refactor: Make assemblyqc (quast) run by default

beiko-lab · Sep 4, 2023 · 6fe9f63 · 6fe9f63
1 parent eeb6f24
commit 6fe9f63
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Showing 3 changed files with 29 additions and 44 deletions.
diff --git a/subworkflows/local/assembly.nf b/subworkflows/local/assembly.nf
@@ -76,34 +76,18 @@ workflow ASSEMBLE_SHORTREADS{
         /*
         * MODULE: Assembly
         */
-
         // unicycler can accept short reads and long reads. For now, shortread only: Pass empty list for optional file args
         ch_unicycler_input = FASTP.out.reads.map { it -> it + [[]]}
         UNICYCLER(ch_unicycler_input)
         ch_software_versions = ch_software_versions.mix(UNICYCLER.out.versions.first().ifEmpty(null))
 
         // Unicycler outputs not quite right for QUAST. Need to re-arrange
         // pattern adapted from nf-core/bacass
-        ch_assembly = Channel.empty()
-        ch_assembly = ch_assembly.mix(UNICYCLER.out.scaffolds.dump(tag: 'unicycler'))
-        ch_assembly
-            .map { meta, fasta -> fasta.toString() }
-            .collectFile(name:'assemblies.txt', newLine: true)
-            .set { ch_to_quast }
-        /*
-        * Module: Evaluate Assembly
-        */
-        QUAST(ch_to_quast, ch_reference_genome, [], use_reference_genome, false)
-        ch_software_versions = ch_software_versions.mix(QUAST.out.versions.ifEmpty(null))
-
         ch_multiqc_files = ch_multiqc_files.mix(RAW_FASTQC.out.zip.collect{it[1]}.ifEmpty([]))
         ch_multiqc_files = ch_multiqc_files.mix(TRIM_FASTQC.out.zip.collect{it[1]}.ifEmpty([]))
-        ch_multiqc_files = ch_multiqc_files.mix(QUAST.out.tsv.collect())
 
     emit:
-        assemblies = ch_assembly
         scaffolds = UNICYCLER.out.scaffolds
-        quast_report = QUAST.out.transposed_report
         assembly_software = ch_software_versions
         multiqc = ch_multiqc_files
 

diff --git a/subworkflows/local/assemblyqc.nf b/subworkflows/local/assemblyqc.nf
@@ -6,7 +6,6 @@ include { CHECKM_LINEAGEWF } from '../../modules/nf-core/checkm/lineagewf/main'
 workflow CHECK_ASSEMBLIES {
     take:
         assemblies
-        krakendb_cache
         reference_genome
         use_reference_genome
 
@@ -15,22 +14,6 @@ workflow CHECK_ASSEMBLIES {
         ch_multiqc_files = Channel.empty()
         ch_software_versions = Channel.empty()
 
-        ///*
-        // * MODULE: Run Kraken2
-        // */
-        if (!params.skip_kraken) {
-            if(krakendb_cache) {
-                GET_DB_CACHE(krakendb_cache)
-                KRAKEN2_RUN(assemblies, GET_DB_CACHE.out.minikraken, false, true)
-            } else {
-                KRAKEN2_DB()
-                KRAKEN2_RUN(assemblies, KRAKEN2_DB.out.minikraken, false, true)
-            }
-
-            ch_software_versions = ch_software_versions.mix(KRAKEN2_RUN.out.versions.first().ifEmpty(null))
-            ch_multiqc_files = ch_multiqc_files.mix(KRAKEN2_RUN.out.report.collect{it[1]}.ifEmpty([]))
-        }
-
         fasta_extension = assemblies.map{ id, path -> path.getExtension() }.first()
 
