Bump versions for Pangolin and Nextclade (#1255)

modules/bcftools/query/main.nf

@@ -8,30 +8,29 @@ process BCFTOOLS_QUERY {
         'quay.io/biocontainers/bcftools:1.14--h88f3f91_0' }"
 
     input:
-    tuple val(meta), path(vcf), path(index)
+    tuple val(meta), path(vcf), path(tbi)
-    path(regions)
+    path regions
-    path(targets)
+    path targets
-    path(samples)
+    path samples
 
     output:
-    tuple val(meta), path("*.gz") , emit: vcf
+    tuple val(meta), path("*.txt"), emit: txt
     path "versions.yml"           , emit: versions
 
     script:
     def args = task.ext.args ?: ''
     def prefix = task.ext.prefix ?: "${meta.id}"
-    def regions_file  = regions ? "--regions-file ${regions}" : ""
+    def regions_file = regions ? "--regions-file ${regions}" : ""
     def targets_file = targets ? "--targets-file ${targets}" : ""
     def samples_file =  samples ? "--samples-file ${samples}" : ""
-
     """
     bcftools query \\
-        --output ${prefix}.vcf.gz \\
+        --output ${prefix}.txt \\
-        ${regions_file} \\
+        $regions_file \\
-        ${targets_file} \\
+        $targets_file \\
-        ${samples_file} \\
+        $samples_file \\
         $args \\
-        ${vcf}
+        $vcf
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":

modules/bcftools/query/meta.yml

@@ -23,22 +23,20 @@ input:
         type: file
         description: |
           The vcf file to be qeuried.
-          e.g. 'file.vcf'
+        pattern: "*.{vcf.gz, vcf}"
-    - index:
+    - tbi:
         type: file
         description: |
           The tab index for the VCF file to be inspected.
-          e.g. 'file.tbi'
+        pattern: "*.tbi"
     - regions:
         type: file
         description: |
           Optionally, restrict the operation to regions listed in this file.
-          e.g. 'file.vcf'
     - targets:
         type: file
         description: |
           Optionally, restrict the operation to regions listed in this file (doesn't rely upon index files)
-          e.g. 'file.vcf'
     - samples:
         type: file
         description: |
@@ -50,13 +48,14 @@ output:
         description: |
           Groovy Map containing sample information
           e.g. [ id:'test', single_end:false ]
-    - vcf:
+    - txt:
         type: file
-        description: VCF query output file
+        description: BCFTools query output file
-        pattern: "*.{vcf.gz}"
+        pattern: "*.txt"
     - versions:
         type: file
         description: File containing software versions
         pattern: "versions.yml"
 authors:
   - "@abhi18av"
+  - "@drpatelh"

modules/nextclade/datasetget/main.nf

@@ -2,10 +2,10 @@ process NEXTCLADE_DATASETGET {
     tag "$dataset"
     label 'process_low'
 
-    conda (params.enable_conda ? "bioconda::nextclade=1.10.1" : null)
+    conda (params.enable_conda ? "bioconda::nextclade=1.10.2" : null)
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/nextclade:1.10.1--h9ee0642_0' :
+        'https://depot.galaxyproject.org/singularity/nextclade:1.10.2--h9ee0642_0' :
-        'quay.io/biocontainers/nextclade:1.10.1--h9ee0642_0' }"
+        'quay.io/biocontainers/nextclade:1.10.2--h9ee0642_0' }"
 
     input:
     val dataset

modules/nextclade/run/main.nf

@@ -2,10 +2,10 @@ process NEXTCLADE_RUN {
     tag "$meta.id"
     label 'process_low'
 
-    conda (params.enable_conda ? "bioconda::nextclade=1.10.1" : null)
+    conda (params.enable_conda ? "bioconda::nextclade=1.10.2" : null)
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/nextclade:1.10.1--h9ee0642_0' :
+        'https://depot.galaxyproject.org/singularity/nextclade:1.10.2--h9ee0642_0' :
-        'quay.io/biocontainers/nextclade:1.10.1--h9ee0642_0' }"
+        'quay.io/biocontainers/nextclade:1.10.2--h9ee0642_0' }"
 
     input:
     tuple val(meta), path(fasta)

modules/pangolin/main.nf

@@ -2,10 +2,10 @@ process PANGOLIN {
     tag "$meta.id"
     label 'process_medium'
 
-    conda (params.enable_conda ? 'bioconda::pangolin=3.1.17' : null)
+    conda (params.enable_conda ? 'bioconda::pangolin=3.1.19' : null)
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/pangolin:3.1.17--pyhdfd78af_0' :
+        'https://depot.galaxyproject.org/singularity/pangolin:3.1.19--pyhdfd78af_0' :
-        'quay.io/biocontainers/pangolin:3.1.17--pyhdfd78af_0' }"
+        'quay.io/biocontainers/pangolin:3.1.19--pyhdfd78af_0' }"
 
     input:
     tuple val(meta), path(fasta)

tests/modules/bcftools/query/main.nf

@@ -6,26 +6,24 @@ include { BCFTOOLS_QUERY } from '../../../../modules/bcftools/query/main.nf'
 
 workflow test_bcftools_query {
 
-    regions = []
-    targets = []
-    samples = []
-
     input = [ [ id:'out' ], // meta map
              file(params.test_data['sarscov2']['illumina']['test_vcf_gz'], checkIfExists: true),
              file(params.test_data['sarscov2']['illumina']['test_vcf_gz_tbi'], checkIfExists: true)]
+    regions = []
+    targets = []
+    samples = []
 
     BCFTOOLS_QUERY ( input, regions, targets, samples )
 }
 
 workflow test_bcftools_query_with_optional_files {
 
+    input = [ [ id:'out' ], // meta map
+             file(params.test_data['sarscov2']['illumina']['test_vcf_gz'], checkIfExists: true),
+             file(params.test_data['sarscov2']['illumina']['test_vcf_gz_tbi'], checkIfExists: true)]
     regions = file(params.test_data['sarscov2']['illumina']['test3_vcf_gz'], checkIfExists: true)
     targets = file(params.test_data['sarscov2']['illumina']['test2_vcf_targets_tsv_gz'], checkIfExists: true)
     samples = []
 
-    input = [ [ id:'out' ], // meta map
-             file(params.test_data['sarscov2']['illumina']['test_vcf_gz'], checkIfExists: true),
-             file(params.test_data['sarscov2']['illumina']['test_vcf_gz_tbi'], checkIfExists: true)]
-
     BCFTOOLS_QUERY ( input, regions, targets, samples )
 }

tests/modules/bcftools/query/test.yml

@@ -4,7 +4,7 @@
     - bcftools
     - bcftools/query
   files:
-    - path: output/bcftools/out.vcf.gz
+    - path: output/bcftools/out.txt
       md5sum: c32a6d28f185822d8fe1eeb7e42ec155
 
 - name: bcftools query with optional files
@@ -13,5 +13,5 @@
     - bcftools
     - bcftools/query
   files:
-    - path: output/bcftools/out.vcf.gz
+    - path: output/bcftools/out.txt
       md5sum: 6bb5df49bfb5af39f7037cdf95032aac

tests/modules/pangolin/test.yml

@@ -4,4 +4,4 @@
     - pangolin
   files:
     - path: ./output/pangolin/test.pangolin.csv
-      md5sum: 2563856ee31ba2a4a05705ff940a28cc
+      md5sum: d92ede51bf3886f696f2089e86189125