From a84f693479340e5ae13f97576d76c42c7320d4c2 Mon Sep 17 00:00:00 2001
From: "Thomas A. Christensen II" <25492070+MillironX@users.noreply.github.com>
Date: Tue, 14 Jun 2022 08:13:36 -0500
Subject: [PATCH 1/8] Install KRAKENTOOLS_KREPORT2KRONA module

---
 modules.json                                  |  3 ++
 .../modules/krakentools/kreport2krona/main.nf | 36 ++++++++++++++++
 .../krakentools/kreport2krona/meta.yml        | 41 +++++++++++++++++++
 3 files changed, 80 insertions(+)
 create mode 100644 modules/nf-core/modules/krakentools/kreport2krona/main.nf
 create mode 100644 modules/nf-core/modules/krakentools/kreport2krona/meta.yml

diff --git a/modules.json b/modules.json
index a8f5a57..b9d9dba 100644
--- a/modules.json
+++ b/modules.json
@@ -48,6 +48,9 @@
             "kraken2/kraken2": {
                 "git_sha": "abe025677cdd805cc93032341ab19885473c1a07"
             },
+            "krakentools/kreport2krona": {
+                "git_sha": "8b2a473f586bed003e72d2b183acc43fc0ddc422"
+            },
             "malt/run": {
                 "git_sha": "72b96f4e504eef673f2b5c13560a9d90b669129b"
             },
diff --git a/modules/nf-core/modules/krakentools/kreport2krona/main.nf b/modules/nf-core/modules/krakentools/kreport2krona/main.nf
new file mode 100644
index 0000000..3bf46ee
--- /dev/null
+++ b/modules/nf-core/modules/krakentools/kreport2krona/main.nf
@@ -0,0 +1,36 @@
+def VERSION = '1.2' // Version information not provided by tool on CLI
+
+process KRAKENTOOLS_KREPORT2KRONA {
+    tag "$meta.id"
+    label 'process_low'
+
+    conda (params.enable_conda ? "bioconda::krakentools=1.2" : null)
+    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+        'https://depot.galaxyproject.org/singularity/krakentools:1.2--pyh5e36f6f_0':
+        'quay.io/biocontainers/krakentools:1.2--pyh5e36f6f_0' }"
+
+    input:
+    tuple val(meta), path(kreport)
+
+    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}"
+    """
+    kreport2krona.py \\
+        -r ${kreport} \\
+        -o ${prefix}.txt \\
+        ${args}
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        kreport2krona.py: ${VERSION}
+    END_VERSIONS
+    """
+}
diff --git a/modules/nf-core/modules/krakentools/kreport2krona/meta.yml b/modules/nf-core/modules/krakentools/kreport2krona/meta.yml
new file mode 100644
index 0000000..2f8a163
--- /dev/null
+++ b/modules/nf-core/modules/krakentools/kreport2krona/meta.yml
@@ -0,0 +1,41 @@
+name: krakentools_kreport2krona
+description: Takes a Kraken report file and prints out a krona-compatible TEXT file
+keywords:
+  - kraken
+  - krona
+  - metagenomics
+  - visualization
+tools:
+  - krakentools:
+      description: KrakenTools is a suite of scripts to be used for post-analysis of Kraken/KrakenUniq/Kraken2/Bracken results. Please cite the relevant paper if using KrakenTools with any of the listed programs.
+      homepage: https://github.com/jenniferlu717/KrakenTools
+      licence: ["GPL v3"]
+
+input:
+  - meta:
+      type: map
+      description: |
+        Groovy Map containing sample information
+        e.g. [ id:'test', single_end:false ]
+  - kreport:
+      type: file
+      description: Kraken report
+      pattern: "*.{txt,kreport}"
+
+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"
+  - krona:
+      type: file
+      description: Krona text-based input file converted from Kraken report
+      pattern: "*.{txt,krona}"
+
+authors:
+  - "@MillironX"

From 87678c127bb5ed16c05f860ff2df59a7c4524f19 Mon Sep 17 00:00:00 2001
From: "Thomas A. Christensen II" <25492070+MillironX@users.noreply.github.com>
Date: Tue, 14 Jun 2022 08:23:47 -0500
Subject: [PATCH 2/8] Add KRONA_CLEANUP process module