         /*
@@ -41,20 +24,23 @@ workflow CHECK_ASSEMBLIES {
         /*
         * Module: QUAST quality check
         */
-        // Need to reformat assembly channel for QUAST
-        // pattern adapted from nf-core/bacass
-        ch_assembly = Channel.empty()
-        ch_assembly = ch_assembly.mix(assemblies.dump(tag: 'assembly'))
-        ch_assembly
-            .map { meta, fasta -> fasta } //QUAST doesn't take the meta tag
+        assemblies
+            .map { meta, fasta -> fasta.toString() }
             .collectFile(name:'assemblies.txt', newLine: true)
-            .set { ch_to_quast }
-        QUAST(ch_to_quast, reference_genome, [], use_reference_genome, false)
+            .set { quast_input }
+
+        QUAST (
+            quast_input,
+            reference_genome,
+            [],
+            use_reference_genome,
+            false
+        )
         ch_software_versions = ch_software_versions.mix(QUAST.out.versions.ifEmpty(null))
-
         ch_multiqc_files = ch_multiqc_files.mix(QUAST.out.tsv.collect())
 
     emit:
+        quast_report = QUAST.out.transposed_report
         assemblyqc_software = ch_software_versions
         multiqc = ch_multiqc_files
 }
diff --git a/workflows/arete.nf b/workflows/arete.nf
@@ -146,6 +146,13 @@ workflow ARETE {
 
     ASSEMBLE_SHORTREADS.out.scaffolds.set { assemblies }
 
+    CHECK_ASSEMBLIES (
+        assemblies,
+        ch_reference_genome,
+        use_reference_genome
+    )
+    ch_software_versions = ch_software_versions.mix(CHECK_ASSEMBLIES.out.assemblyqc_software)
+
     if (db_cache) {
         /////////////////// ANNOTATION ///////////////////////////
         ANNOTATE_ASSEMBLIES(
@@ -198,7 +205,7 @@ workflow ARETE {
             RECOMBINATION (
                 assemblies,
                 RUN_POPPUNK.out.clusters,
-                ASSEMBLE_SHORTREADS.out.quast_report
+                CHECK_ASSEMBLIES.out.quast_report
             )
         }
     }
@@ -240,6 +247,7 @@ workflow ARETE {
     ch_multiqc_files = ch_multiqc_files.mix(ch_workflow_summary.collectFile(name: 'workflow_summary_mqc.yaml'))
     ch_multiqc_files = ch_multiqc_files.mix(GET_SOFTWARE_VERSIONS.out.yaml.collect())
     ch_multiqc_files = ch_multiqc_files.mix(ASSEMBLE_SHORTREADS.out.multiqc)
+    ch_multiqc_files = ch_multiqc_files.mix(CHECK_ASSEMBLIES.out.multiqc)
     ch_multiqc_files = ch_multiqc_files.mix(ANNOTATE_ASSEMBLIES.out.multiqc)
 
     MULTIQC(
@@ -285,6 +293,13 @@ workflow ASSEMBLY {
 
     ch_software_versions = ch_software_versions.mix(ASSEMBLE_SHORTREADS.out.assembly_software)
 
+    CHECK_ASSEMBLIES(
+        ASSEMBLE_SHORTREADS.out.scaffolds,
+        ch_reference_genome,
+        use_reference_genome
+    )
+    ch_software_versions = ch_software_versions.mix(CHECK_ASSEMBLIES.out.assemblyqc_software)
+
     // Get unique list of files containing version information
     ch_software_versions
         .map { it -> if (it) [ it.baseName, it ] }
@@ -300,6 +315,7 @@ workflow ASSEMBLY {
     ch_workflow_summary = Channel.value(workflow_summary)
 
     ch_multiqc_files = Channel.empty()
+    ch_multiqc_files = ch_multiqc_files.mix(CHECK_ASSEMBLIES.out.multiqc)
     ch_multiqc_files = ch_multiqc_files.mix(ch_workflow_summary.collectFile(name: 'workflow_summary_mqc.yaml'))
     ch_multiqc_files = ch_multiqc_files.mix(ASSEMBLE_SHORTREADS.out.multiqc)
 
@@ -480,7 +496,6 @@ workflow QUALITYCHECK {
 
     CHECK_ASSEMBLIES(
         ANNOTATION_INPUT_CHECK.out.genomes,
-        db_cache,
         ch_reference_genome,
         use_reference_genome
     )