From 682f789f93070bd047868300dd018faf3d434e7c Mon Sep 17 00:00:00 2001 From: Harshil Patel Date: Thu, 7 Jul 2022 14:48:04 +0100 Subject: [PATCH] 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 | 6 +- modules/artic/minion/main.nf | 6 +- modules/bcftools/annotate/main.nf | 6 +- modules/bcftools/concat/main.nf | 6 +- modules/bcftools/consensus/main.nf | 6 +- modules/bcftools/filter/main.nf | 6 +- modules/bcftools/index/main.nf | 6 +- modules/bcftools/isec/main.nf | 6 +- modules/bcftools/merge/main.nf | 6 +- modules/bcftools/mpileup/main.nf | 6 +- modules/bcftools/norm/main.nf | 6 +- modules/bcftools/query/main.nf | 6 +- modules/bcftools/reheader/main.nf | 6 +- modules/bcftools/sort/main.nf | 6 +- modules/bcftools/stats/main.nf | 6 +- modules/bcftools/view/main.nf | 6 +- modules/custom/dumpsoftwareversions/main.nf | 6 +- modules/nanoplot/main.nf | 6 +- modules/nextclade/datasetget/main.nf | 8 +-- modules/nextclade/run/main.nf | 32 ++++----- modules/pangolin/main.nf | 6 +- modules/picard/addorreplacereadgroups/main.nf | 6 +- modules/picard/cleansam/main.nf | 6 +- modules/picard/collecthsmetrics/main.nf | 6 +- modules/picard/collectmultiplemetrics/main.nf | 6 +- modules/picard/collectwgsmetrics/main.nf | 6 +- .../picard/createsequencedictionary/main.nf | 6 +- modules/picard/crosscheckfingerprints/main.nf | 6 +- modules/picard/filtersamreads/main.nf | 6 +- modules/picard/fixmateinformation/main.nf | 6 +- modules/picard/liftovervcf/main.nf | 6 +- modules/picard/markduplicates/main.nf | 6 +- modules/picard/mergesamfiles/main.nf | 6 +- modules/picard/sortsam/main.nf | 6 +- modules/picard/sortvcf/main.nf | 6 +- modules/quast/main.nf | 6 +- modules/spades/main.nf | 6 +- modules/vcflib/vcfuniq/main.nf | 6 +- tests/modules/artic/minion/test.yml | 1 - tests/modules/bcftools/annotate/test.yml | 4 +- tests/modules/bcftools/concat/test.yml | 4 +- tests/modules/bcftools/filter/test.yml | 2 +- tests/modules/bcftools/index/test.yml | 4 +- tests/modules/bcftools/isec/test.yml | 8 +-- tests/modules/bcftools/merge/test.yml | 2 +- tests/modules/bcftools/mpileup/test.yml | 14 ++-- tests/modules/bcftools/query/test.yml | 2 +- tests/modules/bcftools/reheader/test.yml | 6 +- tests/modules/bcftools/sort/test.yml | 4 +- tests/modules/bcftools/stats/test.yml | 2 +- tests/modules/bcftools/view/test.yml | 4 +- .../custom/dumpsoftwareversions/main.nf | 2 +- tests/modules/nextclade/run/test.yml | 65 ++++++++++++++++--- tests/modules/pangolin/test.yml | 2 +- .../picard/collectmultiplemetrics/test.yml | 6 -- tests/modules/quast/test.yml | 35 +++++----- tests/modules/spades/test.yml | 6 +- tests/modules/vcflib/vcfuniq/test.yml | 2 +- 58 files changed, 235 insertions(+), 196 deletions(-) diff --git a/modules/artic/guppyplex/main.nf b/modules/artic/guppyplex/main.nf index 8e6b2879..12f6f68c 100644 --- a/modules/artic/guppyplex/main.nf +++ b/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' : - 'quay.io/biocontainers/artic:1.2.1--py_0' }" + 'https://depot.galaxyproject.org/singularity/artic:1.2.2--pyhdfd78af_0' : + 'quay.io/biocontainers/artic:1.2.2--pyhdfd78af_0' }" input: tuple val(meta), path(fastq_dir) diff --git a/modules/artic/minion/main.nf b/modules/artic/minion/main.nf index 22a6fd87..9d00ef6a 100644 --- a/modules/artic/minion/main.nf +++ b/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' : - 'quay.io/biocontainers/artic:1.2.1--py_0' }" + 'https://depot.galaxyproject.org/singularity/artic:1.2.2--pyhdfd78af_0' : + 