update svdb to version 2.5.2 (#1390)

* update svdb version and tests

* update link

modules/svdb/merge/main.nf

@@ -2,10 +2,10 @@ process SVDB_MERGE {
     tag "$meta.id"
     label 'process_medium'
 
-    conda (params.enable_conda ? "bioconda::svdb=2.5.0" : null)
+    conda (params.enable_conda ? "bioconda::svdb=2.5.2" : null)
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/svdb:2.5.0--py39hcbe4a3b_0':
+        'https://depot.galaxyproject.org/singularity/svdb:2.5.2--py39h5371cbf_0':
-        'quay.io/biocontainers/svdb:2.5.0--py39hcbe4a3b_0' }"
+        'quay.io/biocontainers/svdb:2.5.2--py39h5371cbf_0' }"
 
     input:
     tuple val(meta), path(vcfs)

modules/svdb/query/main.nf

@@ -2,36 +2,73 @@ process SVDB_QUERY {
     tag "$meta.id"
     label 'process_medium'
 
-    conda (params.enable_conda ? "bioconda::svdb=2.5.0" : null)
+    conda (params.enable_conda ? "bioconda::svdb=2.5.2" : null)
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/svdb:2.5.0--py39hcbe4a3b_0':
+        'https://depot.galaxyproject.org/singularity/svdb:2.5.2--py39h5371cbf_0':
-        'quay.io/biocontainers/svdb:2.5.0--py39hcbe4a3b_0' }"
+        'quay.io/biocontainers/svdb:2.5.2--py39h5371cbf_0' }"
 
     input:
     tuple val(meta), path(vcf)
-    path (vcf_db)
+    val(in_occs)
+    val(in_frqs)
+    val(out_occs)
+    val(out_frqs)
+    path (vcf_dbs)
 
     output:
-    tuple val(meta), path("*_ann_svdbq.vcf"), emit: vcf
+    tuple val(meta), path("*_query.vcf"), emit: vcf
     path "versions.yml"                     , emit: versions
 
     when:
     task.ext.when == null || task.ext.when
 
     script:
-    def args = task.ext.args ?: ''
+    def args    = task.ext.args ?: ''
-    def prefix = task.ext.prefix ?: "${meta.id}"
+    def prefix  = task.ext.prefix ?: "${meta.id}"
+    def in_occ  = ""
+    def in_frq  = ""
+    def out_occ = ""
+    def out_frq = ""
+    if (in_occs) {
+        in_occ  = "--in_occ ${in_occs.join(',')}"
+    }
+    if (in_frqs) {
+        in_frq  = "--in_frq ${in_frqs.join(',')}"
+    }
+    if (out_occs) {
+        out_occ = "--out_occ ${out_occs.join(',')}"
+    }
+    if (out_frqs) {
+        out_frq = "--out_frq ${out_frqs.join(',')}"
+    }
+
     """
     svdb \\
         --query \\
+        $in_occ \\
+        $in_frq \\
+        $out_occ \\
+        $out_frq \\
         $args \\
-        --db $vcf_db \\
+        --db ${vcf_dbs.join(',')} \\
         --query_vcf $vcf \\
-        >${prefix}_ann_svdbq.vcf
+        --prefix ${prefix}
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
         svdb: \$( echo \$(svdb) | head -1 | sed 's/usage: SVDB-\\([0-9]\\.[0-9]\\.[0-9]\\).*/\\1/' )
     END_VERSIONS
     """
+
+    stub:
+    def prefix = task.ext.prefix ?: "${meta.id}"
+    """
+    touch ${prefix}_query.vcf
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        svdb: \$( echo \$(svdb) | head -1 | sed 's/usage: SVDB-\\([0-9]\\.[0-9]\\.[0-9]\\).*/\\1/' )
+    END_VERSIONS
+    """
+
 }

