will be passed as argument to ktImportTaxonomy.
   - report:
       type: file
       description: "A tab-delimited file with taxonomy IDs and (optionally) query IDs, magnitudes, and scores.  Query IDs are taken from column 1, taxonomy IDs from column 2, and scores from column 3.  Lines beginning with # will be ignored."

modules/krona/ktupdatetaxonomy/main.nf

@@ -0,0 +1,30 @@
+def VERSION='2.7.1' // Version information not provided by tool on CLI
+
+process KRONA_KTUPDATETAXONOMY {
+    label 'process_low'
+
+    conda (params.enable_conda ? "bioconda::krona=2.7.1" : null)
+    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+        'https://depot.galaxyproject.org/singularity/krona:2.7.1--pl526_5' :
+        'quay.io/biocontainers/krona:2.7.1--pl526_5' }"
+
+    output:
+    path 'taxonomy/taxonomy.tab', emit: db
+    path "versions.yml"         , emit: versions
+
+    when:
+    task.ext.when == null || task.ext.when
+
+    script:
+    def args = task.ext.args ?: ''
+    """
+    ktUpdateTaxonomy.sh \\
+        $args \\
+        taxonomy/
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        krona: $VERSION
+    END_VERSIONS
+    """
+}

modules/krona/ktupdatetaxonomy/meta.yml

@@ -0,0 +1,31 @@
+name: krona_ktupdatetaxonomy
+description: KronaTools Update Taxonomy downloads a taxonomy database
+keywords:
+  - database
+  - taxonomy
+  - krona
+  - visualisation
+tools:
+  - krona:
+      description: Krona Tools is a set of scripts to create Krona charts from several Bioinformatics tools as well as from text and XML files.
+      homepage: https://github.com/marbl/Krona/wiki/KronaTools
+      documentation: https://github.com/marbl/Krona/wiki/Installing
+      tool_dev_url:
+      doi: https://doi.org/10.1186/1471-2105-12-385
+      licence:
+
+input:
+  - none: There is no input. This module downloads a pre-built taxonomy database for use with Krona Tools.
+
+output:
+  - versions:
+      type: file
+      description: File containing software versions
+      pattern: "versions.yml"
+  - db:
+      type: file
+      description: A TAB separated file that contains a taxonomy database.
+      pattern: "*.{tab}"
+
+authors:
+  - "@mjakobs"

tests/config/pytest_modules.yml

@@ -1058,6 +1058,10 @@ krona/kronadb:
   - modules/krona/kronadb/**
   - tests/modules/krona/kronadb/**
 
+krona/ktupdatetaxonomy:
+  - modules/krona/ktupdatetaxonomy/**
+  - tests/modules/krona/ktupdatetaxonomy/**
+
 krona/ktimporttaxonomy:
   - modules/krona/ktimporttaxonomy/**
   - tests/modules/krona/ktimporttaxonomy/**

tests/config/test_data.config

@@ -111,7 +111,9 @@ params {
                 test_sequencing_summary                        = "${test_data_dir}/genomics/sarscov2/nanopore/sequencing_summary/test.sequencing_summary.txt"
             }
             'metagenome' {
+                classified_reads_assignment                    = "${test_data_dir}/genomics/sarscov2/metagenome/test_1.kraken2.reads.txt"
                 kraken_report                                  = "${test_data_dir}/genomics/sarscov2/metagenome/test_1.kraken2.report.txt"
+                krona_taxonomy                                 = "${test_data_dir}/genomics/sarscov2/metagenome/krona_taxonomy.tab"
             }
         }
         'homo_sapiens' {

tests/modules/krona/ktimporttaxonomy/main.nf

@@ -2,15 +2,27 @@
 
 nextflow.enable.dsl = 2
 
-include { KRONA_KTIMPORTTAXONOMY } from '../../../../modules/krona/ktimporttaxonomy/main.nf'
+include { KRONA_KTIMPORTTAXONOMY as KRONA_KTIMPORTTAXONOMY_READS  } from '../../../../modules/krona/ktimporttaxonomy/main.nf'
+include { KRONA_KTIMPORTTAXONOMY as KRONA_KTIMPORTTAXONOMY_REPORT } from '../../../../modules/krona/ktimporttaxonomy/main.nf'
 