'quay.io/biocontainers/artic:1.2.2--pyhdfd78af_0' }" input: tuple val(meta), path(fastq) diff --git a/modules/bcftools/annotate/main.nf b/modules/bcftools/annotate/main.nf index 40e32047..da94d3c0 100644 --- a/modules/bcftools/annotate/main.nf +++ b/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': - 'quay.io/biocontainers/bcftools:1.15--haf5b3da_0' }" + 'https://depot.galaxyproject.org/singularity/bcftools:1.15.1--h0ea216a_0': + 'quay.io/biocontainers/bcftools:1.15.1--h0ea216a_0' }" input: tuple val(meta), path(input) diff --git a/modules/bcftools/concat/main.nf b/modules/bcftools/concat/main.nf index 257ee36f..d2a58a55 100644 --- a/modules/bcftools/concat/main.nf +++ b/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' : - 'quay.io/biocontainers/bcftools:1.14--h88f3f91_0' }" + 'https://depot.galaxyproject.org/singularity/bcftools:1.15.1--h0ea216a_0': + 'quay.io/biocontainers/bcftools:1.15.1--h0ea216a_0' }" input: tuple val(meta), path(vcfs), path(tbi) diff --git a/modules/bcftools/consensus/main.nf b/modules/bcftools/consensus/main.nf index a0c436e2..e28dc7f4 100644 --- a/modules/bcftools/consensus/main.nf +++ b/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' : - 'quay.io/biocontainers/bcftools:1.14--h88f3f91_0' }" + 'https://depot.galaxyproject.org/singularity/bcftools:1.15.1--h0ea216a_0': + 'quay.io/biocontainers/bcftools:1.15.1--h0ea216a_0' }" input: tuple val(meta), path(vcf), path(tbi), path(fasta) diff --git a/modules/bcftools/filter/main.nf b/modules/bcftools/filter/main.nf index 82961e32..ef99eda2 100644 --- a/modules/bcftools/filter/main.nf +++ b/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' : - 'quay.io/biocontainers/bcftools:1.14--h88f3f91_0' }" + 'https://depot.galaxyproject.org/singularity/bcftools:1.15.1--h0ea216a_0': + 'quay.io/biocontainers/bcftools:1.15.1--h0ea216a_0' }" input: tuple val(meta), path(vcf) diff --git a/modules/bcftools/index/main.nf b/modules/bcftools/index/main.nf index 548a9277..119019fc 100644 --- a/modules/bcftools/index/main.nf +++ b/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' : - 'quay.io/biocontainers/bcftools:1.14--h88f3f91_0' }" + 'https://depot.galaxyproject.org/singularity/bcftools:1.15.1--h0ea216a_0': + 'quay.io/biocontainers/bcftools:1.15.1--h0ea216a_0' }" input: tuple val(meta), path(vcf) diff --git a/modules/bcftools/isec/main.nf b/modules/bcftools/isec/main.nf index c8f89753..43d7b136 100644 --- a/modules/bcftools/isec/main.nf +++ b/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' : - 'quay.io/biocontainers/bcftools:1.14--h88f3f91_0' }" + 'https://depot.galaxyproject.org/singularity/bcftools:1.15.1--h0ea216a_0': + 'quay.io/biocontainers/bcftools:1.15.1--h0ea216a_0' }" input: tuple val(meta), path(vcfs), path(tbis) diff --git a/modules/bcftools/merge/main.nf b/modules/bcftools/merge/main.nf index 7bee5a9b..082b229c 100644 --- a/modules/bcftools/merge/main.nf +++ b/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' : - 'quay.io/biocontainers/bcftools:1.14--h88f3f91_0' }" + 'https://depot.galaxyproject.org/singularity/bcftools:1.15.1--h0ea216a_0': + 'quay.io/biocontainers/bcftools:1.15.1--h0ea216a_0' }" input: tuple val(meta), path(vcfs), path(tbis) diff --git a/modules/bcftools/mpileup/main.nf b/modules/bcftools/mpileup/main.nf index 676eae7a..b7795bfc 100644 --- a/modules/bcftools/mpileup/main.nf +++ b/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' : - 