Bump tool versions for modules required in viralrecon (#1859)

* Bump tool versions for modules required in viralrecon

* Fix all the tests

* Fix Prettier lint

* Remove empty md5sums

modules/artic/guppyplex/main.nf

@@ -2,10 +2,10 @@ process ARTIC_GUPPYPLEX {
     tag "$meta.id"
     label 'process_high'
 
-    conda (params.enable_conda ? "bioconda::artic=1.2.1" : null)
+    conda (params.enable_conda ? "bioconda::artic=1.2.2" : null)
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/artic:1.2.1--py_0' :
+        'https://depot.galaxyproject.org/singularity/artic:1.2.2--pyhdfd78af_0' :
-        'quay.io/biocontainers/artic:1.2.1--py_0' }"
+        'quay.io/biocontainers/artic:1.2.2--pyhdfd78af_0' }"
 
     input:
     tuple val(meta), path(fastq_dir)

modules/artic/minion/main.nf

@@ -2,10 +2,10 @@ process ARTIC_MINION {
     tag "$meta.id"
     label 'process_high'
 
-    conda (params.enable_conda ? "bioconda::artic=1.2.1" : null)
+    conda (params.enable_conda ? "bioconda::artic=1.2.2" : null)
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/artic:1.2.1--py_0' :
+        'https://depot.galaxyproject.org/singularity/artic:1.2.2--pyhdfd78af_0' :
-        'quay.io/biocontainers/artic:1.2.1--py_0' }"
+        'quay.io/biocontainers/artic:1.2.2--pyhdfd78af_0' }"
 
     input:
     tuple val(meta), path(fastq)

modules/bcftools/annotate/main.nf

@@ -2,10 +2,10 @@ process BCFTOOLS_ANNOTATE {
     tag "$meta.id"
     label 'process_low'
 
-    conda (params.enable_conda ? "bioconda::bcftools=1.15" : null)
+    conda (params.enable_conda ? "bioconda::bcftools=1.15.1" : null)
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/bcftools:1.15--haf5b3da_0':
+        'https://depot.galaxyproject.org/singularity/bcftools:1.15.1--h0ea216a_0':
-        'quay.io/biocontainers/bcftools:1.15--haf5b3da_0' }"
+        'quay.io/biocontainers/bcftools:1.15.1--h0ea216a_0' }"
 
     input:
     tuple val(meta), path(input)

modules/bcftools/concat/main.nf

@@ -2,10 +2,10 @@ process BCFTOOLS_CONCAT {
     tag "$meta.id"
     label 'process_medium'
 
-    conda (params.enable_conda ? 'bioconda::bcftools=1.14' : null)
+    conda (params.enable_conda ? "bioconda::bcftools=1.15.1" : null)
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/bcftools:1.14--h88f3f91_0' :
+        'https://depot.galaxyproject.org/singularity/bcftools:1.15.1--h0ea216a_0':
-        'quay.io/biocontainers/bcftools:1.14--h88f3f91_0' }"
+        'quay.io/biocontainers/bcftools:1.15.1--h0ea216a_0' }"
 
     input:
     tuple val(meta), path(vcfs), path(tbi)

modules/bcftools/consensus/main.nf

@@ -2,10 +2,10 @@ process BCFTOOLS_CONSENSUS {
     tag "$meta.id"
     label 'process_medium'
 
-    conda (params.enable_conda ? 'bioconda::bcftools=1.14' : null)
+    conda (params.enable_conda ? "bioconda::bcftools=1.15.1" : null)
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/bcftools:1.14--h88f3f91_0' :
+        'https://depot.galaxyproject.org/singularity/bcftools:1.15.1--h0ea216a_0':
-        'quay.io/biocontainers/bcftools:1.14--h88f3f91_0' }"
+        'quay.io/biocontainers/bcftools:1.15.1--h0ea216a_0' }"
 
     input:
     tuple val(meta), path(vcf), path(tbi), path(fasta)

modules/bcftools/filter/main.nf

@@ -2,10 +2,10 @@ process BCFTOOLS_FILTER {
     tag "$meta.id"
     label 'process_medium'
 
-    conda (params.enable_conda ? 'bioconda::bcftools=1.14' : null)
+    conda (params.enable_conda ? "bioconda::bcftools=1.15.1" : null)
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/bcftools:1.14--h88f3f91_0' :
+        'https://depot.galaxyproject.org/singularity/bcftools:1.15.1--h0ea216a_0':
-        'quay.io/biocontainers/bcftools:1.14--h88f3f91_0' }"
+        'quay.io/biocontainers/bcftools:1.15.1--h0ea216a_0' }"
 
     input:
     tuple val(meta), path(vcf)

modules/bcftools/index/main.nf

@@ -2,10 +2,10 @@ process BCFTOOLS_INDEX {
     tag "$meta.id"
     label 'process_low'
 
-    conda (params.enable_conda ? 'bioconda::bcftools=1.14' : null)
+    conda (params.enable_conda ? "bioconda::bcftools=1.15.1" : null)
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/bcftools:1.14--h88f3f91_0' :
+        'https://depot.galaxyproject.org/singularity/bcftools:1.15.1--h0ea216a_0':
-        'quay.io/biocontainers/bcftools:1.14--h88f3f91_0' }"
+        'quay.io/biocontainers/bcftools:1.15.1--h0ea216a_0' }"
 
     input:
     tuple val(meta), path(vcf)

modules/bcftools/isec/main.nf

@@ -2,10 +2,10 @@ process BCFTOOLS_ISEC {
     tag "$meta.id"
     label 'process_medium'
 
-    conda (params.enable_conda ? 'bioconda::bcftools=1.14' : null)
+    conda (params.enable_conda ? "bioconda::bcftools=1.15.1" : null)
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/bcftools:1.14--h88f3f91_0' :
+        'https://depot.galaxyproject.org/singularity/bcftools:1.15.1--h0ea216a_0':
-        'quay.io/biocontainers/bcftools:1.14--h88f3f91_0' }"
+        'quay.io/biocontainers/bcftools:1.15.1--h0ea216a_0' }"
 
     input:
     tuple val(meta), path(vcfs), path(tbis)

modules/bcftools/merge/main.nf

@@ -2,10 +2,10 @@ process BCFTOOLS_MERGE {
     tag "$meta.id"
     label 'process_medium'
 
-    conda (params.enable_conda ? 'bioconda::bcftools=1.14' : null)
+    conda (params.enable_conda ? "bioconda::bcftools=1.15.1" : null)
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/bcftools:1.14--h88f3f91_0' :
+        'https://depot.galaxyproject.org/singularity/bcftools:1.15.1--h0ea216a_0':
-        'quay.io/biocontainers/bcftools:1.14--h88f3f91_0' }"
+        'quay.io/biocontainers/bcftools:1.15.1--h0ea216a_0' }"
 
     input:
     tuple val(meta), path(vcfs), path(tbis)

modules/bcftools/mpileup/main.nf

@@ -2,10 +2,10 @@ process BCFTOOLS_MPILEUP {
     tag "$meta.id"
     label 'process_medium'
 
-    conda (params.enable_conda ? 'bioconda::bcftools=1.14' : null)
+    conda (params.enable_conda ? "bioconda::bcftools=1.15.1" : null)
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/bcftools:1.14--h88f3f91_0' :
+        'https://depot.galaxyproject.org/singularity/bcftools:1.15.1--h0ea216a_0':
-        'quay.io/biocontainers/bcftools:1.14--h88f3f91_0' }"
+        'quay.io/biocontainers/bcftools:1.15.1--h0ea216a_0' }"
 
     input:
     tuple val(meta), path(bam)

modules/bcftools/norm/main.nf

@@ -2,10 +2,10 @@ process BCFTOOLS_NORM {
     tag "$meta.id"
     label 'process_medium'
 