---
 modules/local/krona_cleanup.nf | 40 ++++++++++++++++++++++++++++++++++
 1 file changed, 40 insertions(+)
 create mode 100644 modules/local/krona_cleanup.nf

diff --git a/modules/local/krona_cleanup.nf b/modules/local/krona_cleanup.nf
new file mode 100644
index 0000000..804cb69
--- /dev/null
+++ b/modules/local/krona_cleanup.nf
@@ -0,0 +1,40 @@
+process KRONA_CLEANUP {
+    tag "$meta.id"
+    label 'process_low'
+
+    conda (params.enable_conda ? "conda-forge::sed=4.7" : null)
+    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+        'https://containers.biocontainers.pro/s3/SingImgsRepo/biocontainers/v1.2.0_cv1/biocontainers_v1.2.0_cv1.img' :
+        'biocontainers/biocontainers:v1.2.0_cv1' }"
+
+    input:
+    tuple val(meta), path(krona, stageAs: 'uncleaned.krona.txt')
+
+    output:
+    tuple val(meta), path("*.txt"), emit: txt
+    path "versions.yml", emit: versions
+
+    when:
+    task.ext.when == null || task.ext.when
+
+    script:
+    def prefix = task.ext.prefix ?: "${meta.id}"
+    """
+    # Copy the file to a new name
+    cp ${krona} ${prefix}.txt
+
+    # Remove ugly 'x__' prefixes for each of the taxonomic levels
+    LEVELS=(d k p c o f g s)
+    for L in "\${LEVELS[@]}"; do
+        sed -i "s/\${L}__//g" ${prefix}.txt
+    done
+
+    # Remove underscores that are standing in place of spaces
+    sed -i "s/_/ /g" ${prefix}.txt
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        sed: \$(echo \$(sed --version 2>&1) | sed 's/^.*GNU sed) //; s/ .*\$//')
+    END_VERSIONS
+    """
+}

From 5da8d5b7418cc778284f64110f7fe721a29aa148 Mon Sep 17 00:00:00 2001
From: "Thomas A. Christensen II" <25492070+MillironX@users.noreply.github.com>
Date: Tue, 14 Jun 2022 08:27:42 -0500
Subject: [PATCH 3/8] Install KRONA_KTIMPORTTEXT

---
 modules.json                                  |  3 ++
 .../modules/krona/ktimporttext/main.nf        | 34 ++++++++++++++
 .../modules/krona/ktimporttext/meta.yml       | 47 +++++++++++++++++++
 3 files changed, 84 insertions(+)
 create mode 100644 modules/nf-core/modules/krona/ktimporttext/main.nf
 create mode 100644 modules/nf-core/modules/krona/ktimporttext/meta.yml

