From 4d73bd8cf9715a2a5d7b548411ede2de74c4a96f Mon Sep 17 00:00:00 2001 From: Matthias De Smet <11850640+matthdsm@users.noreply.github.com> Date: Thu, 31 Oct 2024 11:21:16 +0100 Subject: [PATCH 1/4] bump gatk4 --- .../nf-core/gatk4/addorreplacereadgroups/environment.yml | 2 +- modules/nf-core/gatk4/addorreplacereadgroups/main.nf | 4 ++-- modules/nf-core/gatk4/annotateintervals/environment.yml | 2 +- modules/nf-core/gatk4/annotateintervals/main.nf | 4 ++-- modules/nf-core/gatk4/applybqsr/environment.yml | 2 +- modules/nf-core/gatk4/applybqsr/main.nf | 4 ++-- modules/nf-core/gatk4/applyvqsr/environment.yml | 2 +- modules/nf-core/gatk4/applyvqsr/main.nf | 4 ++-- modules/nf-core/gatk4/asereadcounter/environment.yml | 2 +- modules/nf-core/gatk4/asereadcounter/main.nf | 4 ++-- modules/nf-core/gatk4/baserecalibrator/environment.yml | 2 +- modules/nf-core/gatk4/baserecalibrator/main.nf | 4 ++-- modules/nf-core/gatk4/bedtointervallist/environment.yml | 2 +- modules/nf-core/gatk4/bedtointervallist/main.nf | 4 ++-- .../nf-core/gatk4/calculatecontamination/environment.yml | 2 +- modules/nf-core/gatk4/calculatecontamination/main.nf | 4 ++-- modules/nf-core/gatk4/calibratedragstrmodel/environment.yml | 2 +- modules/nf-core/gatk4/calibratedragstrmodel/main.nf | 4 ++-- modules/nf-core/gatk4/collectreadcounts/environment.yml | 2 +- modules/nf-core/gatk4/collectreadcounts/main.nf | 4 ++-- modules/nf-core/gatk4/collectsvevidence/environment.yml | 2 +- modules/nf-core/gatk4/collectsvevidence/main.nf | 4 ++-- modules/nf-core/gatk4/combinegvcfs/environment.yml | 2 +- modules/nf-core/gatk4/combinegvcfs/main.nf | 4 ++-- modules/nf-core/gatk4/composestrtablefile/environment.yml | 2 +- modules/nf-core/gatk4/composestrtablefile/main.nf | 4 ++-- modules/nf-core/gatk4/condensedepthevidence/environment.yml | 2 +- modules/nf-core/gatk4/condensedepthevidence/main.nf | 4 ++-- .../gatk4/createreadcountpanelofnormals/environment.yml | 2 +- modules/nf-core/gatk4/createreadcountpanelofnormals/main.nf | 4 ++-- .../nf-core/gatk4/createsequencedictionary/environment.yml | 2 +- modules/nf-core/gatk4/createsequencedictionary/main.nf | 4 ++-- .../gatk4/createsomaticpanelofnormals/environment.yml | 2 +- modules/nf-core/gatk4/createsomaticpanelofnormals/main.nf | 4 ++-- modules/nf-core/gatk4/denoisereadcounts/environment.yml | 2 +- modules/nf-core/gatk4/denoisereadcounts/main.nf | 4 ++-- .../gatk4/determinegermlinecontigploidy/environment.yml | 5 +++++ modules/nf-core/gatk4/determinegermlinecontigploidy/main.nf | 6 ++++-- .../nf-core/gatk4/estimatelibrarycomplexity/environment.yml | 2 +- modules/nf-core/gatk4/estimatelibrarycomplexity/main.nf | 4 ++-- modules/nf-core/gatk4/fastqtosam/environment.yml | 2 +- modules/nf-core/gatk4/fastqtosam/main.nf | 4 ++-- modules/nf-core/gatk4/filterintervals/environment.yml | 2 +- modules/nf-core/gatk4/filterintervals/main.nf | 4 ++-- modules/nf-core/gatk4/filtermutectcalls/environment.yml | 2 +- modules/nf-core/gatk4/filtermutectcalls/main.nf | 4 ++-- modules/nf-core/gatk4/filtervarianttranches/environment.yml | 2 +- modules/nf-core/gatk4/filtervarianttranches/main.nf | 4 ++-- modules/nf-core/gatk4/gatherbqsrreports/environment.yml | 2 +- modules/nf-core/gatk4/gatherbqsrreports/main.nf | 4 ++-- modules/nf-core/gatk4/gatherpileupsummaries/environment.yml | 2 +- modules/nf-core/gatk4/gatherpileupsummaries/main.nf | 4 ++-- modules/nf-core/gatk4/genomicsdbimport/environment.yml | 2 +- modules/nf-core/gatk4/genomicsdbimport/main.nf | 4 ++-- modules/nf-core/gatk4/genotypegvcfs/environment.yml | 2 +- modules/nf-core/gatk4/genotypegvcfs/main.nf | 4 ++-- modules/nf-core/gatk4/germlinecnvcaller/environment.yml | 5 +++++ modules/nf-core/gatk4/germlinecnvcaller/main.nf | 6 ++++-- modules/nf-core/gatk4/getpileupsummaries/environment.yml | 2 +- modules/nf-core/gatk4/getpileupsummaries/main.nf | 4 ++-- modules/nf-core/gatk4/haplotypecaller/environment.yml | 2 +- modules/nf-core/gatk4/haplotypecaller/main.nf | 4 ++-- modules/nf-core/gatk4/indexfeaturefile/environment.yml | 2 +- modules/nf-core/gatk4/indexfeaturefile/main.nf | 4 ++-- modules/nf-core/gatk4/intervallisttobed/environment.yml | 2 +- modules/nf-core/gatk4/intervallisttobed/main.nf | 4 ++-- modules/nf-core/gatk4/intervallisttools/environment.yml | 2 +- modules/nf-core/gatk4/intervallisttools/main.nf | 4 ++-- .../nf-core/gatk4/learnreadorientationmodel/environment.yml | 2 +- modules/nf-core/gatk4/learnreadorientationmodel/main.nf | 4 ++-- .../nf-core/gatk4/leftalignandtrimvariants/environment.yml | 2 +- modules/nf-core/gatk4/leftalignandtrimvariants/main.nf | 4 ++-- modules/nf-core/gatk4/markduplicates/environment.yml | 2 +- modules/nf-core/gatk4/mergebamalignment/environment.yml | 2 +- modules/nf-core/gatk4/mergebamalignment/main.nf | 4 ++-- modules/nf-core/gatk4/mergemutectstats/environment.yml | 2 +- modules/nf-core/gatk4/mergemutectstats/main.nf | 4 ++-- modules/nf-core/gatk4/mergevcfs/environment.yml | 2 +- modules/nf-core/gatk4/mergevcfs/main.nf | 4 ++-- modules/nf-core/gatk4/mutect2/environment.yml | 2 +- modules/nf-core/gatk4/mutect2/main.nf | 4 ++-- modules/nf-core/gatk4/preprocessintervals/environment.yml | 2 +- modules/nf-core/gatk4/preprocessintervals/main.nf | 4 ++-- modules/nf-core/gatk4/printreads/environment.yml | 2 +- modules/nf-core/gatk4/printreads/main.nf | 4 ++-- modules/nf-core/gatk4/printsvevidence/environment.yml | 2 +- modules/nf-core/gatk4/printsvevidence/main.nf | 4 ++-- modules/nf-core/gatk4/reblockgvcf/environment.yml | 2 +- modules/nf-core/gatk4/reblockgvcf/main.nf | 4 ++-- modules/nf-core/gatk4/revertsam/environment.yml | 2 +- modules/nf-core/gatk4/revertsam/main.nf | 4 ++-- modules/nf-core/gatk4/samtofastq/environment.yml | 2 +- modules/nf-core/gatk4/samtofastq/main.nf | 4 ++-- modules/nf-core/gatk4/selectvariants/environment.yml | 2 +- modules/nf-core/gatk4/selectvariants/main.nf | 4 ++-- modules/nf-core/gatk4/shiftfasta/environment.yml | 2 +- modules/nf-core/gatk4/shiftfasta/main.nf | 4 ++-- modules/nf-core/gatk4/sitedepthtobaf/environment.yml | 2 +- modules/nf-core/gatk4/sitedepthtobaf/main.nf | 4 ++-- modules/nf-core/gatk4/splitcram/environment.yml | 2 +- modules/nf-core/gatk4/splitcram/main.nf | 4 ++-- modules/nf-core/gatk4/splitintervals/environment.yml | 2 +- modules/nf-core/gatk4/splitintervals/main.nf | 4 ++-- modules/nf-core/gatk4/splitncigarreads/environment.yml | 2 +- modules/nf-core/gatk4/splitncigarreads/main.nf | 4 ++-- modules/nf-core/gatk4/svannotate/environment.yml | 2 +- modules/nf-core/gatk4/svannotate/main.nf | 4 ++-- modules/nf-core/gatk4/svcluster/environment.yml | 2 +- modules/nf-core/gatk4/svcluster/main.nf | 4 ++-- modules/nf-core/gatk4/variantfiltration/environment.yml | 2 +- modules/nf-core/gatk4/variantfiltration/main.nf | 4 ++-- modules/nf-core/gatk4/variantrecalibrator/environment.yml | 2 +- modules/nf-core/gatk4/variantrecalibrator/main.nf | 4 ++-- modules/nf-core/gatk4/variantstotable/environment.yml | 2 +- modules/nf-core/gatk4/variantstotable/main.nf | 4 ++-- 115 files changed, 184 insertions(+), 170 deletions(-) create mode 100644 modules/nf-core/gatk4/determinegermlinecontigploidy/environment.yml create mode 100644 modules/nf-core/gatk4/germlinecnvcaller/environment.yml diff --git a/modules/nf-core/gatk4/addorreplacereadgroups/environment.yml b/modules/nf-core/gatk4/addorreplacereadgroups/environment.yml index 55993f440cd..e93eac37506 100644 --- a/modules/nf-core/gatk4/addorreplacereadgroups/environment.yml +++ b/modules/nf-core/gatk4/addorreplacereadgroups/environment.yml @@ -2,4 +2,4 @@ channels: - conda-forge - bioconda dependencies: - - bioconda::gatk4=4.5.0.0 + - bioconda::gatk4=4.6.1.0 diff --git a/modules/nf-core/gatk4/addorreplacereadgroups/main.nf b/modules/nf-core/gatk4/addorreplacereadgroups/main.nf index 861f7045a14..8e0142f943d 100644 --- a/modules/nf-core/gatk4/addorreplacereadgroups/main.nf +++ b/modules/nf-core/gatk4/addorreplacereadgroups/main.nf @@ -4,8 +4,8 @@ process GATK4_ADDORREPLACEREADGROUPS { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/gatk4:4.5.0.0--py36hdfd78af_0': - 