'quay.io/biocontainers/bcftools:1.14--h88f3f91_0' }" + 'https://depot.galaxyproject.org/singularity/bcftools:1.15.1--h0ea216a_0': + 'quay.io/biocontainers/bcftools:1.15.1--h0ea216a_0' }" input: tuple val(meta), path(bam) diff --git a/modules/bcftools/norm/main.nf b/modules/bcftools/norm/main.nf index c48aa9bf..96f306bc 100644 --- a/modules/bcftools/norm/main.nf +++ b/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' : - 'quay.io/biocontainers/bcftools:1.14--h88f3f91_0' }" + 'https://depot.galaxyproject.org/singularity/bcftools:1.15.1--h0ea216a_0': + 'quay.io/biocontainers/bcftools:1.15.1--h0ea216a_0' }" input: tuple val(meta), path(vcf), path(tbi) diff --git a/modules/bcftools/query/main.nf b/modules/bcftools/query/main.nf index 8921abdd..5de34a9e 100644 --- a/modules/bcftools/query/main.nf +++ b/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' : - 'quay.io/biocontainers/bcftools:1.14--h88f3f91_0' }" + 'https://depot.galaxyproject.org/singularity/bcftools:1.15.1--h0ea216a_0': + 'quay.io/biocontainers/bcftools:1.15.1--h0ea216a_0' }" input: tuple val(meta), path(vcf), path(tbi) diff --git a/modules/bcftools/reheader/main.nf b/modules/bcftools/reheader/main.nf index 7d2abecf..457cf4d9 100644 --- a/modules/bcftools/reheader/main.nf +++ b/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' : - 'quay.io/biocontainers/bcftools:1.14--h88f3f91_0' }" + 'https://depot.galaxyproject.org/singularity/bcftools:1.15.1--h0ea216a_0': + 'quay.io/biocontainers/bcftools:1.15.1--h0ea216a_0' }" input: tuple val(meta), path(vcf) diff --git a/modules/bcftools/sort/main.nf b/modules/bcftools/sort/main.nf index 8478fe25..9552b57c 100644 --- a/modules/bcftools/sort/main.nf +++ b/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': - 'quay.io/biocontainers/bcftools:1.14--h88f3f91_0' }" + 'https://depot.galaxyproject.org/singularity/bcftools:1.15.1--h0ea216a_0': + 'quay.io/biocontainers/bcftools:1.15.1--h0ea216a_0' }" input: tuple val(meta), path(vcf) diff --git a/modules/bcftools/stats/main.nf b/modules/bcftools/stats/main.nf index 7e150d1f..1e0f3a47 100644 --- a/modules/bcftools/stats/main.nf +++ b/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' : - 'quay.io/biocontainers/bcftools:1.14--h88f3f91_0' }" + 'https://depot.galaxyproject.org/singularity/bcftools:1.15.1--h0ea216a_0': + 'quay.io/biocontainers/bcftools:1.15.1--h0ea216a_0' }" input: tuple val(meta), path(vcf) diff --git a/modules/bcftools/view/main.nf b/modules/bcftools/view/main.nf index ca1121a5..3df08a57 100644 --- a/modules/bcftools/view/main.nf +++ b/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' : - 'quay.io/biocontainers/bcftools:1.14--h88f3f91_0' }" + 'https://depot.galaxyproject.org/singularity/bcftools:1.15.1--h0ea216a_0': + 'quay.io/biocontainers/bcftools:1.15.1--h0ea216a_0' }" input: tuple val(meta), path(vcf), path(index) diff --git a/modules/custom/dumpsoftwareversions/main.nf b/modules/custom/dumpsoftwareversions/main.nf index 327d5100..12293efc 100644 --- a/modules/custom/dumpsoftwareversions/main.nf +++ b/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 "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/multiqc:1.11--pyhdfd78af_0' : - 'quay.io/biocontainers/multiqc:1.11--pyhdfd78af_0' }" + 'https://depot.galaxyproject.org/singularity/multiqc:1.12--pyhdfd78af_0' : + 'quay.io/biocontainers/multiqc:1.12--pyhdfd78af_0' }" input: path versions diff --git a/modules/nanoplot/main.nf b/modules/nanoplot/main.nf index 083e2374..83c0e2ec 