diff --git a/modules.json b/modules.json
index b9d9dba..4956cc8 100644
--- a/modules.json
+++ b/modules.json
@@ -51,6 +51,9 @@
             "krakentools/kreport2krona": {
                 "git_sha": "8b2a473f586bed003e72d2b183acc43fc0ddc422"
             },
+            "krona/ktimporttext": {
+                "git_sha": "cdefbec66999c0b49d8bfeea9d6f9d19056635a2"
+            },
             "malt/run": {
                 "git_sha": "72b96f4e504eef673f2b5c13560a9d90b669129b"
             },
diff --git a/modules/nf-core/modules/krona/ktimporttext/main.nf b/modules/nf-core/modules/krona/ktimporttext/main.nf
new file mode 100644
index 0000000..de0cfc2
--- /dev/null
+++ b/modules/nf-core/modules/krona/ktimporttext/main.nf
@@ -0,0 +1,34 @@
+process KRONA_KTIMPORTTEXT {
+    tag "$meta.id"
+    label 'process_low'
+
+    conda (params.enable_conda ? "bioconda::krona=2.8.1" : null)
+    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+        'https://depot.galaxyproject.org/singularity/krona:2.8.1--pl5321hdfd78af_1':
+        'quay.io/biocontainers/krona:2.8.1--pl5321hdfd78af_1' }"
+
+    input:
+    tuple val(meta), path(report)
+
+    output:
+    tuple val(meta), path ('*.html'), emit: html
+    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}"
+    """
+    ktImportText  \\
+        $args \\
+        -o ${prefix}.html \\
+        $report
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        krona: \$( echo \$(ktImportText 2>&1) | sed 's/^.*KronaTools //g; s/- ktImportText.*\$//g')
+    END_VERSIONS
+    """
+}
diff --git a/modules/nf-core/modules/krona/ktimporttext/meta.yml b/modules/nf-core/modules/krona/ktimporttext/meta.yml
new file mode 100644
index 0000000..a7108e0
--- /dev/null
+++ b/modules/nf-core/modules/krona/ktimporttext/meta.yml
@@ -0,0 +1,47 @@
+name: "krona_ktimporttext"
+description: Creates a Krona chart from text files listing quantities and lineages.
+keywords:
+  - plot
+  - taxonomy
+  - interactive
+  - html
+  - visualisation
+  - krona chart
+  - metagenomics
+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: http://manpages.ubuntu.com/manpages/impish/man1/ktImportTaxonomy.1.html
+      tool_dev_url: https://github.com/marbl/Krona
+      doi: 10.1186/1471-2105-12-385
+      licence: https://raw.githubusercontent.com/marbl/Krona/master/KronaTools/LICENSE.txt
+
+input:
+  - meta:
+      type: map
+      description: |
+        Groovy Map containing sample information
+        e.g. [ id:'test']
+  - report:
+      type: file
+      description: "Tab-delimited text file. Each line should be a number followed by a list of wedges to contribute to (starting from the highest level). If no wedges are listed (and just a quantity is given), it will contribute to the top level. If the same lineage is listed more than once, the values will be added. Quantities can be omitted if -q is specified. Lines beginning with '#' will be ignored."
+      pattern: "*.{txt}"
+
+output:
+  - meta:
+      type: map
+      description: |
+        Groovy Map containing sample information
+        e.g. [ id:'test' ]
+  - versions:
+      type: file
+      description: File containing software versions
+      pattern: "versions.yml"
+  - html:
+      type: file
+      description: A html file containing an interactive krona plot.
+      pattern: "*.{html}"
+
+authors:
+  - "@jianhong"

From a40a442178487dce25aa9f10109098976868a198 Mon Sep 17 00:00:00 2001
From: "Thomas A. Christensen II" <25492070+MillironX@users.noreply.github.com>
Date: Mon, 27 Jun 2022 08:22:47 -0500
Subject: [PATCH 4/8] Create VISUALIZATION_KRONA workflow to create Krona
 charts

---
 subworkflows/local/visualization_krona.nf | 55 +++++++++++++++++++++++
 1 file changed, 55 insertions(+)
 create mode 100644 subworkflows/local/visualization_krona.nf

diff --git a/subworkflows/local/visualization_krona.nf b/subworkflows/local/visualization_krona.nf
new file mode 100644
index 0000000..87db112
--- /dev/null
+++ b/subworkflows/local/visualization_krona.nf
@@ -0,0 +1,55 @@
+//
+// Create Krona visualizations
+//
+
+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:
+    profiles
+
+    main:
+    ch_krona_text = Channel.empty()
+    ch_krona_html = Channel.empty()
+    ch_versions = Channel.empty()
+
+    /*
+        Split profile results based on tool they come from
+    */
+    ch_input_profiles = profiles
+        .branch {
+            kraken2: it[0]['tool'] == 'kraken2'
+            unknown: true
+        }
+
+    /*
+        Convert Kraken2 formatted reports into Krona text files
+    */
+    ch_kraken_reports = ch_input_profiles.kraken2
+    KRAKENTOOLS_KREPORT2KRONA ( ch_kraken_reports )
+    ch_krona_text = ch_krona_text.mix( KRAKENTOOLS_KREPORT2KRONA.out.txt )
+    ch_versions = ch_versions.mix( KRAKENTOOLS_KREPORT2KRONA.out.versions.first() )
+
+    /*
+        Remove taxonomy level annotations from the Krona text files
+    */
+    KRONA_CLEANUP( ch_krona_text )
+    ch_cleaned_krona_text = KRONA_CLEANUP.out.txt
+    ch_versions = ch_versions.mix( KRONA_CLEANUP.out.versions.first() )
+
+    /*
+        Convert Krona text files into html Krona visualizations
+    */
+    ch_krona_text_for_import = ch_cleaned_krona_text
+        .map{[[id: it[0]['db_name']], it[1]]}
+        .groupTuple()
+    KRONA_KTIMPORTTEXT( ch_krona_text_for_import )
+    ch_krona_html = ch_krona_html.mix( KRONA_KTIMPORTTEXT.out.html )
+    ch_versions = ch_versions.mix( KRONA_KTIMPORTTEXT.out.versions.first() )
+
+    emit:
+    html = ch_krona_html
+    versions = ch_versions
+}