'biocontainers/gatk4:4.5.0.0--py36hdfd78af_0' }" + 'https://depot.galaxyproject.org/singularity/gatk4:4.6.1.0--py310hdfd78af_0': + 'biocontainers/gatk4:4.6.1.0--py310hdfd78af_0' }" input: tuple val(meta), path(bam) diff --git a/modules/nf-core/gatk4/annotateintervals/environment.yml b/modules/nf-core/gatk4/annotateintervals/environment.yml index 55993f440cd..e93eac37506 100644 --- a/modules/nf-core/gatk4/annotateintervals/environment.yml +++ b/modules/nf-core/gatk4/annotateintervals/environment.yml @@ -2,4 +2,4 @@ channels: - conda-forge - bioconda dependencies: - - bioconda::gatk4=4.5.0.0 + - bioconda::gatk4=4.6.1.0 diff --git a/modules/nf-core/gatk4/annotateintervals/main.nf b/modules/nf-core/gatk4/annotateintervals/main.nf index dfe9dc27a09..e48156d79ec 100644 --- a/modules/nf-core/gatk4/annotateintervals/main.nf +++ b/modules/nf-core/gatk4/annotateintervals/main.nf @@ -4,8 +4,8 @@ process GATK4_ANNOTATEINTERVALS { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/gatk4:4.5.0.0--py36hdfd78af_0': - 'biocontainers/gatk4:4.5.0.0--py36hdfd78af_0' }" + 'https://depot.galaxyproject.org/singularity/gatk4:4.6.1.0--py310hdfd78af_0': + 'biocontainers/gatk4:4.6.1.0--py310hdfd78af_0' }" input: tuple val(meta), path(intervals) diff --git a/modules/nf-core/gatk4/applybqsr/environment.yml b/modules/nf-core/gatk4/applybqsr/environment.yml index 55993f440cd..e93eac37506 100644 --- a/modules/nf-core/gatk4/applybqsr/environment.yml +++ b/modules/nf-core/gatk4/applybqsr/environment.yml @@ -2,4 +2,4 @@ channels: - conda-forge - bioconda dependencies: - - bioconda::gatk4=4.5.0.0 + - bioconda::gatk4=4.6.1.0 diff --git a/modules/nf-core/gatk4/applybqsr/main.nf b/modules/nf-core/gatk4/applybqsr/main.nf index 4e91c311b0e..7dae410c685 100644 --- a/modules/nf-core/gatk4/applybqsr/main.nf +++ b/modules/nf-core/gatk4/applybqsr/main.nf @@ -4,8 +4,8 @@ process GATK4_APPLYBQSR { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/gatk4:4.5.0.0--py36hdfd78af_0': - 'biocontainers/gatk4:4.5.0.0--py36hdfd78af_0' }" + 'https://depot.galaxyproject.org/singularity/gatk4:4.6.1.0--py310hdfd78af_0': + 'biocontainers/gatk4:4.6.1.0--py310hdfd78af_0' }" input: tuple val(meta), path(input), path(input_index), path(bqsr_table), path(intervals) diff --git a/modules/nf-core/gatk4/applyvqsr/environment.yml b/modules/nf-core/gatk4/applyvqsr/environment.yml index 55993f440cd..e93eac37506 100644 --- a/modules/nf-core/gatk4/applyvqsr/environment.yml +++ b/modules/nf-core/gatk4/applyvqsr/environment.yml @@ -2,4 +2,4 @@ channels: - conda-forge - bioconda dependencies: - - bioconda::gatk4=4.5.0.0 + - bioconda::gatk4=4.6.1.0 diff --git a/modules/nf-core/gatk4/applyvqsr/main.nf b/modules/nf-core/gatk4/applyvqsr/main.nf index 047321b8e9e..e14649aab58 100644 --- a/modules/nf-core/gatk4/applyvqsr/main.nf +++ b/modules/nf-core/gatk4/applyvqsr/main.nf @@ -4,8 +4,8 @@ process GATK4_APPLYVQSR { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/gatk4:4.5.0.0--py36hdfd78af_0': - 'biocontainers/gatk4:4.5.0.0--py36hdfd78af_0' }" + 'https://depot.galaxyproject.org/singularity/gatk4:4.6.1.0--py310hdfd78af_0': + 'biocontainers/gatk4:4.6.1.0--py310hdfd78af_0' }" input: tuple val(meta), path(vcf), path(vcf_tbi), path(recal), path(recal_index), path(tranches) diff --git a/modules/nf-core/gatk4/asereadcounter/environment.yml b/modules/nf-core/gatk4/asereadcounter/environment.yml index 55993f440cd..e93eac37506 100644 --- a/modules/nf-core/gatk4/asereadcounter/environment.yml +++ b/modules/nf-core/gatk4/asereadcounter/environment.yml @@ -2,4 +2,4 @@ channels: - conda-forge - bioconda dependencies: - - bioconda::gatk4=4.5.0.0 + - bioconda::gatk4=4.6.1.0 diff --git a/modules/nf-core/gatk4/asereadcounter/main.nf b/modules/nf-core/gatk4/asereadcounter/main.nf index cb9083e0761..87cd0cce29f 100644 --- a/modules/nf-core/gatk4/asereadcounter/main.nf +++ b/modules/nf-core/gatk4/asereadcounter/main.nf @@ -4,8 +4,8 @@ process GATK4_ASEREADCOUNTER { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/gatk4:4.5.0.0--py36hdfd78af_0': - 