modules/svdb/query/meta.yml

@@ -15,6 +15,12 @@ input:
       description: |
         Groovy Map containing sample information
         e.g. [ id:'test', single_end:false ]
+  - in_occs:
+      type: list
+      description: A list of allele count tags
+  - in_frqs:
+      type: list
+      description: A list of allele frequency tags
   - vcf:
       type: file
       description: query vcf file
@@ -34,10 +40,16 @@ output:
       type: file
       description: File containing software versions
       pattern: "versions.yml"
+  - out_occs:
+      type: list
+      description: A list of allele count tags
+  - out_frqs:
+      type: list
+      description: A list of allele frequency tags
   - vcf:
       type: file
       description: Annotated output VCF file
-      pattern: "*_ann_svdbq.vcf"
+      pattern: "*_query.vcf"
 
 authors:
   - "@ramprasadn"

tests/config/test_data.config

@@ -140,6 +140,7 @@ params {
                 syntheticvcf_short_vcf_gz_tbi                  = "${test_data_dir}/genomics/homo_sapiens/genome/vcf/syntheticvcf_short.vcf.gz.tbi"
                 syntheticvcf_short_score                       = "${test_data_dir}/genomics/homo_sapiens/genome/vcf/syntheticvcf_short.score"
                 gnomad_r2_1_1_sv_vcf_gz                        = "${test_data_dir}/genomics/homo_sapiens/genome/vcf/gnomAD.r2.1.1-sv.vcf.gz"
+                gnomad2_r2_1_1_sv_vcf_gz                       = "${test_data_dir}/genomics/homo_sapiens/genome/vcf/gnomAD2.r2.1.1-sv.vcf.gz"
 
                 hapmap_3_3_hg38_21_vcf_gz                      = "${test_data_dir}/genomics/homo_sapiens/genome/chr21/germlineresources/hapmap_3.3.hg38.vcf.gz"
                 hapmap_3_3_hg38_21_vcf_gz_tbi                  = "${test_data_dir}/genomics/homo_sapiens/genome/chr21/germlineresources/hapmap_3.3.hg38.vcf.gz.tbi"

tests/modules/svdb/query/main.nf

@@ -14,5 +14,29 @@ workflow test_svdb_query {
                 file(params.test_data['homo_sapiens']['genome']['gnomad_r2_1_1_sv_vcf_gz'], checkIfExists: true)
             ]
 
-    SVDB_QUERY ( input, vcf_db )
+    in_occs = ['AC']
+    in_frqs = ['AF']
+    out_occs = ['gnomad_svAC']
+    out_frqs = ['gnomad_svAF']
+
+    SVDB_QUERY ( input, in_occs, in_frqs, out_occs, out_frqs, vcf_db )
+}
+
+workflow test_svdb_query_multiple {
+
+    input = [ [ id:'test' ], // meta map
+              [ file(params.test_data['homo_sapiens']['illumina']['test_sv_vcf'], checkIfExists: true) ]
+            ]
+
+    vcf_db = [
+                file(params.test_data['homo_sapiens']['genome']['gnomad_r2_1_1_sv_vcf_gz'], checkIfExists: true),
+                file(params.test_data['homo_sapiens']['genome']['gnomad2_r2_1_1_sv_vcf_gz'], checkIfExists: true)
+            ]
+
+    in_occs = ['AC','AC']
+    in_frqs = ['AF','AF']
+    out_occs = ['gnomad_svAC','gnomad_svAC']
+    out_frqs = ['gnomad_svAF','gnomad_svAF']
+
+    SVDB_QUERY ( input, in_occs, in_frqs, out_occs, out_frqs, vcf_db )
 }

tests/modules/svdb/query/nextflow.config

@@ -2,8 +2,4 @@ process {
 
     publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
 
-    withName: SVDB_QUERY {
-         ext.args = '--in_occ AC --out_occ gnomad_svAC --in_frq AF --out_frq gnomad_svAF'
-     }
-
 }

tests/modules/svdb/query/test.yml

@@ -4,4 +4,12 @@
     - svdb
     - svdb/query
   files:
-    - path: output/svdb/test_ann_svdbq.vcf
+    - path: output/svdb/test_query.vcf
+
+- name: svdb query multiple
+  command: nextflow run ./tests/modules/svdb/query -entry test_svdb_query_multiple -c ./tests/config/nextflow.config -c ./tests/modules/svdb/query/nextflow.config
+  tags:
+    - svdb
+    - svdb/query
+  files:
+    - path: output/svdb/test_query.vcf