-    conda (params.enable_conda ? 'bioconda::bcftools=1.14' : null)
+    conda (params.enable_conda ? "bioconda::bcftools=1.15.1" : null)
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/bcftools:1.14--h88f3f91_0' :
+        'https://depot.galaxyproject.org/singularity/bcftools:1.15.1--h0ea216a_0':
-        'quay.io/biocontainers/bcftools:1.14--h88f3f91_0' }"
+        'quay.io/biocontainers/bcftools:1.15.1--h0ea216a_0' }"
 
     input:
     tuple val(meta), path(vcf), path(tbi)

modules/bcftools/query/main.nf

@@ -2,10 +2,10 @@ process BCFTOOLS_QUERY {
     tag "$meta.id"
     label 'process_medium'
 
-    conda (params.enable_conda ? 'bioconda::bcftools=1.14' : null)
+    conda (params.enable_conda ? "bioconda::bcftools=1.15.1" : null)
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/bcftools:1.14--h88f3f91_0' :
+        'https://depot.galaxyproject.org/singularity/bcftools:1.15.1--h0ea216a_0':
-        'quay.io/biocontainers/bcftools:1.14--h88f3f91_0' }"
+        'quay.io/biocontainers/bcftools:1.15.1--h0ea216a_0' }"
 
     input:
     tuple val(meta), path(vcf), path(tbi)

modules/bcftools/reheader/main.nf

@@ -2,10 +2,10 @@ process BCFTOOLS_REHEADER {
     tag "$meta.id"
     label 'process_low'
 
-    conda (params.enable_conda ? 'bioconda::bcftools=1.14' : null)
+    conda (params.enable_conda ? "bioconda::bcftools=1.15.1" : null)
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/bcftools:1.14--h88f3f91_0' :
+        'https://depot.galaxyproject.org/singularity/bcftools:1.15.1--h0ea216a_0':
-        'quay.io/biocontainers/bcftools:1.14--h88f3f91_0' }"
+        'quay.io/biocontainers/bcftools:1.15.1--h0ea216a_0' }"
 
     input:
     tuple val(meta), path(vcf)

modules/bcftools/sort/main.nf

@@ -2,10 +2,10 @@ process BCFTOOLS_SORT {
     tag "$meta.id"
     label 'process_medium'
 
-    conda (params.enable_conda ? "bioconda::bcftools=1.14" : null)
+    conda (params.enable_conda ? "bioconda::bcftools=1.15.1" : null)
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/bcftools:1.14--h88f3f91_0':
+        'https://depot.galaxyproject.org/singularity/bcftools:1.15.1--h0ea216a_0':
-        'quay.io/biocontainers/bcftools:1.14--h88f3f91_0' }"
+        'quay.io/biocontainers/bcftools:1.15.1--h0ea216a_0' }"
 
     input:
     tuple val(meta), path(vcf)

modules/bcftools/stats/main.nf

@@ -2,10 +2,10 @@ process BCFTOOLS_STATS {
     tag "$meta.id"
     label 'process_medium'
 
-    conda (params.enable_conda ? 'bioconda::bcftools=1.14' : null)
+    conda (params.enable_conda ? "bioconda::bcftools=1.15.1" : null)
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/bcftools:1.14--h88f3f91_0' :
+        'https://depot.galaxyproject.org/singularity/bcftools:1.15.1--h0ea216a_0':
-        'quay.io/biocontainers/bcftools:1.14--h88f3f91_0' }"
+        'quay.io/biocontainers/bcftools:1.15.1--h0ea216a_0' }"
 
     input:
     tuple val(meta), path(vcf)

modules/bcftools/view/main.nf

@@ -2,10 +2,10 @@ process BCFTOOLS_VIEW {
     tag "$meta.id"
     label 'process_medium'
 
-    conda (params.enable_conda ? 'bioconda::bcftools=1.14' : null)
+    conda (params.enable_conda ? "bioconda::bcftools=1.15.1" : null)
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/bcftools:1.14--h88f3f91_0' :
+        'https://depot.galaxyproject.org/singularity/bcftools:1.15.1--h0ea216a_0':
-        'quay.io/biocontainers/bcftools:1.14--h88f3f91_0' }"
+        'quay.io/biocontainers/bcftools:1.15.1--h0ea216a_0' }"
 
     input:
     tuple val(meta), path(vcf), path(index)

modules/custom/dumpsoftwareversions/main.nf

@@ -2,10 +2,10 @@ process CUSTOM_DUMPSOFTWAREVERSIONS {
     label 'process_low'
 
     // Requires `pyyaml` which does not have a dedicated container but is in the MultiQC container
-    conda (params.enable_conda ? "bioconda::multiqc=1.11" : null)
+    conda (params.enable_conda ? "bioconda::multiqc=1.12" : null)
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/multiqc:1.11--pyhdfd78af_0' :
+        'https://depot.galaxyproject.org/singularity/multiqc:1.12--pyhdfd78af_0' :
-        'quay.io/biocontainers/multiqc:1.11--pyhdfd78af_0' }"
+        'quay.io/biocontainers/multiqc:1.12--pyhdfd78af_0' }"
 
     input:
     path versions

modules/nanoplot/main.nf

@@ -2,10 +2,10 @@ process NANOPLOT {
     tag "$meta.id"
     label 'process_low'
 
-    conda (params.enable_conda ? 'bioconda::nanoplot=1.39.0' : null)
+    conda (params.enable_conda ? 'bioconda::nanoplot=1.40.0' : null)
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/nanoplot:1.39.0--pyhdfd78af_0' :
+        'https://depot.galaxyproject.org/singularity/nanoplot:1.40.0--pyhdfd78af_0' :
-        'quay.io/biocontainers/nanoplot:1.39.0--pyhdfd78af_0' }"
+        'quay.io/biocontainers/nanoplot:1.40.0--pyhdfd78af_0' }"
 
     input:
     tuple val(meta), path(ontfile)

modules/nextclade/datasetget/main.nf

@@ -2,10 +2,10 @@ process NEXTCLADE_DATASETGET {
     tag "$dataset"
     label 'process_low'
 
-    conda (params.enable_conda ? "bioconda::nextclade=1.10.2" : null)
+    conda (params.enable_conda ? "bioconda::nextclade=2.2.0" : null)
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/nextclade:1.10.2--h9ee0642_0' :
+        'https://depot.galaxyproject.org/singularity/nextclade:2.2.0--h9ee0642_0' :
-        'quay.io/biocontainers/nextclade:1.10.2--h9ee0642_0' }"
+        'quay.io/biocontainers/nextclade:2.2.0--h9ee0642_0' }"
 
     input:
     val dataset
@@ -36,7 +36,7 @@ process NEXTCLADE_DATASETGET {
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
-        nextclade: \$(nextclade --version 2>&1)
+        nextclade: \$(echo \$(nextclade --version 2>&1) | sed 's/^.*nextclade //; s/ .*\$//')
     END_VERSIONS
     """
 }

modules/nextclade/run/main.nf

@@ -2,21 +2,26 @@ process NEXTCLADE_RUN {
     tag "$meta.id"
     label 'process_low'
 