'biocontainers/gatk4:4.5.0.0--py36hdfd78af_0' }" + 'https://depot.galaxyproject.org/singularity/gatk4:4.6.1.0--py310hdfd78af_0': + 'biocontainers/gatk4:4.6.1.0--py310hdfd78af_0' }" input: tuple val(meta), path(bam), path(bai), path(vcf), path(tbi) diff --git a/modules/nf-core/gatk4/baserecalibrator/environment.yml b/modules/nf-core/gatk4/baserecalibrator/environment.yml index 55993f440cd..e93eac37506 100644 --- a/modules/nf-core/gatk4/baserecalibrator/environment.yml +++ b/modules/nf-core/gatk4/baserecalibrator/environment.yml @@ -2,4 +2,4 @@ channels: - conda-forge - bioconda dependencies: - - bioconda::gatk4=4.5.0.0 + - bioconda::gatk4=4.6.1.0 diff --git a/modules/nf-core/gatk4/baserecalibrator/main.nf b/modules/nf-core/gatk4/baserecalibrator/main.nf index 1a299862657..3c321159377 100644 --- a/modules/nf-core/gatk4/baserecalibrator/main.nf +++ b/modules/nf-core/gatk4/baserecalibrator/main.nf @@ -4,8 +4,8 @@ process GATK4_BASERECALIBRATOR { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/gatk4:4.5.0.0--py36hdfd78af_0': - 'biocontainers/gatk4:4.5.0.0--py36hdfd78af_0' }" + 'https://depot.galaxyproject.org/singularity/gatk4:4.6.1.0--py310hdfd78af_0': + 'biocontainers/gatk4:4.6.1.0--py310hdfd78af_0' }" input: tuple val(meta), path(input), path(input_index), path(intervals) diff --git a/modules/nf-core/gatk4/bedtointervallist/environment.yml b/modules/nf-core/gatk4/bedtointervallist/environment.yml index 55993f440cd..e93eac37506 100644 --- a/modules/nf-core/gatk4/bedtointervallist/environment.yml +++ b/modules/nf-core/gatk4/bedtointervallist/environment.yml @@ -2,4 +2,4 @@ channels: - conda-forge - bioconda dependencies: - - bioconda::gatk4=4.5.0.0 + - bioconda::gatk4=4.6.1.0 diff --git a/modules/nf-core/gatk4/bedtointervallist/main.nf b/modules/nf-core/gatk4/bedtointervallist/main.nf index 68863d677d7..43db8839ab6 100644 --- a/modules/nf-core/gatk4/bedtointervallist/main.nf +++ b/modules/nf-core/gatk4/bedtointervallist/main.nf @@ -4,8 +4,8 @@ process GATK4_BEDTOINTERVALLIST { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/gatk4:4.5.0.0--py36hdfd78af_0': - 'biocontainers/gatk4:4.5.0.0--py36hdfd78af_0' }" + 'https://depot.galaxyproject.org/singularity/gatk4:4.6.1.0--py310hdfd78af_0': + 'biocontainers/gatk4:4.6.1.0--py310hdfd78af_0' }" input: tuple val(meta), path(bed) diff --git a/modules/nf-core/gatk4/calculatecontamination/environment.yml b/modules/nf-core/gatk4/calculatecontamination/environment.yml index 55993f440cd..e93eac37506 100644 --- a/modules/nf-core/gatk4/calculatecontamination/environment.yml +++ b/modules/nf-core/gatk4/calculatecontamination/environment.yml @@ -2,4 +2,4 @@ channels: - conda-forge - bioconda dependencies: - - bioconda::gatk4=4.5.0.0 + - bioconda::gatk4=4.6.1.0 diff --git a/modules/nf-core/gatk4/calculatecontamination/main.nf b/modules/nf-core/gatk4/calculatecontamination/main.nf index 1ca3fd9d45f..52f5d194b39 100644 --- a/modules/nf-core/gatk4/calculatecontamination/main.nf +++ b/modules/nf-core/gatk4/calculatecontamination/main.nf @@ -4,8 +4,8 @@ process GATK4_CALCULATECONTAMINATION { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/gatk4:4.5.0.0--py36hdfd78af_0': - 'biocontainers/gatk4:4.5.0.0--py36hdfd78af_0' }" + 'https://depot.galaxyproject.org/singularity/gatk4:4.6.1.0--py310hdfd78af_0': + 'biocontainers/gatk4:4.6.1.0--py310hdfd78af_0' }" input: tuple val(meta), path(pileup), path(matched) diff --git a/modules/nf-core/gatk4/calibratedragstrmodel/environment.yml b/modules/nf-core/gatk4/calibratedragstrmodel/environment.yml index 55993f440cd..e93eac37506 100644 --- a/modules/nf-core/gatk4/calibratedragstrmodel/environment.yml +++ b/modules/nf-core/gatk4/calibratedragstrmodel/environment.yml @@ -2,4 +2,4 @@ channels: - conda-forge - bioconda dependencies: - - bioconda::gatk4=4.5.0.0 + - bioconda::gatk4=4.6.1.0 diff --git a/modules/nf-core/gatk4/calibratedragstrmodel/main.nf b/modules/nf-core/gatk4/calibratedragstrmodel/main.nf index 88e108cb01e..7e8f50e21df 