added pirate

nf-core · Jul 13, 2023 · 4f44a00 · 4f44a00
1 parent b61c831
commit 4f44a00
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Showing 7 changed files with 133 additions and 12 deletions.
diff --git a/modules.json b/modules.json
@@ -75,6 +75,11 @@
                         "git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
                         "installed_by": ["modules"]
                     },
+                    "pirate": {
+                        "branch": "master",
+                        "git_sha": "911696ea0b62df80e900ef244d7867d177971f73",
+                        "installed_by": ["modules"]
+                    },
                     "quast": {
                         "branch": "master",
                         "git_sha": "911696ea0b62df80e900ef244d7867d177971f73",

diff --git a/modules/nf-core/pirate/main.nf b/modules/nf-core/pirate/main.nf
diff --git a/modules/nf-core/pirate/meta.yml b/modules/nf-core/pirate/meta.yml
diff --git a/subworkflows/local/bacteriapipeline.nf b/subworkflows/local/bacteriapipeline.nf
@@ -4,6 +4,7 @@ include { ALIGN_READS_TO_REF     } from './align_reads_to_ref'
 include { CALL_VARIANTS          } from './call_variants'
 include { VARIANT_CALLING_REPORT } from './variant_calling_report'
 include { GENOME_ASSEMBLY        } from './genome_assembly'
+include { CORE_GENOME_PHYLOGENY  } from './core_genome_phylogeny'                     
 
 workflow BACTERIAPIPELINE {
 
@@ -38,17 +39,21 @@ workflow BACTERIAPIPELINE {
     )
     ch_versions = ch_versions.mix(CALL_VARIANTS.out.versions)       
 
-    VARIANT_CALLING_REPORT (
-        CALL_VARIANTS.out.vcf,
-        ch_samplesheet
-    )
-    ch_versions = ch_versions.mix(VARIANT_CALLING_REPORT.out.versions)       
+    //VARIANT_CALLING_REPORT (
+    //    CALL_VARIANTS.out.vcf,
+    //    ch_samplesheet
+    //)
+    //ch_versions = ch_versions.mix(VARIANT_CALLING_REPORT.out.versions)       
 
     GENOME_ASSEMBLY (
         ch_reads
         .join(ch_reference)
     )
     ch_versions = ch_versions.mix(GENOME_ASSEMBLY.out.versions)
+
+    CORE_GENOME_PHYLOGENY (
+        GENOME_ASSEMBLY.out.gff.join(ch_reference)
+    )
 
     emit:
     picard_dict  = MAKE_REFERENCE_INDEX.out.picard_dict

diff --git a/subworkflows/local/core_genome_phylogeny.nf b/subworkflows/local/core_genome_phylogeny.nf
@@ -0,0 +1,26 @@
+include { PIRATE         } from '../../modules/nf-core/pirate/main'
+include { SAMTOOLS_FAIDX } from '../../modules/nf-core/samtools/faidx/main'
+
+workflow CORE_GENOME_PHYLOGENY {
+
+    take:
+    ch_input // [ val(meta), file(gff), val(ref_meta), file(reference) ]
+
+    main:
+
+    ch_versions = Channel.empty()
+
+    // group samples by reference genome                                        
+    ch_gff_grouped = ch_input                                                   
+        .groupTuple(by: 2)                                                      
+        .map { [it[2], it[1]] } // remove redundant reference genome paths
+
+    PIRATE ( ch_gff_grouped )
+    ch_versions = ch_versions.mix(PIRATE.out.versions.first())
+
+    emit:
+    pirate_aln      = PIRATE.out.aln        // channel: [ ref_meta, align_fasta ]
+
+    versions = ch_versions                     // channel: [ versions.yml ]
+}
+
diff --git a/subworkflows/local/eukaryotepipeline.nf b/subworkflows/local/eukaryotepipeline.nf
@@ -36,11 +36,11 @@ workflow EUKARYOTEPIPELINE {
     )
     ch_versions = ch_versions.mix(CALL_VARIANTS.out.versions)       
 
-    VARIANT_CALLING_REPORT (
-        CALL_VARIANTS.out.vcf,
-        ch_samplesheet
-    )
-    ch_versions = ch_versions.mix(VARIANT_CALLING_REPORT.out.versions)       
+    //VARIANT_CALLING_REPORT (
+    //    CALL_VARIANTS.out.vcf,
+    //    ch_samplesheet
+    //)
+    //ch_versions = ch_versions.mix(VARIANT_CALLING_REPORT.out.versions)       
 
     emit:
     picard_dict  = MAKE_REFERENCE_INDEX.out.picard_dict

diff --git a/subworkflows/local/genome_assembly.nf b/subworkflows/local/genome_assembly.nf
@@ -44,14 +44,16 @@ workflow GENOME_ASSEMBLY {
 
     ch_bakta_db = Channel.value("$projectDir/assets/bakta_db/db-light")
     BAKTA_BAKTA (
-        SPADES.out.scaffolds, // Genome assembly
+        FILTER_ASSEMBLY.out.filtered, // Genome assembly
         ch_bakta_db, // Bakta database
         [], // proteins (optional)
         [] // prodigal_tf (optional)
     )
 
     emit:
-    reads    = FASTP.out.reads           // channel: [ val(meta), [ fastq_1, fastq_2 ] ]
+    reads     = FASTP.out.reads           // channel: [ val(meta), [ fastq_1, fastq_2 ] ]
+    gff       = BAKTA_BAKTA.out.gff
+    scaffolds = FILTER_ASSEMBLY.out.filtered
 
     versions = ch_versions                     // channel: [ versions.yml ]
 }