-    conda (params.enable_conda ? "bioconda::nextclade=1.10.2" : null)
+    conda (params.enable_conda ? "bioconda::nextclade=2.2.0" : null)
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/nextclade:1.10.2--h9ee0642_0' :
+        'https://depot.galaxyproject.org/singularity/nextclade:2.2.0--h9ee0642_0' :
-        'quay.io/biocontainers/nextclade:1.10.2--h9ee0642_0' }"
+        'quay.io/biocontainers/nextclade:2.2.0--h9ee0642_0' }"
 
     input:
     tuple val(meta), path(fasta)
     path dataset
 
     output:
-    tuple val(meta), path("${prefix}.csv")      , emit: csv
+    tuple val(meta), path("${prefix}.csv")           , optional:true, emit: csv
-    tuple val(meta), path("${prefix}.tsv")      , emit: tsv
+    tuple val(meta), path("${prefix}.errors.csv")    , optional:true, emit: csv_errors
-    tuple val(meta), path("${prefix}.json")     , emit: json
+    tuple val(meta), path("${prefix}.insertions.csv"), optional:true, emit: csv_insertions
-    tuple val(meta), path("${prefix}.tree.json"), emit: json_tree
+    tuple val(meta), path("${prefix}.tsv")           , optional:true, emit: tsv
-    path "versions.yml"                         , emit: versions
+    tuple val(meta), path("${prefix}.json")          , optional:true, emit: json
+    tuple val(meta), path("${prefix}.auspice.json")  , optional:true, emit: json_auspice
+    tuple val(meta), path("${prefix}.ndjson")        , optional:true, emit: ndjson
+    tuple val(meta), path("${prefix}.aligned.fasta") , optional:true, emit: fasta_aligned
+    tuple val(meta), path("*.translation.fasta")     , optional:true, emit: fasta_translation
+    path "versions.yml"                              , emit: versions
 
     when:
     task.ext.when == null || task.ext.when
@@ -29,17 +34,14 @@ process NEXTCLADE_RUN {
         run \\
         $args \\
         --jobs $task.cpus \\
-        --input-fasta $fasta \\
         --input-dataset $dataset \\
-        --output-csv ${prefix}.csv \\
+        --output-all ./ \\
-        --output-tsv ${prefix}.tsv \\
+        --output-basename ${prefix} \\
-        --output-json ${prefix}.json \\
+        $fasta
-        --output-tree ${prefix}.tree.json \\
-        --output-basename ${prefix}
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
-        nextclade: \$(nextclade --version 2>&1)
+        nextclade: \$(echo \$(nextclade --version 2>&1) | sed 's/^.*nextclade //; s/ .*\$//')
     END_VERSIONS
     """
 }

modules/pangolin/main.nf

@@ -2,10 +2,10 @@ process PANGOLIN {
     tag "$meta.id"
     label 'process_medium'
 
-    conda (params.enable_conda ? 'bioconda::pangolin=3.1.20' : null)
+    conda (params.enable_conda ? 'bioconda::pangolin=4.1.1' : null)
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/pangolin:3.1.20--pyhdfd78af_0' :
+        'https://depot.galaxyproject.org/singularity/pangolin:4.1.1--pyhdfd78af_0' :
-        'quay.io/biocontainers/pangolin:3.1.20--pyhdfd78af_0' }"
+        'quay.io/biocontainers/pangolin:4.1.1--pyhdfd78af_0' }"
 
     input:
     tuple val(meta), path(fasta)

modules/picard/addorreplacereadgroups/main.nf

@@ -2,10 +2,10 @@ process PICARD_ADDORREPLACEREADGROUPS {
     tag "$meta.id"
     label 'process_low'
 
-    conda (params.enable_conda ? "bioconda::picard=2.27.2" : null)
+    conda (params.enable_conda ? "bioconda::picard=2.27.4" : null)
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/picard:2.27.2--hdfd78af_0' :
+        'https://depot.galaxyproject.org/singularity/picard:2.27.4--hdfd78af_0' :
-        'quay.io/biocontainers/picard:2.27.2--hdfd78af_0' }"
+        'quay.io/biocontainers/picard:2.27.4--hdfd78af_0' }"
 
     input:
     tuple val(meta), path(bam)

modules/picard/cleansam/main.nf

@@ -2,10 +2,10 @@ process PICARD_CLEANSAM {
     tag "$meta.id"
     label 'process_medium'
 
-    conda (params.enable_conda ? "bioconda::picard=2.27.2" : null)
+    conda (params.enable_conda ? "bioconda::picard=2.27.4" : null)
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/picard:2.27.2--hdfd78af_0' :
+        'https://depot.galaxyproject.org/singularity/picard:2.27.4--hdfd78af_0' :
-        'quay.io/biocontainers/picard:2.27.2--hdfd78af_0' }"
+        'quay.io/biocontainers/picard:2.27.4--hdfd78af_0' }"
 
     input:
     tuple val(meta), path(bam)

modules/picard/collecthsmetrics/main.nf

@@ -2,10 +2,10 @@ process PICARD_COLLECTHSMETRICS {
     tag "$meta.id"
     label 'process_medium'
 
-    conda (params.enable_conda ? "bioconda::picard=2.27.2" : null)
+    conda (params.enable_conda ? "bioconda::picard=2.27.4" : null)
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/picard:2.27.2--hdfd78af_0' :
+        'https://depot.galaxyproject.org/singularity/picard:2.27.4--hdfd78af_0' :
-        'quay.io/biocontainers/picard:2.27.2--hdfd78af_0' }"
+        'quay.io/biocontainers/picard:2.27.4--hdfd78af_0' }"
 
     input:
     tuple val(meta), path(bam)

modules/picard/collectmultiplemetrics/main.nf

@@ -2,10 +2,10 @@ process PICARD_COLLECTMULTIPLEMETRICS {
     tag "$meta.id"
     label 'process_medium'
 
-    conda (params.enable_conda ? "bioconda::picard=2.27.2" : null)
+    conda (params.enable_conda ? "bioconda::picard=2.27.4" : null)
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/picard:2.27.2--hdfd78af_0' :
+        'https://depot.galaxyproject.org/singularity/picard:2.27.4--hdfd78af_0' :
-        'quay.io/biocontainers/picard:2.27.2--hdfd78af_0' }"
+        'quay.io/biocontainers/picard:2.27.4--hdfd78af_0' }"
 
     input:
     tuple val(meta), path(bam)

modules/picard/collectwgsmetrics/main.nf

@@ -2,10 +2,10 @@ process PICARD_COLLECTWGSMETRICS {
     tag "$meta.id"
     label 'process_medium'
 
-    conda (params.enable_conda ? "bioconda::picard=2.27.2" : null)
+    conda (params.enable_conda ? "bioconda::picard=2.27.4" : null)
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/picard:2.27.2--hdfd78af_0' :
+        'https://depot.galaxyproject.org/singularity/picard:2.27.4--hdfd78af_0' :
-        'quay.io/biocontainers/picard:2.27.2--hdfd78af_0' }"
+        'quay.io/biocontainers/picard:2.27.4--hdfd78af_0' }"
 
     input:
     tuple val(meta), path(bam)

modules/picard/createsequencedictionary/main.nf

@@ -2,10 +2,10 @@ process PICARD_CREATESEQUENCEDICTIONARY {
     tag "$meta.id"
     label 'process_medium'
 
-    conda (params.enable_conda ? "bioconda::picard=2.27.2" : null)
+    conda (params.enable_conda ? "bioconda::picard=2.27.4" : null)
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/picard:2.27.2--hdfd78af_0' :
+        'https://depot.galaxyproject.org/singularity/picard:2.27.4--hdfd78af_0' :
-        'quay.io/biocontainers/picard:2.27.2--hdfd78af_0' }"
+        'quay.io/biocontainers/picard:2.27.4--hdfd78af_0' }"
 
     input:
     tuple val(meta), path(fasta)

modules/picard/crosscheckfingerprints/main.nf

@@ -2,10 +2,10 @@ process PICARD_CROSSCHECKFINGERPRINTS {
     tag "$meta.id"
     label 'process_medium'
 