100644 --- a/modules/nf-core/gatk4/calibratedragstrmodel/main.nf +++ b/modules/nf-core/gatk4/calibratedragstrmodel/main.nf @@ -4,8 +4,8 @@ process GATK4_CALIBRATEDRAGSTRMODEL { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/gatk4:4.5.0.0--py36hdfd78af_0': - 'biocontainers/gatk4:4.5.0.0--py36hdfd78af_0' }" + 'https://depot.galaxyproject.org/singularity/gatk4:4.6.1.0--py310hdfd78af_0': + 'biocontainers/gatk4:4.6.1.0--py310hdfd78af_0' }" input: tuple val(meta), path(bam), path(bam_index) diff --git a/modules/nf-core/gatk4/collectreadcounts/environment.yml b/modules/nf-core/gatk4/collectreadcounts/environment.yml index 55993f440cd..e93eac37506 100644 --- a/modules/nf-core/gatk4/collectreadcounts/environment.yml +++ b/modules/nf-core/gatk4/collectreadcounts/environment.yml @@ -2,4 +2,4 @@ channels: - conda-forge - bioconda dependencies: - - bioconda::gatk4=4.5.0.0 + - bioconda::gatk4=4.6.1.0 diff --git a/modules/nf-core/gatk4/collectreadcounts/main.nf b/modules/nf-core/gatk4/collectreadcounts/main.nf index 2c545d22432..7007d28bfef 100644 --- a/modules/nf-core/gatk4/collectreadcounts/main.nf +++ b/modules/nf-core/gatk4/collectreadcounts/main.nf @@ -4,8 +4,8 @@ process GATK4_COLLECTREADCOUNTS { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/gatk4:4.5.0.0--py36hdfd78af_0': - 'biocontainers/gatk4:4.5.0.0--py36hdfd78af_0' }" + 'https://depot.galaxyproject.org/singularity/gatk4:4.6.1.0--py310hdfd78af_0': + 'biocontainers/gatk4:4.6.1.0--py310hdfd78af_0' }" input: tuple val(meta), path(input), path(input_index), path(intervals) diff --git a/modules/nf-core/gatk4/collectsvevidence/environment.yml b/modules/nf-core/gatk4/collectsvevidence/environment.yml index 55993f440cd..e93eac37506 100644 --- a/modules/nf-core/gatk4/collectsvevidence/environment.yml +++ b/modules/nf-core/gatk4/collectsvevidence/environment.yml @@ -2,4 +2,4 @@ channels: - conda-forge - bioconda dependencies: - - bioconda::gatk4=4.5.0.0 + - bioconda::gatk4=4.6.1.0 diff --git a/modules/nf-core/gatk4/collectsvevidence/main.nf b/modules/nf-core/gatk4/collectsvevidence/main.nf index 9e6dd4a284b..47c264108c1 100644 --- a/modules/nf-core/gatk4/collectsvevidence/main.nf +++ b/modules/nf-core/gatk4/collectsvevidence/main.nf @@ -4,8 +4,8 @@ process GATK4_COLLECTSVEVIDENCE { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/gatk4:4.5.0.0--py36hdfd78af_0': - 'biocontainers/gatk4:4.5.0.0--py36hdfd78af_0' }" + 'https://depot.galaxyproject.org/singularity/gatk4:4.6.1.0--py310hdfd78af_0': + 'biocontainers/gatk4:4.6.1.0--py310hdfd78af_0' }" input: tuple val(meta), path(input), path(input_index), path(site_depth_vcf), path(site_depth_vcf_tbi) diff --git a/modules/nf-core/gatk4/combinegvcfs/environment.yml b/modules/nf-core/gatk4/combinegvcfs/environment.yml index 55993f440cd..e93eac37506 100644 --- a/modules/nf-core/gatk4/combinegvcfs/environment.yml +++ b/modules/nf-core/gatk4/combinegvcfs/environment.yml @@ -2,4 +2,4 @@ channels: - conda-forge - bioconda dependencies: - - bioconda::gatk4=4.5.0.0 + - bioconda::gatk4=4.6.1.0 diff --git a/modules/nf-core/gatk4/combinegvcfs/main.nf b/modules/nf-core/gatk4/combinegvcfs/main.nf index 56db0c12c86..8b66e3eef7d 100644 --- a/modules/nf-core/gatk4/combinegvcfs/main.nf +++ b/modules/nf-core/gatk4/combinegvcfs/main.nf @@ -4,8 +4,8 @@ process GATK4_COMBINEGVCFS { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/gatk4:4.5.0.0--py36hdfd78af_0': - 'biocontainers/gatk4:4.5.0.0--py36hdfd78af_0' }" + 'https://depot.galaxyproject.org/singularity/gatk4:4.6.1.0--py310hdfd78af_0': + 'biocontainers/gatk4:4.6.1.0--py310hdfd78af_0' }" input: tuple val(meta), path(vcf), path(vcf_idx) diff --git a/modules/nf-core/gatk4/composestrtablefile/environment.yml b/modules/nf-core/gatk4/composestrtablefile/environment.yml index 55993f440cd..e93eac37506 100644 --- a/modules/nf-core/gatk4/composestrtablefile/environment.yml +++ b/modules/nf-core/gatk4/composestrtablefile/environment.yml @@ -2,4 +2,4 @@ channels: - conda-forge - bioconda dependencies: - - bioconda::gatk4=4.5.0.0 + - bioconda::gatk4=4.6.1.0 diff --git a/modules/nf-core/gatk4/composestrtablefile/main.nf b/modules/nf-core/gatk4/composestrtablefile/main.nf index 5073ab64200..b6e2ef65a89 100644 --- a/modules/nf-core/gatk4/composestrtablefile/main.nf +++ b/modules/nf-core/gatk4/composestrtablefile/main.nf @@ -4,8 +4,8 @@ process GATK4_COMPOSESTRTABLEFILE { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/gatk4:4.5.0.0--py36hdfd78af_0': - 'biocontainers/gatk4:4.5.0.0--py36hdfd78af_0' }" + 'https://depot.galaxyproject.org/singularity/gatk4:4.6.1.0--py310hdfd78af_0': + 'biocontainers/gatk4:4.6.1.0--py310hdfd78af_0' }" input: path(fasta) diff --git a/modules/nf-core/gatk4/condensedepthevidence/environment.yml b/modules/nf-core/gatk4/condensedepthevidence/environment.yml index 55993f440cd..e93eac37506 100644 --- a/modules/nf-core/gatk4/condensedepthevidence/environment.yml +++ b/modules/nf-core/gatk4/condensedepthevidence/environment.yml @@ -2,4 +2,4 @@ channels: - conda-forge - bioconda dependencies: - - bioconda::gatk4=4.5.0.0 + - bioconda::gatk4=4.6.1.0 diff --git a/modules/nf-core/gatk4/condensedepthevidence/main.nf b/modules/nf-core/gatk4/condensedepthevidence/main.nf index a37b6693f39..0313b46b635 100644 --- a/modules/nf-core/gatk4/condensedepthevidence/main.nf +++ b/modules/nf-core/gatk4/condensedepthevidence/main.nf @@ -4,8 +4,8 @@ process GATK4_CONDENSEDEPTHEVIDENCE { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/gatk4:4.5.0.0--py36hdfd78af_0': - 'biocontainers/gatk4:4.5.0.0--py36hdfd78af_0' }" + 'https://depot.galaxyproject.org/singularity/gatk4:4.6.1.0--py310hdfd78af_0': + 'biocontainers/gatk4:4.6.1.0--py310hdfd78af_0' }" input: tuple val(meta), path(depth_evidence), path(depth_evidence_index) diff --git a/modules/nf-core/gatk4/createreadcountpanelofnormals/environment.yml b/modules/nf-core/gatk4/createreadcountpanelofnormals/environment.yml index 55993f440cd..e93eac37506 100644 --- a/modules/nf-core/gatk4/createreadcountpanelofnormals/environment.yml +++ b/modules/nf-core/gatk4/createreadcountpanelofnormals/environment.yml @@ -2,4 +2,4 @@ channels: - conda-forge - bioconda dependencies: - - bioconda::gatk4=4.5.0.0 + - bioconda::gatk4=4.6.1.0 diff --git a/modules/nf-core/gatk4/createreadcountpanelofnormals/main.nf b/modules/nf-core/gatk4/createreadcountpanelofnormals/main.nf index 332f9d9247f..a31a20d0b44 100644 --- a/modules/nf-core/gatk4/createreadcountpanelofnormals/main.nf +++ b/modules/nf-core/gatk4/createreadcountpanelofnormals/main.nf @@ -4,8 +4,8 @@ process GATK4_CREATEREADCOUNTPANELOFNORMALS { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/gatk4:4.5.0.0--py36hdfd78af_0': - 'biocontainers/gatk4:4.5.0.0--py36hdfd78af_0' }" + 'https://depot.galaxyproject.org/singularity/gatk4:4.6.1.0--py310hdfd78af_0': + 'biocontainers/gatk4:4.6.1.0--py310hdfd78af_0' }" input: tuple val(meta), path(counts) diff --git a/modules/nf-core/gatk4/createsequencedictionary/environment.yml b/modules/nf-core/gatk4/createsequencedictionary/environment.yml index 55993f440cd..e93eac37506 100644 --- a/modules/nf-core/gatk4/createsequencedictionary/environment.yml +++ b/modules/nf-core/gatk4/createsequencedictionary/environment.yml @@ -2,4 +2,4 @@ channels: - conda-forge - bioconda dependencies: - - bioconda::gatk4=4.5.0.0 + - bioconda::gatk4=4.6.1.0 diff --git a/modules/nf-core/gatk4/createsequencedictionary/main.nf b/modules/nf-core/gatk4/createsequencedictionary/main.nf index c7f1d75b3c1..e42735af6b1 100644 --- a/modules/nf-core/gatk4/createsequencedictionary/main.nf +++ b/modules/nf-core/gatk4/createsequencedictionary/main.nf @@ -4,8 +4,8 @@ process GATK4_CREATESEQUENCEDICTIONARY { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/gatk4:4.5.0.0--py36hdfd78af_0': - 'biocontainers/gatk4:4.5.0.0--py36hdfd78af_0' }" + 'https://depot.galaxyproject.org/singularity/gatk4:4.6.1.0--py310hdfd78af_0': + 'biocontainers/gatk4:4.6.1.0--py310hdfd78af_0' }" input: tuple val(meta), path(fasta) diff --git a/modules/nf-core/gatk4/createsomaticpanelofnormals/environment.yml