From ad9bc4b7e9d2ec09bcd8fd53a6ea67f86a1e2f73 Mon Sep 17 00:00:00 2001
From: "Thomas A. Christensen II" <25492070+MillironX@users.noreply.github.com>
Date: Mon, 20 Jun 2022 09:03:47 -0500
Subject: [PATCH 5/8] Add the visualization workflow to the main workflow

---
 workflows/taxprofiler.nf | 7 +++++++
 1 file changed, 7 insertions(+)

diff --git a/workflows/taxprofiler.nf b/workflows/taxprofiler.nf
index f29a366..313790c 100644
--- a/workflows/taxprofiler.nf
+++ b/workflows/taxprofiler.nf
@@ -62,6 +62,7 @@ include { SHORTREAD_HOSTREMOVAL         } from '../subworkflows/local/shortread_
 include { LONGREAD_HOSTREMOVAL          } from '../subworkflows/local/longread_hostremoval'
 include { SHORTREAD_COMPLEXITYFILTERING } from '../subworkflows/local/shortread_complexityfiltering'
 include { PROFILING                     } from '../subworkflows/local/profiling'
+include { VISUALIZATION_KRONA           } from '../subworkflows/local/visualization_krona'
 
 /*
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
@@ -209,6 +210,12 @@ workflow TAXPROFILER {
     PROFILING ( ch_reads_runmerged, DB_CHECK.out.dbs )
     ch_versions = ch_versions.mix( PROFILING.out.versions )
 
+    /*
+        SUBWORKFLOW: VISUALIZATION_KRONA
+    */
+    VISUALIZATION_KRONA ( PROFILING.out.profiles )
+    ch_versions = ch_versions.mix( VISUALIZATION_KRONA.out.versions )
+
     /*
         MODULE: MultiQC
     */

From 0e8edd5b2f097e2c7a6c1b7a39fb5a19671395ce Mon Sep 17 00:00:00 2001
From: "Thomas A. Christensen II" <25492070+MillironX@users.noreply.github.com>
Date: Tue, 14 Jun 2022 08:48:16 -0500
Subject: [PATCH 6/8] Add output configuration for Kraken Krona chart

---
 conf/modules.config | 8 ++++++++
 1 file changed, 8 insertions(+)

diff --git a/conf/modules.config b/conf/modules.config
index 46320cf..f9d0329 100644
--- a/conf/modules.config
+++ b/conf/modules.config
@@ -293,6 +293,14 @@ process {
         ]
     }
 
+    withName: KRONA_KTIMPORTTEXT {
+        publishDir = [
+            path: { "${params.outdir}/krona" },
+            mode: params.publish_dir_mode,
+            pattern: '*.{html}'
+        ]
+    }
+
     withName: METAPHLAN3 {
         ext.args = { "${meta.db_params}" }
         ext.prefix = params.perform_runmerging ? { "${meta.id}-${meta.db_name}" } : { "${meta.id}-${meta.run_accession}-${meta.db_name}" }

From 15ac8b39fa8a2e6b490d05d69e1634f48eb35117 Mon Sep 17 00:00:00 2001
From: "Thomas A. Christensen II" <25492070+MillironX@users.noreply.github.com>
Date: Tue, 14 Jun 2022 10:54:10 -0500
Subject: [PATCH 7/8] Add citation for Krona

---
 CITATIONS.md | 4 ++++
 1 file changed, 4 insertions(+)

diff --git a/CITATIONS.md b/CITATIONS.md
index 8044658..1ce4ec2 100644
--- a/CITATIONS.md
+++ b/CITATIONS.md
@@ -36,6 +36,10 @@
 
   > Wood, Derrick E., Jennifer Lu, and Ben Langmead. 2019. Improved Metagenomic Analysis with Kraken 2. Genome Biology 20 (1): 257. doi: 10.1186/s13059-019-1891-0.
 