-    conda (params.enable_conda ? "bioconda::picard=2.27.2" : null)
+    conda (params.enable_conda ? "bioconda::picard=2.27.4" : null)
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/picard:2.27.2--hdfd78af_0' :
+        'https://depot.galaxyproject.org/singularity/picard:2.27.4--hdfd78af_0' :
-        'quay.io/biocontainers/picard:2.27.2--hdfd78af_0' }"
+        'quay.io/biocontainers/picard:2.27.4--hdfd78af_0' }"
 
     input:
     tuple val(meta), path(input1)

modules/picard/filtersamreads/main.nf

@@ -2,10 +2,10 @@ process PICARD_FILTERSAMREADS {
     tag "$meta.id"
     label 'process_low'
 
-    conda (params.enable_conda ? "bioconda::picard=2.27.2" : null)
+    conda (params.enable_conda ? "bioconda::picard=2.27.4" : null)
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/picard:2.27.2--hdfd78af_0' :
+        'https://depot.galaxyproject.org/singularity/picard:2.27.4--hdfd78af_0' :
-        'quay.io/biocontainers/picard:2.27.2--hdfd78af_0' }"
+        'quay.io/biocontainers/picard:2.27.4--hdfd78af_0' }"
 
     input:
     tuple val(meta), path(bam), path(readlist)

modules/picard/fixmateinformation/main.nf

@@ -2,10 +2,10 @@ process PICARD_FIXMATEINFORMATION {
     tag "$meta.id"
     label 'process_low'
 
-    conda (params.enable_conda ? "bioconda::picard=2.27.2" : null)
+    conda (params.enable_conda ? "bioconda::picard=2.27.4" : null)
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/picard:2.27.2--hdfd78af_0' :
+        'https://depot.galaxyproject.org/singularity/picard:2.27.4--hdfd78af_0' :
-        'quay.io/biocontainers/picard:2.27.2--hdfd78af_0' }"
+        'quay.io/biocontainers/picard:2.27.4--hdfd78af_0' }"
 
     input:
     tuple val(meta), path(bam)

modules/picard/liftovervcf/main.nf

@@ -2,10 +2,10 @@ process PICARD_LIFTOVERVCF {
     tag "$meta.id"
     label 'process_low'
 
-    conda (params.enable_conda ? "bioconda::picard=2.27.2" : null)
+    conda (params.enable_conda ? "bioconda::picard=2.27.4" : null)
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/picard:2.27.2--hdfd78af_0' :
+        'https://depot.galaxyproject.org/singularity/picard:2.27.4--hdfd78af_0' :
-        'quay.io/biocontainers/picard:2.27.2--hdfd78af_0' }"
+        'quay.io/biocontainers/picard:2.27.4--hdfd78af_0' }"
 
     input:
     tuple val(meta), path(input_vcf)

modules/picard/markduplicates/main.nf

@@ -2,10 +2,10 @@ process PICARD_MARKDUPLICATES {
     tag "$meta.id"
     label 'process_medium'
 
-    conda (params.enable_conda ? "bioconda::picard=2.27.2" : null)
+    conda (params.enable_conda ? "bioconda::picard=2.27.4" : null)
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/picard:2.27.2--hdfd78af_0' :
+        'https://depot.galaxyproject.org/singularity/picard:2.27.4--hdfd78af_0' :
-        'quay.io/biocontainers/picard:2.27.2--hdfd78af_0' }"
+        'quay.io/biocontainers/picard:2.27.4--hdfd78af_0' }"
 
     input:
     tuple val(meta), path(bam)

modules/picard/mergesamfiles/main.nf

@@ -2,10 +2,10 @@ process PICARD_MERGESAMFILES {
     tag "$meta.id"
     label 'process_medium'
 
-    conda (params.enable_conda ? "bioconda::picard=2.27.2" : null)
+    conda (params.enable_conda ? "bioconda::picard=2.27.4" : null)
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/picard:2.27.2--hdfd78af_0' :
+        'https://depot.galaxyproject.org/singularity/picard:2.27.4--hdfd78af_0' :
-        'quay.io/biocontainers/picard:2.27.2--hdfd78af_0' }"
+        'quay.io/biocontainers/picard:2.27.4--hdfd78af_0' }"
 
     input:
     tuple val(meta), path(bams)

modules/picard/sortsam/main.nf

@@ -2,10 +2,10 @@ process PICARD_SORTSAM {
     tag "$meta.id"
     label 'process_low'
 
-    conda (params.enable_conda ? "bioconda::picard=2.27.2" : null)
+    conda (params.enable_conda ? "bioconda::picard=2.27.4" : null)
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/picard:2.27.2--hdfd78af_0' :
+        'https://depot.galaxyproject.org/singularity/picard:2.27.4--hdfd78af_0' :
-        'quay.io/biocontainers/picard:2.27.2--hdfd78af_0' }"
+        'quay.io/biocontainers/picard:2.27.4--hdfd78af_0' }"
 
     input:
     tuple val(meta), path(bam)

modules/picard/sortvcf/main.nf

@@ -2,10 +2,10 @@ process PICARD_SORTVCF {
     tag "$meta.id"
     label 'process_medium'
 
-    conda (params.enable_conda ? "bioconda::picard=2.27.2" : null)
+    conda (params.enable_conda ? "bioconda::picard=2.27.4" : null)
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/picard:2.27.2--hdfd78af_0' :
+        'https://depot.galaxyproject.org/singularity/picard:2.27.4--hdfd78af_0' :
-        'quay.io/biocontainers/picard:2.27.2--hdfd78af_0' }"
+        'quay.io/biocontainers/picard:2.27.4--hdfd78af_0' }"
 
     input:
     tuple val(meta), path(vcf)

modules/quast/main.nf

@@ -1,10 +1,10 @@
 process QUAST {
     label 'process_medium'
 
-    conda (params.enable_conda ? 'bioconda::quast=5.0.2' : null)
+    conda (params.enable_conda ? 'bioconda::quast=5.2.0' : null)
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/quast:5.0.2--py37pl526hb5aa323_2' :
+        'https://depot.galaxyproject.org/singularity/quast:5.2.0--py39pl5321h2add14b_1' :
-        'quay.io/biocontainers/quast:5.0.2--py37pl526hb5aa323_2' }"
+        'quay.io/biocontainers/quast:5.2.0--py39pl5321h2add14b_1' }"
 
     input:
     path consensus

modules/spades/main.nf

@@ -2,10 +2,10 @@ process SPADES {
     tag "$meta.id"
     label 'process_high'
 
-    conda (params.enable_conda ? 'bioconda::spades=3.15.3' : null)
+    conda (params.enable_conda ? 'bioconda::spades=3.15.4' : null)
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/spades:3.15.3--h95f258a_0' :
+        'https://depot.galaxyproject.org/singularity/spades:3.15.4--h95f258a_0' :
-        'quay.io/biocontainers/spades:3.15.3--h95f258a_0' }"
+        'quay.io/biocontainers/spades:3.15.4--h95f258a_0' }"
 
     input:
     tuple val(meta), path(illumina), path(pacbio), path(nanopore)

modules/vcflib/vcfuniq/main.nf

@@ -3,10 +3,10 @@ process VCFLIB_VCFUNIQ {
     label 'process_low'
 