100644 --- a/modules/nanoplot/main.nf +++ b/modules/nanoplot/main.nf @@ -2,10 +2,10 @@ process NANOPLOT { tag "$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 "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/nanoplot:1.39.0--pyhdfd78af_0' : - 'quay.io/biocontainers/nanoplot:1.39.0--pyhdfd78af_0' }" + 'https://depot.galaxyproject.org/singularity/nanoplot:1.40.0--pyhdfd78af_0' : + 'quay.io/biocontainers/nanoplot:1.40.0--pyhdfd78af_0' }" input: tuple val(meta), path(ontfile) diff --git a/modules/nextclade/datasetget/main.nf b/modules/nextclade/datasetget/main.nf index 4dd82ee3..a9f52c84 100644 --- a/modules/nextclade/datasetget/main.nf +++ b/modules/nextclade/datasetget/main.nf @@ -2,10 +2,10 @@ process NEXTCLADE_DATASETGET { tag "$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 "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/nextclade:1.10.2--h9ee0642_0' : - 'quay.io/biocontainers/nextclade:1.10.2--h9ee0642_0' }" + 'https://depot.galaxyproject.org/singularity/nextclade:2.2.0--h9ee0642_0' : + 'quay.io/biocontainers/nextclade:2.2.0--h9ee0642_0' }" input: val dataset @@ -36,7 +36,7 @@ process NEXTCLADE_DATASETGET { cat <<-END_VERSIONS > versions.yml "${task.process}": - nextclade: \$(nextclade --version 2>&1) + nextclade: \$(echo \$(nextclade --version 2>&1) | sed 's/^.*nextclade //; s/ .*\$//') END_VERSIONS """ } diff --git a/modules/nextclade/run/main.nf b/modules/nextclade/run/main.nf index 4d4bdb88..22f72781 100644 --- a/modules/nextclade/run/main.nf +++ b/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' : - 'quay.io/biocontainers/nextclade:1.10.2--h9ee0642_0' }" + 'https://depot.galaxyproject.org/singularity/nextclade:2.2.0--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}.tsv") , emit: tsv - tuple val(meta), path("${prefix}.json") , emit: json - tuple val(meta), path("${prefix}.tree.json"), emit: json_tree - path "versions.yml" , emit: versions + tuple val(meta), path("${prefix}.csv") , optional:true, emit: csv + tuple val(meta), path("${prefix}.errors.csv") , optional:true, emit: csv_errors + tuple val(meta), path("${prefix}.insertions.csv"), optional:true, emit: csv_insertions + tuple val(meta), path("${prefix}.tsv") , optional:true, emit: tsv + 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-tsv ${prefix}.tsv \\ - --output-json ${prefix}.json \\ - --output-tree ${prefix}.tree.json \\ - --output-basename ${prefix} + --output-all ./ \\ + --output-basename ${prefix} \\ + $fasta cat <<-END_VERSIONS > versions.yml "${task.process}": - nextclade: \$(nextclade --version 2>&1) + nextclade: \$(echo \$(nextclade --version 2>&1) | sed 's/^.*nextclade //; s/ .*\$//') END_VERSIONS """ } diff --git a/modules/pangolin/main.nf b/modules/pangolin/main.nf index 5af557ac..6414b5d3 100644 --- a/modules/pangolin/main.nf +++ b/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' : - 'quay.io/biocontainers/pangolin:3.1.20--pyhdfd78af_0' }" + 'https://depot.galaxyproject.org/singularity/pangolin:4.1.1--pyhdfd78af_0' : + 'quay.io/biocontainers/pangolin:4.1.1--pyhdfd78af_0' }" input: tuple val(meta), path(fasta) diff --git a/modules/picard/addorreplacereadgroups/main.nf b/modules/picard/addorreplacereadgroups/main.nf index aff83c9f..8e9bda07 100644 --- a/modules/picard/addorreplacereadgroups/main.nf +++ b/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' : - 'quay.io/biocontainers/picard:2.27.2--hdfd78af_0' }" + 