Add subworkflows for ensemblvep and snpeff (#1124)

* greatly simplify syntax

* feat: add subworkflows to annotate (+ bgzip/tabix index) with ensemblvep and snpeff

* feat: get versions from all tools

* add commented infor for new annotation modules

subworkflows/nf-core/annotation_ensemblvep/main.nf

@@ -0,0 +1,26 @@
+//
+// Run VEP to annotate VCF files
+//
+
+include { ENSEMBLVEP                                } from '../../../modules/ensemblvep/main'
+include { TABIX_BGZIPTABIX as ANNOTATION_BGZIPTABIX } from '../../../modules/tabix/bgziptabix/main'
+
+workflow ANNOTATION_ENSEMBLVEP {
+    take:
+    vcf               // channel: [ val(meta), vcf ]
+    vep_genome        //   value: which genome
+    vep_species       //   value: which species
+    vep_cache_version //   value: which cache version
+    vep_cache         //    path: path_to_vep_cache (optionnal)
+
+    main:
+    ENSEMBLVEP(vcf, vep_genome, vep_species, vep_cache_version, vep_cache)
+    ANNOTATION_BGZIPTABIX(ENSEMBLVEP.out.vcf)
+
+    ch_versions = ENSEMBLVEP.out.versions.first().mix(ANNOTATION_BGZIPTABIX.out.versions.first())
+
+    emit:
+    vcf_tbi  = ANNOTATION_BGZIPTABIX.out.gz_tbi // channel: [ val(meta), vcf.gz, vcf.gz.tbi ]
+    reports  = ENSEMBLVEP.out.report            //    path: *.html
+    versions = ch_versions                      //    path: versions.yml
+}

subworkflows/nf-core/annotation_ensemblvep/meta.yml

@@ -0,0 +1,29 @@
+name: annotation_ensemblvep
+description: |
+  Perform annotation with ensemblvep and bgzip + tabix index the resulting VCF file
+keywords:
+  - ensemblvep
+modules:
+  - ensemblvep
+  - tabix/bgziptabix
+input:
+  - meta:
+      type: map
+      description: |
+        Groovy Map containing sample information
+        e.g. [ id:'test' ]
+  - input:
+      type: vcf
+      description: list containing one vcf file
+      pattern: "[ *.{vcf,vcf.gz} ]"
+output:
+  - versions:
+      type: file
+      description: File containing software versions
+      pattern: 'versions.yml'
+  - vcf_tbi:
+      type: file
+      description: Compressed vcf file + tabix index
+      pattern: "[ *{.vcf.gz,vcf.gz.tbi} ]"
+authors:
+  - '@maxulysse'

subworkflows/nf-core/annotation_snpeff/main.nf

@@ -0,0 +1,23 @@
+//
+// Run SNPEFF to annotate VCF files
+//
+
+include { SNPEFF                                    } from '../../../modules/snpeff/main'
+include { TABIX_BGZIPTABIX as ANNOTATION_BGZIPTABIX } from '../../../modules/tabix/bgziptabix/main'
+
+workflow ANNOTATION_SNPEFF {
+    take:
+    vcf            // channel: [ val(meta), vcf ]
+    snpeff_db      //   value: version of db to use
+    snpeff_cache   //    path: path_to_snpeff_cache (optionnal)
+
+    main:
+    SNPEFF(vcf, snpeff_db, snpeff_cache)
+    ANNOTATION_BGZIPTABIX(SNPEFF.out.vcf)
+    ch_versions = SNPEFF.out.versions.first().mix(ANNOTATION_BGZIPTABIX.out.versions.first())
+
+    emit:
+    vcf_tbi  = ANNOTATION_BGZIPTABIX.out.gz_tbi // channel: [ val(meta), vcf.gz, vcf.gz.tbi ]
+    reports  = SNPEFF.out.report                //    path: *.html
+    versions = ch_versions                      //    path: versions.yml
+}

subworkflows/nf-core/annotation_snpeff/meta.yml

@@ -0,0 +1,29 @@
+name: annotation_snpeff
+description: |
+  Perform annotation with snpeff and bgzip + tabix index the resulting VCF file
+keywords:
+  - snpeff
+modules:
+  - snpeff
+  - tabix/bgziptabix
+input:
+  - meta:
+      type: map
+      description: |
+        Groovy Map containing sample information
+        e.g. [ id:'test' ]
+  - input:
+      type: vcf
+      description: list containing one vcf file
+      pattern: "[ *.{vcf,vcf.gz} ]"
+output:
+  - versions:
+      type: file
+      description: File containing software versions
+      pattern: 'versions.yml'
+  - vcf_tbi:
+      type: file
+      description: Compressed vcf file + tabix index
+      pattern: "[ *{.vcf.gz,vcf.gz.tbi} ]"
+authors:
+  - '@maxulysse'

tests/config/pytest_modules.yml

@@ -1451,6 +1451,19 @@ yara/mapper:
   - modules/yara/mapper/**
   - tests/modules/yara/mapper/**
 