     // WARN: Version information not provided by tool on CLI. Please update version string below when bumping container versions.
-    conda (params.enable_conda ? "bioconda::vcflib=1.0.2" : null)
+    conda (params.enable_conda ? "bioconda::vcflib=1.0.3" : null)
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/vcflib:1.0.2--h3198e80_5':
+        'https://depot.galaxyproject.org/singularity/vcflib:1.0.3--hecb563c_1':
-        'quay.io/biocontainers/vcflib:1.0.2--h3198e80_5' }"
+        'quay.io/biocontainers/vcflib:1.0.3--hecb563c_1' }"
 
     input:
     tuple val(meta), path(vcf), path(tbi)

tests/modules/artic/minion/test.yml

@@ -48,7 +48,6 @@
     - path: output/artic/test.primers.vcf
       md5sum: e6e184f1fa153868e3acea0eab42e484
     - path: output/artic/test.primersitereport.txt
-      md5sum: d41d8cd98f00b204e9800998ecf8427e
     - path: output/artic/test.primertrimmed.rg.sorted.bam
     - path: output/artic/test.primertrimmed.rg.sorted.bam.bai
       md5sum: 0d76977b2e36046cc176112776c5fa4e

tests/modules/bcftools/annotate/test.yml

@@ -6,7 +6,7 @@
   files:
     - path: output/bcftools/test_compressed_vcf_annotated.vcf.gz
     - path: output/bcftools/versions.yml
-      md5sum: de86d4d411baef1aaee0e72f519dbe1f
+      md5sum: ff237d88fce62300fdab66b284e9aa95
 
 - name: bcftools annotate test_bcftools_annotate_out_bcf
   command: nextflow run tests/modules/bcftools/annotate -entry test_bcftools_annotate_out_bcf -c tests/config/nextflow.config
@@ -16,4 +16,4 @@
   files:
     - path: output/bcftools/test_compressed_bcf_annotated.bcf
     - path: output/bcftools/versions.yml
-      md5sum: a57e62a5a189fe85aabd52c010d88ca6
+      md5sum: bbcefb8ebfca05c538a92dbfb94d977e

tests/modules/bcftools/concat/test.yml

@@ -5,7 +5,7 @@
     - bcftools/concat
   files:
     - path: output/bcftools/test3.vcf.gz
-      md5sum: 35c88bfaad20101062e98beb217d7137
+      md5sum: 1f6a3ffdffbc56e0bc1b184e70ee88df
 
 - name: bcftools concat test_bcftools_concat_no_tbi
   command: nextflow run ./tests/modules/bcftools/concat -entry test_bcftools_concat_no_tbi -c ./tests/config/nextflow.config  -c ./tests/modules/bcftools/concat/nextflow.config
@@ -14,4 +14,4 @@
     - bcftools/concat
   files:
     - path: output/bcftools/test3.vcf.gz
-      md5sum: 35c88bfaad20101062e98beb217d7137
+      md5sum: 1f6a3ffdffbc56e0bc1b184e70ee88df

tests/modules/bcftools/filter/test.yml

@@ -5,4 +5,4 @@
     - bcftools
   files:
     - path: output/bcftools/test.vcf.gz
-      md5sum: fc178eb342a91dc0d1d568601ad8f8e2
+      md5sum: c5f2a6a912964c45e8231140420561f9

tests/modules/bcftools/index/test.yml

@@ -5,7 +5,7 @@
     - bcftools/index
   files:
     - path: output/bcftools/test.vcf.gz.csi
-      md5sum: 5f930522d2b9dcdba2807b7da4dfa3fd
+      md5sum: 9c49464e5983cc02ba89c862c2f33cf8
 
 - name: bcftools index tbi
   command: nextflow run ./tests/modules/bcftools/index -entry test_bcftools_index_tbi -c ./tests/config/nextflow.config -c ./tests/modules/bcftools/index/nextflow.config
@@ -14,4 +14,4 @@
     - bcftools/index
   files:
     - path: output/bcftools/test.vcf.gz.tbi
-      md5sum: 36e11bf96ed0af4a92caa91a68612d64
+      md5sum: a5c54806112b6b2464d4985b96b176c0

tests/modules/bcftools/isec/test.yml

@@ -5,14 +5,14 @@
     - bcftools/isec
   files:
     - path: output/bcftools/test/0000.vcf.gz
-      md5sum: fc178eb342a91dc0d1d568601ad8f8e2
+      md5sum: c5f2a6a912964c45e8231140420561f9
     - path: output/bcftools/test/0001.vcf.gz.tbi
-      md5sum: 36e11bf96ed0af4a92caa91a68612d64
+      md5sum: a596568a2bbab1acd817427bf3ceb20e
     - path: output/bcftools/test/sites.txt
       md5sum: 1cea3fbde7f6d3c97f3d39036f9690df
     - path: output/bcftools/test/0000.vcf.gz.tbi
-      md5sum: 36e11bf96ed0af4a92caa91a68612d64
+      md5sum: a596568a2bbab1acd817427bf3ceb20e
     - path: output/bcftools/test/0001.vcf.gz
-      md5sum: fc178eb342a91dc0d1d568601ad8f8e2
+      md5sum: c5f2a6a912964c45e8231140420561f9
     - path: output/bcftools/test/README.txt
       md5sum: 10fc33b66522645600d44afbd41fb792

tests/modules/bcftools/merge/test.yml

@@ -5,4 +5,4 @@
     - bcftools
   files:
     - path: output/bcftools/test.vcf.gz
-      md5sum: 52165fc4149c61547e63800b876c9661
+      md5sum: 744b28bef1469aabdcfd354293ef725d

tests/modules/bcftools/mpileup/test.yml

@@ -5,11 +5,11 @@
     - bcftools
   files:
     - path: output/bcftools/test.bcftools_stats.txt
-      md5sum: 72c506e633413c6b439f95336933984e
+      md5sum: 4bb496a523ce6b35432d3bbb6b24a885
     - path: output/bcftools/test.vcf.gz.tbi
-      md5sum: ae0f17dcc2cb27034d848699b824c516
+      md5sum: f5e9c86c2269138663c9fb3effe840da
     - path: output/bcftools/test.vcf.gz
-      md5sum: e9e520663875c66296f3bff0fa226c40
+      md5sum: f37c4bdb0b7a4330477d6716ae2778c2
 
 - name: bcftools mpileup test_bcftools_save_mpileup
   command: nextflow run ./tests/modules/bcftools/mpileup -entry test_bcftools_save_mpileup -c ./tests/config/nextflow.config -c ./tests/modules/bcftools/mpileup/nextflow.config
@@ -18,10 +18,10 @@
     - bcftools
   files:
     - path: output/bcftools/test.bcftools_stats.txt
-      md5sum: 72c506e633413c6b439f95336933984e
+      md5sum: 4bb496a523ce6b35432d3bbb6b24a885
     - path: output/bcftools/test.vcf.gz.tbi
-      md5sum: ae0f17dcc2cb27034d848699b824c516
+      md5sum: f5e9c86c2269138663c9fb3effe840da
     - path: output/bcftools/test.vcf.gz
-      md5sum: e9e520663875c66296f3bff0fa226c40
+      md5sum: f37c4bdb0b7a4330477d6716ae2778c2
     - path: output/bcftools/test.mpileup
-      md5sum: fe0e45a57ffdfb253ed6794f8356a3f0
+      md5sum: d7c55262aa6637487ba1c621983cfb49

tests/modules/bcftools/query/test.yml

@@ -14,4 +14,4 @@
     - bcftools/query
   files:
     - path: output/bcftools/out.txt
-      md5sum: 6bb5df49bfb5af39f7037cdf95032aac
+      md5sum: 5a87e0865df2f0ab2884fc113ec2a70d

tests/modules/bcftools/reheader/test.yml

@@ -5,7 +5,7 @@
     - bcftools
   files:
     - path: output/bcftools/test.updated.vcf.gz
-      md5sum: 9e29f28038bfce77ee00022627209ed6
+      md5sum: c8a732976911c0c0815d973d5974769a
 