'https://depot.galaxyproject.org/singularity/picard:2.27.4--hdfd78af_0' : + 'quay.io/biocontainers/picard:2.27.4--hdfd78af_0' }" input: tuple val(meta), path(bam) diff --git a/modules/picard/cleansam/main.nf b/modules/picard/cleansam/main.nf index 0042c3f1..36b86502 100644 --- a/modules/picard/cleansam/main.nf +++ b/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' : - 'quay.io/biocontainers/picard:2.27.2--hdfd78af_0' }" + 'https://depot.galaxyproject.org/singularity/picard:2.27.4--hdfd78af_0' : + 'quay.io/biocontainers/picard:2.27.4--hdfd78af_0' }" input: tuple val(meta), path(bam) diff --git a/modules/picard/collecthsmetrics/main.nf b/modules/picard/collecthsmetrics/main.nf index 52d5c84a..6cc04dbf 100644 --- a/modules/picard/collecthsmetrics/main.nf +++ b/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' : - 'quay.io/biocontainers/picard:2.27.2--hdfd78af_0' }" + 'https://depot.galaxyproject.org/singularity/picard:2.27.4--hdfd78af_0' : + 'quay.io/biocontainers/picard:2.27.4--hdfd78af_0' }" input: tuple val(meta), path(bam) diff --git a/modules/picard/collectmultiplemetrics/main.nf b/modules/picard/collectmultiplemetrics/main.nf index 2f991321..63f4e872 100644 --- a/modules/picard/collectmultiplemetrics/main.nf +++ b/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' : - 'quay.io/biocontainers/picard:2.27.2--hdfd78af_0' }" + 'https://depot.galaxyproject.org/singularity/picard:2.27.4--hdfd78af_0' : + 'quay.io/biocontainers/picard:2.27.4--hdfd78af_0' }" input: tuple val(meta), path(bam) diff --git a/modules/picard/collectwgsmetrics/main.nf b/modules/picard/collectwgsmetrics/main.nf index e231afe2..d3153eed 100644 --- a/modules/picard/collectwgsmetrics/main.nf +++ b/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' : - 'quay.io/biocontainers/picard:2.27.2--hdfd78af_0' }" + 'https://depot.galaxyproject.org/singularity/picard:2.27.4--hdfd78af_0' : + 'quay.io/biocontainers/picard:2.27.4--hdfd78af_0' }" input: tuple val(meta), path(bam) diff --git a/modules/picard/createsequencedictionary/main.nf b/modules/picard/createsequencedictionary/main.nf index 16a5ff19..0976f049 100644 --- a/modules/picard/createsequencedictionary/main.nf +++ b/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' : - 'quay.io/biocontainers/picard:2.27.2--hdfd78af_0' }" + 'https://depot.galaxyproject.org/singularity/picard:2.27.4--hdfd78af_0' : + 'quay.io/biocontainers/picard:2.27.4--hdfd78af_0' }" input: tuple val(meta), path(fasta) diff --git a/modules/picard/crosscheckfingerprints/main.nf b/modules/picard/crosscheckfingerprints/main.nf index c7c4766c..d4eef2f2 100644 --- a/modules/picard/crosscheckfingerprints/main.nf +++ b/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' : - 'quay.io/biocontainers/picard:2.27.2--hdfd78af_0' }" + 'https://depot.galaxyproject.org/singularity/picard:2.27.4--hdfd78af_0' : + 'quay.io/biocontainers/picard:2.27.4--hdfd78af_0' }" input: tuple val(meta), path(input1) diff --git a/modules/picard/filtersamreads/main.nf b/modules/picard/filtersamreads/main.nf index e17c4686..fda97803 100644 --- a/modules/picard/filtersamreads/main.nf +++ b/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' : - 'quay.io/biocontainers/picard:2.27.2--hdfd78af_0' }" + 'https://depot.galaxyproject.org/singularity/picard:2.27.4--hdfd78af_0' : + 'quay.io/biocontainers/picard:2.27.4--hdfd78af_0' }" input: tuple val(meta), path(bam), path(readlist) diff --git a/modules/picard/fixmateinformation/main.nf