+- [Krona](https://doi.org/10.1186/1471-2105-12-385)
+
+  > Ondov, Brian D., Nicholas H. Bergman, and Adam M. Phillippy. 2011. Interactive metagenomic visualization in a Web browser. BMC Bioinformatics 12 (1): 385. doi: 10.1186/1471-2105-12-385.
+
 - [MALT](https://doi.org/10.1038/s41559-017-0446-6)
 
   > Vågene, Åshild J., Alexander Herbig, Michael G. Campana, Nelly M. Robles García, Christina Warinner, Susanna Sabin, Maria A. Spyrou, et al. 2018. Salmonella Enterica Genomes from Victims of a Major Sixteenth-Century Epidemic in Mexico. Nature Ecology & Evolution 2 (3): 520-28. doi: 10.1038/s41559-017-0446-6.

From 18284e6e32d1090336f37fd024bb5703cc80503b Mon Sep 17 00:00:00 2001
From: "Thomas A. Christensen II" <25492070+MillironX@users.noreply.github.com>
Date: Mon, 27 Jun 2022 08:41:42 -0500
Subject: [PATCH 8/8] Add run_krona option to allow skipping Krona chart
 creation

---
 conf/test.config                 | 1 +
 conf/test_nopreprocessing.config | 1 +
 nextflow.config                  | 3 +++
 nextflow_schema.json             | 3 +++
 workflows/taxprofiler.nf         | 6 ++++--
 5 files changed, 12 insertions(+), 2 deletions(-)

diff --git a/conf/test.config b/conf/test.config
index e9fa62e..04dfb4d 100644
--- a/conf/test.config
+++ b/conf/test.config
@@ -37,6 +37,7 @@ params {
     run_metaphlan3                        = true
     run_centrifuge                        = true
     run_diamond                           = true
+    run_krona                             = true
     malt_save_reads                       = true
     kraken2_save_reads                    = true
     centrifuge_save_reads                 = true
diff --git a/conf/test_nopreprocessing.config b/conf/test_nopreprocessing.config
index 60cdde8..92fd29d 100644
--- a/conf/test_nopreprocessing.config
+++ b/conf/test_nopreprocessing.config
@@ -37,6 +37,7 @@ params {
     run_metaphlan3                        = true
     run_centrifuge                        = true
     run_diamond                           = true
+    run_krona                             = true
 }
 
 process {
diff --git a/nextflow.config b/nextflow.config
index 73fd0b3..29c87cd 100644
--- a/nextflow.config
+++ b/nextflow.config
@@ -125,6 +125,9 @@ params {
     run_diamond                = false
     diamond_output_format      = 'tsv'  // TSV is only format with taxonomic information apparently
     diamond_save_reads         = false // this will override default diamond output format so no taxonomic profile is generated!
+
+    // krona
+    run_krona                  = false
 }
 
 // Load base.config by default for all pipelines
diff --git a/nextflow_schema.json b/nextflow_schema.json
index 2c00348..682bf2f 100644
--- a/nextflow_schema.json
+++ b/nextflow_schema.json
@@ -433,6 +433,9 @@
         },
         "diamond_save_reads": {
             "type": "boolean"
+        },
+        "run_krona": {
+            "type": "boolean"
         }
     }
 }
diff --git a/workflows/taxprofiler.nf b/workflows/taxprofiler.nf
index 313790c..f7ef07a 100644
--- a/workflows/taxprofiler.nf
+++ b/workflows/taxprofiler.nf
@@ -213,8 +213,10 @@ workflow TAXPROFILER {
     /*
         SUBWORKFLOW: VISUALIZATION_KRONA
     */
-    VISUALIZATION_KRONA ( PROFILING.out.profiles )
-    ch_versions = ch_versions.mix( VISUALIZATION_KRONA.out.versions )
+    if ( params.run_krona ) {
+        VISUALIZATION_KRONA ( PROFILING.out.profiles )
+        ch_versions = ch_versions.mix( VISUALIZATION_KRONA.out.versions )
+    }
 
     /*
         MODULE: MultiQC