+# subworkflows/align_bowtie2:
+#   - subworkflows/nf-core/align_bowtie2/**
+#   - tests/subworkflows/nf-core/align_bowtie2/**
+#   - *subworkflows_bam_sort_samtools
+
+# subworkflows/annotation_ensemblvep: &subworkflows_annotation_ensemblvep
+#   - subworkflows/nf-core/annotation_ensemblvep/**
+#   - tests/subworkflows/nf-core/annotation_ensemblvep/**
+
+# subworkflows/annotation_snpeff: &subworkflows_annotation_snpeff
+#   - subworkflows/nf-core/annotation_snpeff/**
+#   - tests/subworkflows/nf-core/annotation_snpeff/**
+
 # subworkflows/bam_stats_samtools: &subworkflows_bam_stats_samtools
 #   - subworkflows/nf-core/bam_stats_samtools/**
 #   - tests/subworkflows/nf-core/bam_stats_samtools/**
@@ -1462,17 +1475,6 @@ yara/mapper:
 #   - *samtools_index
 #   - *subworkflows_bam_stats_samtools
 
-# subworkflows/align_bowtie2:
-#   - subworkflows/nf-core/align_bowtie2/**
-#   - tests/subworkflows/nf-core/align_bowtie2/**
-#   - *subworkflows_bam_sort_samtools
-
-# subworkflows/sra_fastq:
-#   - subworkflows/nf-core/sra_fastq/**
-#   - tests/subworkflows/nf-core/sra_fastq/**
-#   - *sratools_fasterqdump
-#   - *sratools_prefetch
-
 # subworkflows/gatk_create_som_pon:
 #   - subworkflows/nf-core/gatk_create_som_pon/**
 #   - tests/subworkflows/nf-core/gatk_create_som_pon/**
@@ -1495,3 +1497,9 @@ yara/mapper:
 #   - *gatk4_getpileupsummaries
 #   - *gatk4_calculatecontamination
 #   - *gatk4_filtermutectcalls
+
+# subworkflows/sra_fastq:
+#   - subworkflows/nf-core/sra_fastq/**
+#   - tests/subworkflows/nf-core/sra_fastq/**
+#   - *sratools_fasterqdump
+#   - *sratools_prefetch

tests/subworkflows/nf-core/annotation_ensemblvep/main.nf

@@ -0,0 +1,14 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { ANNOTATION_ENSEMBLVEP } from '../../../../subworkflows/nf-core/annotation_ensemblvep/main'
+
+workflow annotation_ensemblvep {
+    input = [
+        [ id:'test' ], // meta map
+        file(params.test_data['sarscov2']['illumina']['test_vcf'], checkIfExists: true)
+    ]
+
+    ANNOTATION_ENSEMBLVEP ( input, "WBcel235", "caenorhabditis_elegans", "104", [] )
+}

tests/subworkflows/nf-core/annotation_ensemblvep/nextflow.config

@@ -0,0 +1,14 @@
+process {
+
+    publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
+
+    withName: ENSEMBLVEP {
+        container  = 'nfcore/vep:104.3.WBcel235'
+        publishDir = [ enabled: false ]
+    }
+
+    withName: ANNOTATION_BGZIPTABIX {
+        ext.prefix = { "${meta.id}_VEP.ann.vcf" }
+    }
+
+}

tests/subworkflows/nf-core/annotation_ensemblvep/test.yml

@@ -0,0 +1,7 @@
+- name: ensemblvep annotation_ensemblvep
+  command: nextflow run ./tests/subworkflows/nf-core/annotation_ensemblvep -entry annotation_ensemblvep -c ./tests/config/nextflow.config -c ./tests/subworkflows/nf-core/annotation_ensemblvep/nextflow.config
+  tags:
+    - annotation_ensemblvep
+  files:
+    - path: output/annotation/test_VEP.ann.vcf.gz
+    - path: output/annotation/test_VEP.ann.vcf.gz.tbi

tests/subworkflows/nf-core/annotation_snpeff/main.nf

@@ -0,0 +1,14 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { ANNOTATION_SNPEFF } from '../../../../subworkflows/nf-core/annotation_snpeff/main'
+
+workflow annotation_snpeff {
+    input = [
+        [ id:'test' ], // meta map
+        file(params.test_data['sarscov2']['illumina']['test_vcf'], checkIfExists: true)
+    ]
+
+    ANNOTATION_SNPEFF ( input, "WBcel235.99", [] )
+}

tests/subworkflows/nf-core/annotation_snpeff/nextflow.config

@@ -0,0 +1,14 @@
+process {
+
+    publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
+
+    withName: SNPEFF {
+        container  = 'nfcore/snpeff:5.0.WBcel235'
+        publishDir = [ enabled: false ]
+    }
+
+    withName: ANNOTATION_BGZIPTABIX {
+        ext.prefix = { "${meta.id}_snpEff.ann.vcf" }
+    }
+
+}

tests/subworkflows/nf-core/annotation_snpeff/test.yml

@@ -0,0 +1,7 @@
+- name: snpeff annotation_snpeff
+  command: nextflow run ./tests/subworkflows/nf-core/annotation_snpeff -entry annotation_snpeff -c ./tests/config/nextflow.config -c ./tests/subworkflows/nf-core/annotation_snpeff/nextflow.config
+  tags:
+    - annotation_snpeff
+  files:
+    - path: output/annotation/test_snpEff.ann.vcf.gz
+    - path: output/annotation/test_snpEff.ann.vcf.gz.tbi