b/modules/picard/fixmateinformation/main.nf index 616acce8..eea9eca9 100644 --- a/modules/picard/fixmateinformation/main.nf +++ b/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' : - 'quay.io/biocontainers/picard:2.27.2--hdfd78af_0' }" + 'https://depot.galaxyproject.org/singularity/picard:2.27.4--hdfd78af_0' : + 'quay.io/biocontainers/picard:2.27.4--hdfd78af_0' }" input: tuple val(meta), path(bam) diff --git a/modules/picard/liftovervcf/main.nf b/modules/picard/liftovervcf/main.nf index a82f1466..062f2086 100644 --- a/modules/picard/liftovervcf/main.nf +++ b/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' : - 'quay.io/biocontainers/picard:2.27.2--hdfd78af_0' }" + 'https://depot.galaxyproject.org/singularity/picard:2.27.4--hdfd78af_0' : + 'quay.io/biocontainers/picard:2.27.4--hdfd78af_0' }" input: tuple val(meta), path(input_vcf) diff --git a/modules/picard/markduplicates/main.nf b/modules/picard/markduplicates/main.nf index 87f913d4..4e559fea 100644 --- a/modules/picard/markduplicates/main.nf +++ b/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' : - 'quay.io/biocontainers/picard:2.27.2--hdfd78af_0' }" + 'https://depot.galaxyproject.org/singularity/picard:2.27.4--hdfd78af_0' : + 'quay.io/biocontainers/picard:2.27.4--hdfd78af_0' }" input: tuple val(meta), path(bam) diff --git a/modules/picard/mergesamfiles/main.nf b/modules/picard/mergesamfiles/main.nf index d65f518c..cccf4d3d 100644 --- a/modules/picard/mergesamfiles/main.nf +++ b/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' : - 'quay.io/biocontainers/picard:2.27.2--hdfd78af_0' }" + 'https://depot.galaxyproject.org/singularity/picard:2.27.4--hdfd78af_0' : + 'quay.io/biocontainers/picard:2.27.4--hdfd78af_0' }" input: tuple val(meta), path(bams) diff --git a/modules/picard/sortsam/main.nf b/modules/picard/sortsam/main.nf index 5e09d907..759c2c3d 100644 --- a/modules/picard/sortsam/main.nf +++ b/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' : - 'quay.io/biocontainers/picard:2.27.2--hdfd78af_0' }" + 'https://depot.galaxyproject.org/singularity/picard:2.27.4--hdfd78af_0' : + 'quay.io/biocontainers/picard:2.27.4--hdfd78af_0' }" input: tuple val(meta), path(bam) diff --git a/modules/picard/sortvcf/main.nf b/modules/picard/sortvcf/main.nf index 8f886393..b57b39c6 100644 --- a/modules/picard/sortvcf/main.nf +++ b/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' : - 'quay.io/biocontainers/picard:2.27.2--hdfd78af_0' }" + 'https://depot.galaxyproject.org/singularity/picard:2.27.4--hdfd78af_0' : + 'quay.io/biocontainers/picard:2.27.4--hdfd78af_0' }" input: tuple val(meta), path(vcf) diff --git a/modules/quast/main.nf b/modules/quast/main.nf index beb797d4..5585491b 100644 --- a/modules/quast/main.nf +++ b/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 "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/quast:5.0.2--py37pl526hb5aa323_2' : - 'quay.io/biocontainers/quast:5.0.2--py37pl526hb5aa323_2' }" + 'https://depot.galaxyproject.org/singularity/quast:5.2.0--py39pl5321h2add14b_1' : + 'quay.io/biocontainers/quast:5.2.0--py39pl5321h2add14b_1' }" input: path consensus diff --git a/modules/spades/main.nf b/modules/spades/main.nf index b7ece6f6..a467fcd7 100644 --- a/modules/spades/main.nf +++ b/modules/spades/main.nf @@ -2,10 +2,10 @@ process SPADES { tag "$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 "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/spades:3.15.3--h95f258a_0' : - 