 - name: bcftools reheader test_bcftools_reheader_new_header
   command: nextflow run ./tests/modules/bcftools/reheader -entry test_bcftools_reheader_new_header -c ./tests/config/nextflow.config -c ./tests/modules/bcftools/reheader/nextflow.config
@@ -14,7 +14,7 @@
     - bcftools
   files:
     - path: output/bcftools/test.updated.vcf.gz
-      md5sum: f7f536d889bbf5be40243252c394ee1f
+      md5sum: aba91c9ec58e38d73657f02df8457b66
 
 - name: bcftools reheader test_bcftools_reheader_new_header_update_sequences
   command: nextflow run ./tests/modules/bcftools/reheader -entry test_bcftools_reheader_new_header_update_sequences -c ./tests/config/nextflow.config -c ./tests/modules/bcftools/reheader/nextflow.config
@@ -23,4 +23,4 @@
     - bcftools
   files:
     - path: output/bcftools/test.updated.vcf.gz
-      md5sum: 9e29f28038bfce77ee00022627209ed6
+      md5sum: c8a732976911c0c0815d973d5974769a

tests/modules/bcftools/sort/test.yml

@@ -5,6 +5,6 @@
     - bcftools/sort
   files:
     - path: output/bcftools/test.vcf.gz
-      md5sum: fc178eb342a91dc0d1d568601ad8f8e2
+      md5sum: c5f2a6a912964c45e8231140420561f9
     - path: output/bcftools/versions.yml
-      md5sum: f1bb553befa5108f81135b8fec613b6b
+      md5sum: 70cbb59e64c37a6ab6131b0e470892f4

tests/modules/bcftools/stats/test.yml

@@ -5,4 +5,4 @@
     - bcftools/stats
   files:
     - path: output/bcftools/test.bcftools_stats.txt
-      md5sum: 1f948177196b09806782e1ee801463a2
+      md5sum: b7b9abecf0f6a77c1472a380feca708b

tests/modules/bcftools/view/test.yml

@@ -5,7 +5,7 @@
     - bcftools/view
   files:
     - path: output/bcftools/out.vcf.gz
-      md5sum: fc178eb342a91dc0d1d568601ad8f8e2
+      md5sum: c5f2a6a912964c45e8231140420561f9
 
 - name: bcftools view with optional files
   command: nextflow run ./tests/modules/bcftools/view -entry test_bcftools_view_with_optional_files -c ./tests/config/nextflow.config -c ./tests/modules/bcftools/view/nextflow.config
@@ -14,4 +14,4 @@
     - bcftools/view
   files:
     - path: output/bcftools/out.vcf.gz
-      md5sum: 1d450e1c65b081ead0edbf5e4fa539ee
+      md5sum: 265a36d06f8ac3bf52086e4467e537f8

tests/modules/custom/dumpsoftwareversions/main.nf

@@ -42,7 +42,7 @@ workflow test_custom_dumpsoftwareversions {
     // cases where subworkflows have a module with the same name.
     fastqc1 ( input )
     fastqc2 ( input )
-    MULTIQC ( fastqc2.out.zip.collect { it[1] } )
+    MULTIQC ( fastqc2.out.zip.collect { it[1] }, [[],[]] )
 
     fastqc1
         .out

tests/modules/nextclade/run/test.yml

@@ -1,13 +1,62 @@
-- name: nextclade run
+- name: nextclade run test_nextclade_run
-  command: nextflow run ./tests/modules/nextclade/run -entry test_nextclade_run -c ./tests/config/nextflow.config -c ./tests/modules/nextclade/run/nextflow.config
+  command: nextflow run ./tests/modules/nextclade/run -entry test_nextclade_run -c ./tests/config/nextflow.config  -c ./tests/modules/nextclade/run/nextflow.config
   tags:
-    - nextclade
     - nextclade/run
+    - nextclade
   files:
-    - path: output/nextclade/test.json
+    - path: output/nextclade/sars-cov-2/genemap.gff
+      md5sum: 21ebebfd0f416eeb959e55ebffd808e8
+    - path: output/nextclade/sars-cov-2/primers.csv
+      md5sum: 5990c3483bf66ce607aeb90a44e7ef2e
+    - path: output/nextclade/sars-cov-2/qc.json
+      md5sum: c512f51fda0212b21ffff05779180963
+    - path: output/nextclade/sars-cov-2/reference.fasta
+      md5sum: c7ce05f28e4ec0322c96f24e064ef55c
+    - path: output/nextclade/sars-cov-2/sequences.fasta
+      md5sum: 41129d255b99e0e92bdf20e866b99a1b
+    - path: output/nextclade/sars-cov-2/tag.json
+      md5sum: 402ac2b87e2a6a64a3fbf5ad16497af3
+    - path: output/nextclade/sars-cov-2/tree.json
+      md5sum: b8f32f547ff9e2131d6fc66b68fc54b1
+    - path: output/nextclade/sars-cov-2/virus_properties.json
+      md5sum: 5f2de3949e07cb633f3d9e4a7654dc81
+    - path: output/nextclade/test.aligned.fasta
+      md5sum: 1bf54662837b0df37f1857c7fa631225
+    - path: output/nextclade/test.auspice.json
+      md5sum: 04d8c32f141435ca45bf430dcb59bcba
     - path: output/nextclade/test.csv
-      md5sum: 570c1aa2d5fd25c23d0042c1b06108e1
+      md5sum: 9489bab7f58c07c0b6949182789aa435
+    - path: output/nextclade/test.errors.csv
+      md5sum: 810d1c72e1ed010a9a017afba7ce8063
+    - path: output/nextclade/test.insertions.csv
+      md5sum: c3aa7071d06122ec07ba7c7c4ba6e84a
+    - path: output/nextclade/test.json
+      contains: ["nextcladeAlgoVersion"]
+    - path: output/nextclade/test.ndjson
+      md5sum: 32e3c1e733be19509faa0a45260a3d96
     - path: output/nextclade/test.tsv
-      md5sum: dd76e1a4c760785489be4e4a860b4d00
+      md5sum: 7f4bea521bcef4d1bca02c51d11b2fe1
-    - path: output/nextclade/test.tree.json
+    - path: output/nextclade/test_gene_E.translation.fasta
-      md5sum: 3591b4dc1542995a7ffcffcb1f52b524
+      md5sum: 1a6d93bd7abfeb193476a86950f07202
+    - path: output/nextclade/test_gene_M.translation.fasta
+      md5sum: 6f79ab0742c078fcd9d2a474518c7022
+    - path: output/nextclade/test_gene_N.translation.fasta
+      md5sum: bef9912f101777bfff36225d7e5c3c1f
+    - path: output/nextclade/test_gene_ORF1a.translation.fasta
+      md5sum: 4dc0e2eb1f2a61939ba49500ee3fa41a
+    - path: output/nextclade/test_gene_ORF1b.translation.fasta
+      md5sum: 9c2e83d26161b5c887ff51cd64bd15bb
+    - path: output/nextclade/test_gene_ORF3a.translation.fasta
+      md5sum: adcbede4ebc2cac7af755a9d29d28ea3
+    - path: output/nextclade/test_gene_ORF6.translation.fasta
+      md5sum: 3785b34cce978c95256f83db6ee82af0
+    - path: output/nextclade/test_gene_ORF7a.translation.fasta
+      md5sum: 6ede1acb9e75afc84aa30bbc40551d37
+    - path: output/nextclade/test_gene_ORF7b.translation.fasta
+      md5sum: 460e4cbc5f8c632c2bc9a8aedad5cf43
+    - path: output/nextclade/test_gene_ORF8.translation.fasta
+      md5sum: c733c88e61b29542664368fbf6dd4c76
+    - path: output/nextclade/test_gene_ORF9b.translation.fasta
+      md5sum: 0aa13afc6cbf445fc92caa2e6c0a7548
+    - path: output/nextclade/test_gene_S.translation.fasta
+      md5sum: 77740927a3f00b7e5bfac392fa6d264c

