Merge remote-tracking branch 'origin/dev' into malt-to-krona

conf/modules.config

@@ -351,6 +351,10 @@ process {
         ]
     }
 
+    withName: KAIJU_KAIJU2KRONA {
+        ext.args = '-v -u'
+    }
+
     withName: DIAMOND_BLASTX {
         ext.args = { "${meta.db_params}" }
         ext.prefix = params.perform_runmerging ? { "${meta.id}-${meta.db_name}" } : { "${meta.id}-${meta.run_accession}-${meta.db_name}" }

modules.json

@@ -42,6 +42,9 @@
             "kaiju/kaiju": {
                 "git_sha": "8856f127c58f6af479128be8b8df4d42e442ddbe"
             },
+            "kaiju/kaiju2krona": {
+                "git_sha": "2f0b19240430de6807b1232e6d9d0e8084e8a28f"
+            },
             "kaiju/kaiju2table": {
                 "git_sha": "538dbac98ba9c8f799536cd5a617195501439457"
             },

modules/nf-core/modules/kaiju/kaiju2krona/main.nf

@@ -0,0 +1,39 @@
+process KAIJU_KAIJU2KRONA {
+    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--h5b5514e_1' }"
+
+    input:
+    tuple val(meta), path(tsv)
+    path(db)
+
+    output:
+    tuple val(meta), path("*.txt"), emit: txt
+    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"`
+    dbnames=`find -L ${db} -name "*names.dmp"`
+    kaiju2krona \\
+        $args \\
+        -t \$dbnodes \\
+        -n \$dbnames \\
+        -i ${tsv} \\
+        -o ${prefix}.txt
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        kaiju: \$(echo \$( kaiju -h 2>&1 | sed -n 1p | sed 's/^.*Kaiju //' ))
+    END_VERSIONS
+    """
+}

modules/nf-core/modules/kaiju/kaiju2krona/meta.yml

@@ -0,0 +1,44 @@
+name: kaiju_kaiju2krona
+description: Convert Kaiju's tab-separated output file into a tab-separated text file which can be imported into Krona.
+keywords:
+  - taxonomy
+  - visualisation
+  - krona chart
+  - 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 ]
+  - tsv:
+      type: file
+      description: Kaiju tab-separated output file
+      pattern: "*.{tsv,txt}"
+
+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"
+  - txt:
+      type: file
+      description: Krona text-based input file converted from Kaiju report
+      pattern: "*.{txt,krona}"
+
+authors:
+  - "@MillironX"

subworkflows/local/profiling.nf

@@ -21,7 +21,8 @@ workflow PROFILING {
     main:
     ch_versions             = Channel.empty()
     ch_multiqc_files        = Channel.empty()
-    ch_raw_profiles    = Channel.empty()
+    ch_raw_classifications  = Channel.empty()
+    ch_raw_profiles         = Channel.empty()
 
 /*
         COMBINE READS WITH POSSIBLE DATABASES
@@ -108,9 +109,10 @@ workflow PROFILING {
                                 }
 
         MEGAN_RMA2INFO (ch_maltrun_for_megan, params.malt_generate_megansummary )
-        ch_multiqc_files   = ch_multiqc_files.mix( MALT_RUN.out.log.collect{it[1]}.ifEmpty([])  )
-        ch_versions        = ch_versions.mix( MALT_RUN.out.versions.first(), MEGAN_RMA2INFO.out.versions.first() )
-        ch_raw_profiles    = ch_raw_profiles.mix( MEGAN_RMA2INFO.out.txt )
+        ch_multiqc_files       = ch_multiqc_files.mix( MALT_RUN.out.log.collect{it[1]}.ifEmpty([])  )
+        ch_versions            = ch_versions.mix( MALT_RUN.out.versions.first(), MEGAN_RMA2INFO.out.versions.first() )
+        ch_raw_classifications = ch_raw_classifications.mix( ch_maltrun_for_megan )
+        ch_raw_profiles        = ch_raw_profiles.mix( MEGAN_RMA2INFO.out.txt )
 
     }
 
@@ -124,9 +126,10 @@ workflow PROFILING {
                                 }
 
         KRAKEN2_KRAKEN2 ( ch_input_for_kraken2.reads, ch_input_for_kraken2.db, params.kraken2_save_reads, params.kraken2_save_readclassification )
-        ch_multiqc_files   = ch_multiqc_files.mix( KRAKEN2_KRAKEN2.out.report.collect{it[1]}.ifEmpty([])  )
-        ch_versions        = ch_versions.mix( KRAKEN2_KRAKEN2.out.versions.first() )
-        ch_raw_profiles    = ch_raw_profiles.mix( KRAKEN2_KRAKEN2.out.report )
+        ch_multiqc_files       = ch_multiqc_files.mix( KRAKEN2_KRAKEN2.out.report.collect{it[1]}.ifEmpty([])  )
+        ch_versions            = ch_versions.mix( KRAKEN2_KRAKEN2.out.versions.first() )
+        ch_raw_classifications = ch_raw_classifications.mix( KRAKEN2_KRAKEN2.out.classified_reads_assignment )
+        ch_raw_profiles        = ch_raw_profiles.mix( KRAKEN2_KRAKEN2.out.report )
 