'quay.io/biocontainers/spades:3.15.3--h95f258a_0' }" + 'https://depot.galaxyproject.org/singularity/spades:3.15.4--h95f258a_0' : + 'quay.io/biocontainers/spades:3.15.4--h95f258a_0' }" input: tuple val(meta), path(illumina), path(pacbio), path(nanopore) diff --git a/modules/vcflib/vcfuniq/main.nf b/modules/vcflib/vcfuniq/main.nf index 05d9b9d5..707f074b 100644 --- a/modules/vcflib/vcfuniq/main.nf +++ b/modules/vcflib/vcfuniq/main.nf @@ -3,10 +3,10 @@ process VCFLIB_VCFUNIQ { label 'process_low' // WARN: Version information not provided by tool on CLI. Please update version string below when bumping container versions. - conda (params.enable_conda ? "bioconda::vcflib=1.0.2" : null) + conda (params.enable_conda ? "bioconda::vcflib=1.0.3" : null) container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/vcflib:1.0.2--h3198e80_5': - 'quay.io/biocontainers/vcflib:1.0.2--h3198e80_5' }" + 'https://depot.galaxyproject.org/singularity/vcflib:1.0.3--hecb563c_1': + 'quay.io/biocontainers/vcflib:1.0.3--hecb563c_1' }" input: tuple val(meta), path(vcf), path(tbi) diff --git a/tests/modules/artic/minion/test.yml b/tests/modules/artic/minion/test.yml index 401a8470..c8ad52d7 100644 --- a/tests/modules/artic/minion/test.yml +++ b/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 diff --git a/tests/modules/bcftools/annotate/test.yml b/tests/modules/bcftools/annotate/test.yml index e8cdcc4b..c3a183b0 100644 --- a/tests/modules/bcftools/annotate/test.yml +++ b/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 diff --git a/tests/modules/bcftools/concat/test.yml b/tests/modules/bcftools/concat/test.yml index 0d12badc..cffe3d66 100644 --- a/tests/modules/bcftools/concat/test.yml +++ b/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 diff --git a/tests/modules/bcftools/filter/test.yml b/tests/modules/bcftools/filter/test.yml index da842538..096071bd 100644 --- a/tests/modules/bcftools/filter/test.yml +++ b/tests/modules/bcftools/filter/test.yml @@ -5,4 +5,4 @@ - bcftools files: - path: output/bcftools/test.vcf.gz - md5sum: fc178eb342a91dc0d1d568601ad8f8e2 + md5sum: c5f2a6a912964c45e8231140420561f9 diff --git a/tests/modules/bcftools/index/test.yml b/tests/modules/bcftools/index/test.yml index f1a29437..b8a7d705 100644 --- a/tests/modules/bcftools/index/test.yml +++ b/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 diff --git a/tests/modules/bcftools/isec/test.yml b/tests/modules/bcftools/isec/test.yml index fc887d9d..6329c34e 100644 --- a/tests/modules/bcftools/isec/test.yml +++ b/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 diff --git a/tests/modules/bcftools/merge/test.yml b/tests/modules/bcftools/merge/test.yml index 6c9dd556..cc3621d4 100644 --- a/tests/modules/bcftools/merge/test.yml +++ b/tests/modules/bcftools/merge/test.yml @@ -5,4 +5,4 @@ - bcftools files: - path: output/bcftools/test.vcf.gz - md5sum: 52165fc4149c61547e63800b876c9661 + md5sum: 744b28bef1469aabdcfd354293ef725d diff --git a/tests/modules/bcftools/mpileup/test.yml b/tests/modules/bcftools/mpileup/test.yml index 35c33553..85749cdb 100644 --- a/tests/modules/bcftools/mpileup/test.yml +++ b/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 diff --git a/tests/modules/bcftools/query/test.yml b/tests/modules/bcftools/query/test.yml index 647c62bb..69199109 100644 --- a/tests/modules/bcftools/query/test.yml +++ b/tests/modules/bcftools/query/test.yml @@ -14,4 +14,4 @@ - bcftools/query files: - path: output/bcftools/out.txt - md5sum: 