-workflow test_krona_ktimporttaxonomy {
+workflow test_krona_ktimporttaxonomy_reads {
 
     input = [
         [ id:'test', single_end:false ], // meta map
-        file(params.test_data['generic']['txt']['hello'], checkIfExists: true)
+        file(params.test_data['sarscov2']['metagenome']['classified_reads_assignment'], checkIfExists: true)
     ]
-    taxonomy = file(params.test_data['generic']['txt']['hello'], checkIfExists: true)
+    taxonomy = file(params.test_data['sarscov2']['metagenome']['krona_taxonomy'], checkIfExists: true)
 
-    KRONA_KTIMPORTTAXONOMY ( input, taxonomy )
+    KRONA_KTIMPORTTAXONOMY_READS ( input, taxonomy )
+}
+
+workflow test_krona_ktimporttaxonomy_report {
+
+    input = [
+        [ id:'test', single_end:false ], // meta map
+        file(params.test_data['sarscov2']['metagenome']['kraken_report'], checkIfExists: true)
+    ]
+    taxonomy = file(params.test_data['sarscov2']['metagenome']['krona_taxonomy'], checkIfExists: true)
+
+    KRONA_KTIMPORTTAXONOMY_REPORT ( input, taxonomy )
 }

tests/modules/krona/ktimporttaxonomy/nextflow.config

@@ -2,4 +2,12 @@ process {
 
     publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
 
+    withName: KRONA_KTIMPORTTAXONOMY_READS {
+        ext.args = '-t 3'
+    }
+
+    withName: KRONA_KTIMPORTTAXONOMY_REPORT {
+        ext.args = '-m 3 -t 5'
+    }
+
 }

tests/modules/krona/ktimporttaxonomy/test.yml

@@ -1,9 +1,23 @@
-- name: krona ktimporttaxonomy test_krona_ktimporttaxonomy
+- name: krona ktimporttaxonomy test_krona_ktimporttaxonomy_reads
-  command: nextflow run ./tests/modules/krona/ktimporttaxonomy -entry test_krona_ktimporttaxonomy -c ./tests/config/nextflow.config -c ./tests/modules/krona/ktimporttaxonomy/nextflow.config
+  command: nextflow run tests/modules/krona/ktimporttaxonomy -entry test_krona_ktimporttaxonomy_reads -c tests/config/nextflow.config
   tags:
-    - krona/ktimporttaxonomy
     - krona
+    - krona/ktimporttaxonomy
   files:
     - path: output/krona/taxonomy.krona.html
       contains:
         - "DOCTYPE html PUBLIC"
+    - path: output/krona/versions.yml
+      md5sum: 660a8c151191bf4c63bd96db2c7fe503
+
+- name: krona ktimporttaxonomy test_krona_ktimporttaxonomy_report
+  command: nextflow run tests/modules/krona/ktimporttaxonomy -entry test_krona_ktimporttaxonomy_report -c tests/config/nextflow.config
+  tags:
+    - krona
+    - krona/ktimporttaxonomy
+  files:
+    - path: output/krona/taxonomy.krona.html
+      contains:
+        - "DOCTYPE html PUBLIC"
+    - path: output/krona/versions.yml
+      md5sum: 8a593c16bb2d4132638fb0fc342fe2b7

tests/modules/krona/ktupdatetaxonomy/main.nf

@@ -0,0 +1,9 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { KRONA_KTUPDATETAXONOMY } from '../../../../modules/krona/ktupdatetaxonomy/main.nf'
+
+workflow test_krona_ktupdatetaxonomy {
+    KRONA_KTUPDATETAXONOMY ( )
+}

tests/modules/krona/ktupdatetaxonomy/nextflow.config

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

tests/modules/krona/ktupdatetaxonomy/test.yml

@@ -0,0 +1,7 @@
+- name: krona ktupdatetaxonomy test_krona_ktupdatetaxonomy
+  command: nextflow run ./tests/modules/krona/ktupdatetaxonomy -entry test_krona_ktupdatetaxonomy -c ./tests/config/nextflow.config -c ./tests/modules/krona/ktupdatetaxonomy/nextflow.config
+  tags:
+    - krona
+    - krona/ktupdatetaxonomy
+  files:
+    - path: output/krona/taxonomy/taxonomy.tab