     }
 
@@ -145,8 +148,9 @@ workflow PROFILING {
 
         CENTRIFUGE_CENTRIFUGE ( ch_input_for_centrifuge.reads, ch_input_for_centrifuge.db, params.centrifuge_save_reads, params.centrifuge_save_reads, params.centrifuge_save_reads  )
         CENTRIFUGE_KREPORT (CENTRIFUGE_CENTRIFUGE.out.results, ch_input_for_centrifuge.db)
-        ch_versions        = ch_versions.mix( CENTRIFUGE_CENTRIFUGE.out.versions.first() )
-        ch_raw_profiles    = ch_raw_profiles.mix( CENTRIFUGE_KREPORT.out.kreport )
+        ch_versions            = ch_versions.mix( CENTRIFUGE_CENTRIFUGE.out.versions.first() )
+        ch_raw_classifications = ch_raw_classifications.mix( CENTRIFUGE_CENTRIFUGE.out.results )
+        ch_raw_profiles        = ch_raw_profiles.mix( CENTRIFUGE_KREPORT.out.kreport )
 
     }
 
@@ -182,6 +186,7 @@ workflow PROFILING {
         KAIJU_KAIJU2TABLE (KAIJU_KAIJU.out.results, ch_input_for_kaiju.db, params.kaiju_taxon_name)
         ch_multiqc_files = ch_multiqc_files.mix( KAIJU_KAIJU2TABLE.out.summary.collect{it[1]}.ifEmpty([])  )
         ch_versions = ch_versions.mix( KAIJU_KAIJU.out.versions.first() )
+        ch_raw_classifications = ch_raw_classifications.mix( KAIJU_KAIJU.out.results )
         ch_raw_profiles = ch_raw_profiles.mix( KAIJU_KAIJU2TABLE.out.summary )
 
     }
@@ -206,8 +211,8 @@ workflow PROFILING {
     }
 
     emit:
-    profiles = ch_raw_profiles    // channel: [ val(meta), [ reads ] ] - should be text files or biom
-    versions = ch_versions          // channel: [ versions.yml ]
-    mqc      = ch_multiqc_files
+    classifications = ch_raw_classifications
+    profiles        = ch_raw_profiles    // channel: [ val(meta), [ reads ] ] - should be text files or biom
+    versions        = ch_versions          // channel: [ versions.yml ]
+    mqc             = ch_multiqc_files
 }
-

subworkflows/local/visualization_krona.nf

@@ -2,13 +2,16 @@
 // Create Krona visualizations
 //
 
+include { KAIJU_KAIJU2KRONA         } from '../../modules/nf-core/modules/kaiju/kaiju2krona/main'
 include { KRAKENTOOLS_KREPORT2KRONA } from '../../modules/nf-core/modules/krakentools/kreport2krona/main'
 include { KRONA_CLEANUP             } from '../../modules/local/krona_cleanup'
 include { KRONA_KTIMPORTTEXT        } from '../../modules/nf-core/modules/krona/ktimporttext/main'
 
 workflow VISUALIZATION_KRONA {
     take:
+    classifications
     profiles
+    databases
 
     main:
     ch_krona_text = Channel.empty()
@@ -24,6 +27,11 @@ workflow VISUALIZATION_KRONA {
             kraken2: it[0]['tool'] == 'kraken2'
             unknown: true
         }
+    ch_input_classifications = classifications
+        .branch {
+            kaiju: it[0]['tool'] == 'kaiju'
+            unknown: true
+        }
 
     /*
         Convert Kraken2 formatted reports into Krona text files
@@ -34,6 +42,25 @@ workflow VISUALIZATION_KRONA {
     ch_krona_text = ch_krona_text.mix( KRAKENTOOLS_KREPORT2KRONA.out.txt )
     ch_versions = ch_versions.mix( KRAKENTOOLS_KREPORT2KRONA.out.versions.first() )
 
+    /*
+        Combine Kaiju profiles with their databases
+    */
+    ch_input_for_kaiju2krona = ch_input_classifications.kaiju
+        .map{ [it[0]['db_name'], it[0], it[1]] }
+        .combine( databases.map{ [it[0]['db_name'], it[1]] }, by: 0 )
+        .multiMap{
+            it ->
+                profiles: [it[1], it[2]]
+                db: it[3]
+        }
+
+    /*
+        Convert Kaiju formatted reports into Krona text files
+    */
+    KAIJU_KAIJU2KRONA( ch_input_for_kaiju2krona.profiles, ch_input_for_kaiju2krona.db )
+    ch_krona_text = ch_krona_text.mix( KAIJU_KAIJU2KRONA.out.txt )
+    ch_versions = ch_versions.mix( KAIJU_KAIJU2KRONA.out.versions.first() )
+
     /*
         Remove taxonomy level annotations from the Krona text files
     */

workflows/taxprofiler.nf

@@ -214,7 +214,7 @@ workflow TAXPROFILER {
         SUBWORKFLOW: VISUALIZATION_KRONA
     */
     if ( params.run_krona ) {
-        VISUALIZATION_KRONA ( PROFILING.out.profiles )
+        VISUALIZATION_KRONA ( PROFILING.out.classifications, PROFILING.out.profiles, DB_CHECK.out.dbs )
         ch_versions = ch_versions.mix( VISUALIZATION_KRONA.out.versions )
     }