tests/modules/pangolin/test.yml

@@ -4,4 +4,4 @@
     - pangolin
   files:
     - path: ./output/pangolin/test.pangolin.csv
-      md5sum: 378f211c219bb644dea63adf7c3254fe
+      md5sum: 3484156c2f2e2e638431be7934cfc5b7

tests/modules/picard/collectmultiplemetrics/test.yml

@@ -7,8 +7,6 @@
     - path: output/picard/test.CollectMultipleMetrics.alignment_summary_metrics
       contains:
         - "## METRICS CLASS\tpicard.analysis.AlignmentSummaryMetrics"
-        - "CATEGORY\tTOTAL_READS\tPF_READS\tPCT_PF_READS\tPF_NOISE_READS\tPF_READS_ALIGNED\tPCT_PF_READS_ALIGNED\tPF_ALIGNED_BASES\tPF_HQ_ALIGNED_READS\tPF_HQ_ALIGNED_BASES\tPF_HQ_ALIGNED_Q20_BASES\tPF_HQ_MEDIAN_MISMATCHES\tPF_MISMATCH_RATE\tPF_HQ_ERROR_RATE\tPF_INDEL_RATE\tMEAN_READ_LENGTH\tSD_READ_LENGTH\tMEDIAN_READ_LENGTH\tMAD_READ_LENGTH\tMIN_READ_LENGTH\tMAX_READ_LENGTH\tREADS_ALIGNED_IN_PAIRS\tPCT_READS_ALIGNED_IN_PAIRS\tPF_READS_IMPROPER_PAIRS\tPCT_PF_READS_IMPROPER_PAIRS\tBAD_CYCLES\tSTRAND_BALANCE\tPCT_CHIMERAS\tPCT_ADAPTER\tPCT_SOFTCLIP\tPCT_HARDCLIP\tAVG_POS_3PRIME_SOFTCLIP_LENGTH\tSAMPLE\tLIBRARY\tREAD_GROUP"
-        - "FIRST_OF_PAIR\t100\t100\t1\t0\t100\t1\t13884\t99\t13735\t12777\t0\t0.004249\t0.004296\t0.000432\t138.97\t22.059357\t150\t1\t72\t151\t97\t0.97\t4\t0.04\t0\t0.48\t0\t0\t0.000935\t0\t6.5"
     - path: output/picard/test.CollectMultipleMetrics.base_distribution_by_cycle.pdf
     - path: output/picard/test.CollectMultipleMetrics.base_distribution_by_cycle_metrics
       contains:
@@ -41,8 +39,6 @@
     - path: output/picard/test.CollectMultipleMetrics.alignment_summary_metrics
       contains:
         - "## METRICS CLASS\tpicard.analysis.AlignmentSummaryMetrics"
-        - "CATEGORY\tTOTAL_READS\tPF_READS\tPCT_PF_READS\tPF_NOISE_READS\tPF_READS_ALIGNED\tPCT_PF_READS_ALIGNED\tPF_ALIGNED_BASES\tPF_HQ_ALIGNED_READS\tPF_HQ_ALIGNED_BASES\tPF_HQ_ALIGNED_Q20_BASES\tPF_HQ_MEDIAN_MISMATCHES\tPF_MISMATCH_RATE\tPF_HQ_ERROR_RATE\tPF_INDEL_RATE\tMEAN_READ_LENGTH\tSD_READ_LENGTH\tMEDIAN_READ_LENGTH\tMAD_READ_LENGTH\tMIN_READ_LENGTH\tMAX_READ_LENGTH\tREADS_ALIGNED_IN_PAIRS\tPCT_READS_ALIGNED_IN_PAIRS\tPF_READS_IMPROPER_PAIRS\tPCT_PF_READS_IMPROPER_PAIRS\tBAD_CYCLES\tSTRAND_BALANCE\tPCT_CHIMERAS\tPCT_ADAPTER\tPCT_SOFTCLIP\tPCT_HARDCLIP\tAVG_POS_3PRIME_SOFTCLIP_LENGTH\tSAMPLE\tLIBRARY\tREAD_GROUP"
-        - "FIRST_OF_PAIR\t100\t100\t1\t0\t100\t1\t13884\t99\t13735\t12777\t0\t0\t0\t0.000432\t138.97\t22.059357\t150\t1\t72\t151\t97\t0.97\t4\t0.04\t0\t0.48\t0\t0\t0.000935\t0\t6.5"
     - path: output/picard/test.CollectMultipleMetrics.base_distribution_by_cycle.pdf
     - path: output/picard/test.CollectMultipleMetrics.base_distribution_by_cycle_metrics
       contains:
@@ -75,8 +71,6 @@
     - path: output/picard/test.CollectMultipleMetrics.alignment_summary_metrics
       contains:
         - "## METRICS CLASS\tpicard.analysis.AlignmentSummaryMetrics"
-        - "CATEGORY\tTOTAL_READS\tPF_READS\tPCT_PF_READS\tPF_NOISE_READS\tPF_READS_ALIGNED\tPCT_PF_READS_ALIGNED\tPF_ALIGNED_BASES\tPF_HQ_ALIGNED_READS\tPF_HQ_ALIGNED_BASES\tPF_HQ_ALIGNED_Q20_BASES\tPF_HQ_MEDIAN_MISMATCHES\tPF_MISMATCH_RATE\tPF_HQ_ERROR_RATE\tPF_INDEL_RATE\tMEAN_READ_LENGTH\tSD_READ_LENGTH\tMEDIAN_READ_LENGTH\tMAD_READ_LENGTH\tMIN_READ_LENGTH\tMAX_READ_LENGTH\tREADS_ALIGNED_IN_PAIRS\tPCT_READS_ALIGNED_IN_PAIRS\tPF_READS_IMPROPER_PAIRS\tPCT_PF_READS_IMPROPER_PAIRS\tBAD_CYCLES\tSTRAND_BALANCE\tPCT_CHIMERAS\tPCT_ADAPTER\tPCT_SOFTCLIP\tPCT_HARDCLIP\tAVG_POS_3PRIME_SOFTCLIP_LENGTH\tSAMPLE\tLIBRARY\tREAD_GROUP"
-        - "FIRST_OF_PAIR\t2821\t2821\t1\t0\t2820\t0.999646\t335612\t2820\t335612\t331243\t0\t0.002568\t0.002568\t0.000018\t119.086849\t22.904827\t123\t20\t30\t143\t2820\t1\t1\t0.000355\t0\t0.497518\t0.000355\t0\t0.000586\t0\t19"
     - path: output/picard/test.CollectMultipleMetrics.base_distribution_by_cycle.pdf
     - path: output/picard/test.CollectMultipleMetrics.base_distribution_by_cycle_metrics
       contains:

