feat: Implement microview into taxonomy subwf (#33)

* feat: Add MicroView module * refactor: Allow mixing kaiju and kraken results * chore: Remove hidden default logo param
dalmolingroup · Mar 31, 2024 · 86ab63f · 86ab63f
1 parent 6ab04ad
commit 86ab63f
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Showing 7 changed files with 74 additions and 6 deletions.
diff --git a/conf/modules.config b/conf/modules.config
@@ -75,6 +75,13 @@ process {
         ]
     }
 
+    withName: MICROVIEW {
+        publishDir = [
+            path: { "${params.outdir}/taxonomy/microview" },
+            mode: params.publish_dir_mode,
+            saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
+        ]
+    }
 
     withName: MEGAHIT {
         publishDir = [

diff --git a/docs/params.md b/docs/params.md
@@ -24,6 +24,7 @@ Choose to skip pipeline steps
 | `skip_alignment` | Skip alignment | `boolean` |  |  |  |
 | `skip_functional` | Skip functional annotation | `boolean` |  |  |  |
 | `skip_host_removal` | Skip host removal | `boolean` |  |  |  |
+| `skip_microview` | Skip MicroView report | `boolean` |  |  |  |
 
 ## Decontamination
 

diff --git a/modules/local/microview.nf b/modules/local/microview.nf
@@ -0,0 +1,43 @@
+process MICROVIEW {
+    tag 'report'
+    label 'process_low'
+
+    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+        'docker://docker.io/jvfe/microview:v0.10.0':
+        'docker.io/jvfe/microview:v0.10.0' }"
+
+    input:
+    path reports
+
+    output:
+    path "microview_report.html", emit: report
+    path "versions.yml"         , emit: versions
+
+    when:
+    task.ext.when == null || task.ext.when
+
+    script:
+    def args = task.ext.args ?: ''
+    """
+    microview \\
+        --taxonomy . \\
+        --output microview_report.html
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        MicroView: \$(microview --version | sed 's/.*version \\([0-9.]\\+\\).*/\\1/')
+    END_VERSIONS
+    """
+
+    stub:
+    def args = task.ext.args ?: ''
+
+    """
+    touch microview_report.html
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        MicroView: \$(microview --version | sed 's/.*version \\([0-9.]\\+\\).*/\\1/')
+    END_VERSIONS
+    """
+}
diff --git a/nextflow.config b/nextflow.config
@@ -47,6 +47,7 @@ params {
     skip_classification        = false
     skip_functional            = false
     skip_alignment             = false
+    skip_microview             = false
 
     // MultiQC options
     multiqc_config             = null

diff --git a/nextflow_schema.json b/nextflow_schema.json
@@ -74,6 +74,11 @@
                     "type": "boolean",
                     "description": "Skip host removal",
                     "fa_icon": "fab fa-ioxhost"
+                },
+                "skip_microview": {
+                    "type": "boolean",
+                    "fa_icon": "fas fa-glasses",
+                    "description": "Skip MicroView report"
                 }
             },
             "fa_icon": "fas fa-angle-double-right"

diff --git a/subworkflows/local/taxonomy.nf b/subworkflows/local/taxonomy.nf
@@ -6,6 +6,8 @@ include { KAIJU_KAIJU2TABLE } from '../../modules/nf-core/kaiju/kaiju2table/main
 include { KAIJU_KAIJU2KRONA } from '../../modules/nf-core/kaiju/kaiju2krona/main'
 include { KRONA_KTIMPORTTEXT } from '../../modules/nf-core/krona/ktimporttext/main'
 
+include { MICROVIEW } from '../../modules/local/microview.nf'
+
 workflow TAXONOMY {
     take:
     reads
@@ -14,6 +16,8 @@ workflow TAXONOMY {
 
     main:
 
+    tax_report = Channel.empty()
+    krona_input = Channel.empty()
     ch_versions = Channel.empty()
 
     if (params.run_kaiju) {
@@ -33,10 +37,10 @@ workflow TAXONOMY {
             "species"
         )
 
-        KAIJU_KAIJU2TABLE.out.summary.set { tax_report }
+        tax_report = tax_report.mix(KAIJU_KAIJU2TABLE.out.summary)
 
         KAIJU_KAIJU2KRONA (kaiju_out, kaiju_db_files)
-        KAIJU_KAIJU2KRONA.out.txt.set { krona_input }
+        krona_input = krona_input.mix(KAIJU_KAIJU2KRONA.out.txt)
         ch_versions = ch_versions.mix(KAIJU_KAIJU2KRONA.out.versions)
     }
 
@@ -47,17 +51,24 @@ workflow TAXONOMY {
             false,
             false
         )
-        KRAKEN2_KRAKEN2.out.report.set { tax_report }
+        tax_report = tax_report.mix(KRAKEN2_KRAKEN2.out.report)
         ch_versions = ch_versions.mix(KRAKEN2_KRAKEN2.out.versions.first())
 
         KRAKENTOOLS_KREPORT2KRONA (
-            tax_report
+            KRAKEN2_KRAKEN2.out.report
         )
-        KRAKENTOOLS_KREPORT2KRONA.out.txt.set { krona_input }
+        krona_input = krona_input.mix(KRAKENTOOLS_KREPORT2KRONA.out.txt)
         ch_versions = ch_versions.mix(KRAKENTOOLS_KREPORT2KRONA.out.versions.first())
     }
 
 
+    if (!params.skip_microview) {
+        MICROVIEW (
+            tax_report.collect{it[1]}
+        )
+        ch_versions = ch_versions.mix(MICROVIEW.out.versions)
+    }
+
     KRONA_KTIMPORTTEXT (krona_input)
     ch_versions = ch_versions.mix(KRONA_KTIMPORTTEXT.out.versions)
 

diff --git a/workflows/euryale.nf b/workflows/euryale.nf
@@ -37,6 +37,7 @@ ch_multiqc_custom_methods_description = params.multiqc_methods_description ? fil
 // MODULES
 //
 include { FASTX_COLLAPSER } from '../modules/local/fastx_toolkit/collapser'
+include { MICROVIEW } from '../modules/local/microview.nf'
 
 //
 // SUBWORKFLOW: Consisting of a mix of local and nf-core/modules
@@ -167,7 +168,6 @@ workflow EURYALE {
         ch_multiqc_files = ch_multiqc_files.mix(TAXONOMY.out.tax_report.collect{it[1]}.ifEmpty([]))
     }
 
-
     if (!params.skip_functional && !params.skip_alignment) {
         FUNCTIONAL (
             alignments,