6bb5df49bfb5af39f7037cdf95032aac + md5sum: 5a87e0865df2f0ab2884fc113ec2a70d diff --git a/tests/modules/bcftools/reheader/test.yml b/tests/modules/bcftools/reheader/test.yml index 1ce0b104..2a3e4868 100644 --- a/tests/modules/bcftools/reheader/test.yml +++ b/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 diff --git a/tests/modules/bcftools/sort/test.yml b/tests/modules/bcftools/sort/test.yml index 694fc307..fbb18300 100644 --- a/tests/modules/bcftools/sort/test.yml +++ b/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 diff --git a/tests/modules/bcftools/stats/test.yml b/tests/modules/bcftools/stats/test.yml index 59f3b991..a9366f54 100644 --- a/tests/modules/bcftools/stats/test.yml +++ b/tests/modules/bcftools/stats/test.yml @@ -5,4 +5,4 @@ - bcftools/stats files: - path: output/bcftools/test.bcftools_stats.txt - md5sum: 1f948177196b09806782e1ee801463a2 + md5sum: b7b9abecf0f6a77c1472a380feca708b diff --git a/tests/modules/bcftools/view/test.yml b/tests/modules/bcftools/view/test.yml index fa926dd6..b66402a3 100644 --- a/tests/modules/bcftools/view/test.yml +++ b/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 diff --git a/tests/modules/custom/dumpsoftwareversions/main.nf b/tests/modules/custom/dumpsoftwareversions/main.nf index 95a43a82..b1761656 100644 --- a/tests/modules/custom/dumpsoftwareversions/main.nf +++ b/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 diff --git a/tests/modules/nextclade/run/test.yml b/tests/modules/nextclade/run/test.yml index ea846378..5cf25e42 100644 --- a/tests/modules/nextclade/run/test.yml +++ b/tests/modules/nextclade/run/test.yml @@ -1,13 +1,62 @@ -- name: 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 +- 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 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 - - path: output/nextclade/test.tree.json - md5sum: 3591b4dc1542995a7ffcffcb1f52b524 + md5sum: 7f4bea521bcef4d1bca02c51d11b2fe1 + - path: output/nextclade/test_gene_E.translation.fasta + 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 diff --git a/tests/modules/pangolin/test.yml b/tests/modules/pangolin/test.yml index f11c5c1d..0ddb2195 100644 --- a/tests/modules/pangolin/test.yml +++ b/tests/modules/pangolin/test.yml @@ -4,4 +4,4 @@ - pangolin files: - path: ./output/pangolin/test.pangolin.csv - md5sum: 378f211c219bb644dea63adf7c3254fe + md5sum: 3484156c2f2e2e638431be7934cfc5b7 diff --git a/tests/modules/picard/collectmultiplemetrics/test.yml b/tests/modules/picard/collectmultiplemetrics/test.yml index bccc0d0b..4f3cecc4 100644 --- a/tests/modules/picard/collectmultiplemetrics/test.yml +++ b/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: diff --git a/tests/modules/quast/test.yml b/tests/modules/quast/test.yml index 166cd896..beb895f3 100644 --- a/tests/modules/quast/test.yml +++ b/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 diff --git a/tests/modules/spades/test.yml b/tests/modules/spades/test.yml index 98bc9c8c..d016c1a0 100644 --- a/tests/modules/spades/test.yml +++ b/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 diff --git a/tests/modules/vcflib/vcfuniq/test.yml b/tests/modules/vcflib/vcfuniq/test.yml index 6d998225..aadcd77f 100644 --- a/tests/modules/vcflib/vcfuniq/test.yml +++ b/tests/modules/vcflib/vcfuniq/test.yml @@ -5,4 +5,4 @@ - vcflib/vcfuniq files: - path: output/vcflib/test.uniq.vcf.gz - md5sum: fc178eb342a91dc0d1d568601ad8f8e2 + md5sum: c5f2a6a912964c45e8231140420561f9