tests/modules/quast/test.yml

@@ -5,18 +5,18 @@
   files:
     - path: ./output/quast/report.tsv
     - path: ./output/quast/quast/transposed_report.txt
-      md5sum: 5dee51af1e7f916200d0a80f0c66be60
+      md5sum: 1dacbc04dfea073cbd74488d8b3cf821
     - path: ./output/quast/quast/transposed_report.tex
-      md5sum: 336ec8d7b403fe1e0519e3a39eadd691
+      md5sum: 8d74e5b3d7967820b0e61acdeeee6dcb
     - path: ./output/quast/quast/icarus.html
     - path: ./output/quast/quast/transposed_report.tsv
-      md5sum: 0e1b2eff1e8fd91a0bf80165d8f31ae5
+      md5sum: c0a0d2f998087b307f1a372ed31f5cde
     - path: ./output/quast/quast/report.tex
-      md5sum: a9aac7d2ac2263df7e4599e4431c7393
+      md5sum: 881df38fdcd5ce2a7b78ac3cbfebbde1
     - path: ./output/quast/quast/report.txt
-      md5sum: 2da78350f20819f2625bd467800700ad
+      md5sum: dd24fa9b6f95676006dc0928130d7d0b
     - path: ./output/quast/quast/report.tsv
-      md5sum: 38fb41afadc09ffcbef62e42fea49f5e
+      md5sum: f9b9f817bde917c1672a17ad1d072d6c
     - path: ./output/quast/quast/report.html
     - path: ./output/quast/quast/report.pdf
     - path: ./output/quast/quast/quast.log
@@ -32,14 +32,13 @@
     - path: ./output/quast/quast/basic_stats/Nx_plot.pdf
     - path: ./output/quast/quast/basic_stats/transcriptome_GC_content_plot.pdf
     - path: ./output/quast/quast/basic_stats/gc.icarus.txt
-      md5sum: b3a770802ff9b2dd4ee8e47bddb2df3e
+      md5sum: bdf3e7481880ee7dafbd53add5291da1
     - path: ./output/quast/quast/basic_stats/NGx_plot.pdf
     - path: ./output/quast/quast/basic_stats/GC_content_plot.pdf
     - path: ./output/quast/quast/aligned_stats/cumulative_plot.pdf
     - path: ./output/quast/quast/aligned_stats/NGAx_plot.pdf
     - path: ./output/quast/quast/aligned_stats/NAx_plot.pdf
     - path: ./output/quast/quast/contigs_reports/contigs_report_transcriptome.mis_contigs.info
-      md5sum: d41d8cd98f00b204e9800998ecf8427e
     - path: ./output/quast/quast/contigs_reports/misassemblies_frcurve_plot.pdf
     - path: ./output/quast/quast/contigs_reports/contigs_report_transcriptome.unaligned.info
       md5sum: a8505cf206bf53ca369f7e3073fee587
@@ -53,7 +52,6 @@
     - path: ./output/quast/quast/contigs_reports/misassemblies_report.tex
       md5sum: ec1f7a1d1fb4a1b465057cf897b90b51
     - path: ./output/quast/quast/contigs_reports/transcriptome.mis_contigs.fa
-      md5sum: d41d8cd98f00b204e9800998ecf8427e
     - path: ./output/quast/quast/contigs_reports/transposed_report_misassemblies.txt
       md5sum: fdb440c653e2f0306286798cacceaadb
     - path: ./output/quast/quast/contigs_reports/unaligned_report.tsv
@@ -71,13 +69,10 @@
       md5sum: ec9191d0acb5d5bce56b4842551a8598
     - path: ./output/quast/quast/contigs_reports/minimap_output/transcriptome.coords
       md5sum: dda3fc0addc41ecc0d5183dee6f95886
-    - path: ./output/quast/quast/contigs_reports/minimap_output/transcriptome.used_snps.gz
-      md5sum: 7b1db1b433cd95243a949bcb72e7e3a6
     - path: ./output/quast/quast/contigs_reports/minimap_output/transcriptome.sf
     - path: ./output/quast/quast/contigs_reports/minimap_output/transcriptome.unaligned
-      md5sum: d41d8cd98f00b204e9800998ecf8427e
     - path: ./output/quast/quast/contigs_reports/minimap_output/transcriptome.coords_tmp
-      md5sum: ce66eaeb99fdc11e4d50efadc1816e04
+      md5sum: e5e26685b36489cbcff906fb07320cde
     - path: ./output/quast/quast/icarus_viewers/alignment_viewer.html
     - path: ./output/quast/quast/icarus_viewers/contig_size_viewer.html
 
@@ -87,21 +82,21 @@
     - quast
   files:
     - path: ./output/quast/report.tsv
-      md5sum: 074e239aac0f298cf4cd2a28a9bb5690
+      md5sum: 40e321250db460120563bd0449d76fe3
     - path: ./output/quast/quast/transposed_report.txt
-      md5sum: 8784d7c7349498e1507e09fbf554625d
+      md5sum: 28d6c8051278e9fe4e2facef69329b67
     - path: ./output/quast/quast/transposed_report.tex
-      md5sum: 4c2a9dd0c1d3cbb80a2ac2577b5d363b
+      md5sum: 1cb47c314d9b0c1759375e88f7f91018
     - path: ./output/quast/quast/icarus.html
       md5sum: ecc0b67f3d4ff54568dfb83d8ac5911b
     - path: ./output/quast/quast/transposed_report.tsv
-      md5sum: f0b5f65b2050af83b6d170d384c7616b
+      md5sum: 5de57a794763ced1015c1e81eaa0b32b
     - path: ./output/quast/quast/report.tex
-      md5sum: 3da038cc5a02ef83e225c5277b87970b
+      md5sum: a2c8b9b1811fa948b0ccad1907f8d21b
     - path: ./output/quast/quast/report.txt
-      md5sum: bd2faaef244f02aa072d544c0d6d6e71
+      md5sum: 97f0306d20056e0efd213de88488b895
     - path: ./output/quast/quast/report.tsv
-      md5sum: 074e239aac0f298cf4cd2a28a9bb5690
+      md5sum: 40e321250db460120563bd0449d76fe3
     - path: ./output/quast/quast/report.html
     - path: ./output/quast/quast/report.pdf
     - path: ./output/quast/quast/quast.log

tests/modules/spades/test.yml

@@ -43,10 +43,10 @@
     - spades
   files:
     - path: output/spades/test.assembly.gfa.gz
-      md5sum: e12aaf83d8dbfc313339b7636ba43447
+      md5sum: 22f92cbade8f25be3ac170eaf09f4c7b
     - path: output/spades/test.contigs.fa.gz
-      md5sum: 78523f66d34ac4d5a4890f353c1a6ec6
+      md5sum: bb2d294a5752a6f3a208834b8799ec98
     - path: output/spades/test.scaffolds.fa.gz
-      md5sum: 78523f66d34ac4d5a4890f353c1a6ec6
+      md5sum: 65aa6e3364925ec617fffda3e84b4cbc
     - path: output/spades/test.spades.log
     - path: output/spades/warnings.log

tests/modules/vcflib/vcfuniq/test.yml

@@ -5,4 +5,4 @@
     - vcflib/vcfuniq
   files:
     - path: output/vcflib/test.uniq.vcf.gz
-      md5sum: fc178eb342a91dc0d1d568601ad8f8e2
+      md5sum: c5f2a6a912964c45e8231140420561f9