feat: Add recombination entry

Signed-off-by: jvfe <[email protected]>
beiko-lab · Nov 7, 2023 · a31e488 · a31e488
1 parent 946837b
commit a31e488
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Showing 2 changed files with 69 additions and 1 deletion.
diff --git a/main.nf b/main.nf
@@ -39,7 +39,7 @@ include { QUALITYCHECK } from './workflows/arete'
 include { POPPUNK } from './workflows/arete'
 include { RUN_RSPR } from './workflows/arete'
 include { RUN_EVOLCCM } from './workflows/arete'
-
+include { RUN_RECOMBINATION } from './workflows/arete'
 
 //
 // WORKFLOW: Run main nf-core/arete analysis pipeline
@@ -77,6 +77,10 @@ workflow rspr {
 workflow evolccm {
     RUN_EVOLCCM()
 }
+
+workflow recombination {
+    RUN_RECOMBINATION()
+}
 /*
 ========================================================================================
     RUN ALL WORKFLOWS

diff --git a/workflows/arete.nf b/workflows/arete.nf
@@ -615,6 +615,70 @@ workflow RUN_EVOLCCM {
     )
 }
 
+workflow RUN_RECOMBINATION {
+    if (params.input_sample_table){ ch_input = file(params.input_sample_table) } else { exit 1, 'Input samplesheet not specified!' }
+    if (params.reference_genome) {
+        ch_reference_genome = file(params.reference_genome)
+        use_reference_genome = true
+        }
+    else {
+        ch_reference_genome = []
+        use_reference_genome = false
+    }
+    if (params.poppunk_model == null) { exit 1, 'A model must be specified with --poppunk_model in order to run PopPunk' }
+    ch_software_versions = Channel.empty()
+
+    ANNOTATION_INPUT_CHECK(ch_input)
+    ANNOTATION_INPUT_CHECK.out.genomes.set { assemblies }
+
+    CHECK_ASSEMBLIES(
+        assemblies,
+        ch_reference_genome,
+        use_reference_genome
+    )
+    ch_software_versions = ch_software_versions.mix(CHECK_ASSEMBLIES.out.assemblyqc_software)
+
+    if (params.apply_filtering) {
+        CHECK_ASSEMBLIES.out.assemblies
+            .set { assemblies }
+    }
+
+    RUN_POPPUNK(assemblies)
+    ch_software_versions = ch_software_versions.mix(RUN_POPPUNK.out.poppunk_version)
+
+
+    RECOMBINATION (
+        assemblies,
+        RUN_POPPUNK.out.clusters,
+        CHECK_ASSEMBLIES.out.quast_report
+    )
+
+    CUSTOM_DUMPSOFTWAREVERSIONS (
+        ch_software_versions.unique().collectFile(name: 'collated_versions.yml')
+    )
+
+    /*
+     * MODULE: MultiQC
+     */
+    workflow_summary    = WorkflowArete.paramsSummaryMultiqc(workflow, summary_params)
+    ch_workflow_summary = Channel.value(workflow_summary)
+
+    //Mix QUAST results into one report file
+    ch_multiqc_files = Channel.empty()
+    ch_multiqc_files = ch_multiqc_files.mix(ch_workflow_summary.collectFile(name: 'workflow_summary_mqc.yaml'))
+    ch_multiqc_files = ch_multiqc_files.mix(CUSTOM_DUMPSOFTWAREVERSIONS.out.mqc_yml.collect())
+    ch_multiqc_files = ch_multiqc_files.mix(CHECK_ASSEMBLIES.out.multiqc)
+
+    MULTIQC(
+        ch_multiqc_files.collect(),
+        ch_multiqc_config.collect().ifEmpty([]),
+        ch_multiqc_custom_config.collect().ifEmpty([]),
+        ch_multiqc_logo.collect().ifEmpty([])
+    )
+    multiqc_report       = MULTIQC.out.report.toList()
+    ch_software_versions = ch_software_versions.mix(MULTIQC.out.versions.ifEmpty(null))
+
+}
 /*
 ========================================================================================
     COMPLETION EMAIL AND SUMMARY