b/modules/nf-core/gatk4/createsomaticpanelofnormals/environment.yml index 55993f440cd..e93eac37506 100644 --- a/modules/nf-core/gatk4/createsomaticpanelofnormals/environment.yml +++ b/modules/nf-core/gatk4/createsomaticpanelofnormals/environment.yml @@ -2,4 +2,4 @@ channels: - conda-forge - bioconda dependencies: - - bioconda::gatk4=4.5.0.0 + - bioconda::gatk4=4.6.1.0 diff --git a/modules/nf-core/gatk4/createsomaticpanelofnormals/main.nf b/modules/nf-core/gatk4/createsomaticpanelofnormals/main.nf index 27a50dc208d..ffd77888ed0 100644 --- a/modules/nf-core/gatk4/createsomaticpanelofnormals/main.nf +++ b/modules/nf-core/gatk4/createsomaticpanelofnormals/main.nf @@ -4,8 +4,8 @@ process GATK4_CREATESOMATICPANELOFNORMALS { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/gatk4:4.5.0.0--py36hdfd78af_0': - 'biocontainers/gatk4:4.5.0.0--py36hdfd78af_0' }" + 'https://depot.galaxyproject.org/singularity/gatk4:4.6.1.0--py310hdfd78af_0': + 'biocontainers/gatk4:4.6.1.0--py310hdfd78af_0' }" input: tuple val(meta), path(genomicsdb) diff --git a/modules/nf-core/gatk4/denoisereadcounts/environment.yml b/modules/nf-core/gatk4/denoisereadcounts/environment.yml index 55993f440cd..e93eac37506 100644 --- a/modules/nf-core/gatk4/denoisereadcounts/environment.yml +++ b/modules/nf-core/gatk4/denoisereadcounts/environment.yml @@ -2,4 +2,4 @@ channels: - conda-forge - bioconda dependencies: - - bioconda::gatk4=4.5.0.0 + - bioconda::gatk4=4.6.1.0 diff --git a/modules/nf-core/gatk4/denoisereadcounts/main.nf b/modules/nf-core/gatk4/denoisereadcounts/main.nf index 878e85c6f97..3d4637d8539 100644 --- a/modules/nf-core/gatk4/denoisereadcounts/main.nf +++ b/modules/nf-core/gatk4/denoisereadcounts/main.nf @@ -4,8 +4,8 @@ process GATK4_DENOISEREADCOUNTS { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/gatk4:4.5.0.0--py36hdfd78af_0': - 'biocontainers/gatk4:4.5.0.0--py36hdfd78af_0' }" + 'https://depot.galaxyproject.org/singularity/gatk4:4.6.1.0--py310hdfd78af_0': + 'biocontainers/gatk4:4.6.1.0--py310hdfd78af_0' }" input: tuple val(meta), path(counts) diff --git a/modules/nf-core/gatk4/determinegermlinecontigploidy/environment.yml b/modules/nf-core/gatk4/determinegermlinecontigploidy/environment.yml new file mode 100644 index 00000000000..e93eac37506 --- /dev/null +++ b/modules/nf-core/gatk4/determinegermlinecontigploidy/environment.yml @@ -0,0 +1,5 @@ +channels: + - conda-forge + - bioconda +dependencies: + - bioconda::gatk4=4.6.1.0 diff --git a/modules/nf-core/gatk4/determinegermlinecontigploidy/main.nf b/modules/nf-core/gatk4/determinegermlinecontigploidy/main.nf index 71a67f70320..97a4f5a6269 100644 --- a/modules/nf-core/gatk4/determinegermlinecontigploidy/main.nf +++ b/modules/nf-core/gatk4/determinegermlinecontigploidy/main.nf @@ -3,8 +3,10 @@ process GATK4_DETERMINEGERMLINECONTIGPLOIDY { tag "$meta.id" label 'process_single' - //Conda is not supported at the moment: https://github.com/broadinstitute/gatk/issues/7811 - container "nf-core/gatk:4.5.0.0" //Biocontainers is missing a package + conda "${moduleDir}/environment.yml" + container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + 'https://depot.galaxyproject.org/singularity/gatk4:4.6.1.0--py310hdfd78af_0': + 'biocontainers/gatk4:4.6.1.0--py310hdfd78af_0' }" input: tuple val(meta), path(counts), path(bed), path(exclude_beds) diff --git a/modules/nf-core/gatk4/estimatelibrarycomplexity/environment.yml b/modules/nf-core/gatk4/estimatelibrarycomplexity/environment.yml index 55993f440cd..e93eac37506 100644 --- a/modules/nf-core/gatk4/estimatelibrarycomplexity/environment.yml +++ b/modules/nf-core/gatk4/estimatelibrarycomplexity/environment.yml @@ -2,4 +2,4 @@ channels: - conda-forge - bioconda dependencies: - - bioconda::gatk4=4.5.0.0 + - bioconda::gatk4=4.6.1.0 diff --git a/modules/nf-core/gatk4/estimatelibrarycomplexity/main.nf b/modules/nf-core/gatk4/estimatelibrarycomplexity/main.nf index e0744e16f7d..31430a94291 100644 --- a/modules/nf-core/gatk4/estimatelibrarycomplexity/main.nf +++ b/modules/nf-core/gatk4/estimatelibrarycomplexity/main.nf @@ -4,8 +4,8 @@ process GATK4_ESTIMATELIBRARYCOMPLEXITY { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/gatk4:4.5.0.0--py36hdfd78af_0': - 'biocontainers/gatk4:4.5.0.0--py36hdfd78af_0' }" + 'https://depot.galaxyproject.org/singularity/gatk4:4.6.1.0--py310hdfd78af_0': + 'biocontainers/gatk4:4.6.1.0--py310hdfd78af_0' }" input: tuple val(meta), path(input) diff --git a/modules/nf-core/gatk4/fastqtosam/environment.yml b/modules/nf-core/gatk4/fastqtosam/environment.yml index 55993f440cd..e93eac37506 100644 --- a/modules/nf-core/gatk4/fastqtosam/environment.yml +++ b/modules/nf-core/gatk4/fastqtosam/environment.yml @@ -2,4 +2,4 @@ channels: - conda-forge - bioconda dependencies: - - bioconda::gatk4=4.5.0.0 + - bioconda::gatk4=4.6.1.0 diff --git a/modules/nf-core/gatk4/fastqtosam/main.nf b/modules/nf-core/gatk4/fastqtosam/main.nf index 452d1ca1f35..acd0e71a527 100644 --- a/modules/nf-core/gatk4/fastqtosam/main.nf +++ b/modules/nf-core/gatk4/fastqtosam/main.nf @@ -4,8 +4,8 @@ process GATK4_FASTQTOSAM { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/gatk4:4.5.0.0--py36hdfd78af_0': - 'biocontainers/gatk4:4.5.0.0--py36hdfd78af_0' }" + 'https://depot.galaxyproject.org/singularity/gatk4:4.6.1.0--py310hdfd78af_0': + 'biocontainers/gatk4:4.6.1.0--py310hdfd78af_0' }" input: tuple val(meta), path(reads) diff --git a/modules/nf-core/gatk4/filterintervals/environment.yml b/modules/nf-core/gatk4/filterintervals/environment.yml index 55993f440cd..e93eac37506 100644 --- a/modules/nf-core/gatk4/filterintervals/environment.yml +++ b/modules/nf-core/gatk4/filterintervals/environment.yml @@ -2,4 +2,4 @@ channels: - conda-forge - bioconda dependencies: - - bioconda::gatk4=4.5.0.0 + - bioconda::gatk4=4.6.1.0 diff --git a/modules/nf-core/gatk4/filterintervals/main.nf b/modules/nf-core/gatk4/filterintervals/main.nf index bf1f3a0e369..c2a3ccfc4a1 100644 --- a/modules/nf-core/gatk4/filterintervals/main.nf +++ b/modules/nf-core/gatk4/filterintervals/main.nf @@ -4,8 +4,8 @@ process GATK4_FILTERINTERVALS { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/gatk4:4.5.0.0--py36hdfd78af_0': - 'biocontainers/gatk4:4.5.0.0--py36hdfd78af_0' }" + 'https://depot.galaxyproject.org/singularity/gatk4:4.6.1.0--py310hdfd78af_0': + 'biocontainers/gatk4:4.6.1.0--py310hdfd78af_0' }" input: tuple val(meta), path(intervals) diff --git a/modules/nf-core/gatk4/filtermutectcalls/environment.yml b/modules/nf-core/gatk4/filtermutectcalls/environment.yml index 55993f440cd..e93eac37506 100644 --- a/modules/nf-core/gatk4/filtermutectcalls/environment.yml +++ b/modules/nf-core/gatk4/filtermutectcalls/environment.yml @@ -2,4 +2,4 @@ channels: - conda-forge - bioconda dependencies: - - bioconda::gatk4=4.5.0.0 + - bioconda::gatk4=4.6.1.0 diff --git a/modules/nf-core/gatk4/filtermutectcalls/main.nf b/modules/nf-core/gatk4/filtermutectcalls/main.nf index 0532ec02582..927c514ebd6 100644 --- a/modules/nf-core/gatk4/filtermutectcalls/main.nf +++ b/modules/nf-core/gatk4/filtermutectcalls/main.nf @@ -4,8 +4,8 @@ process GATK4_FILTERMUTECTCALLS { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/gatk4:4.5.0.0--py36hdfd78af_0': - 'biocontainers/gatk4:4.5.0.0--py36hdfd78af_0' }" + 'https://depot.galaxyproject.org/singularity/gatk4:4.6.1.0--py310hdfd78af_0': + 'biocontainers/gatk4:4.6.1.0--py310hdfd78af_0' }" input: tuple val(meta), path(vcf), path(vcf_tbi), path(stats), path(orientationbias), path(segmentation), path(table), val(estimate) diff --git a/modules/nf-core/gatk4/filtervarianttranches/environment.yml b/modules/nf-core/gatk4/filtervarianttranches/environment.yml index 55993f440cd..e93eac37506 100644 --- a/modules/nf-core/gatk4/filtervarianttranches/environment.yml +++ b/modules/nf-core/gatk4/filtervarianttranches/environment.yml @@ -2,4 +2,4 @@ channels: - conda-forge - bioconda dependencies: - - bioconda::gatk4=4.5.0.0 + - bioconda::gatk4=4.6.1.0 diff --git a/modules/nf-core/gatk4/filtervarianttranches/main.nf b/modules/nf-core/gatk4/filtervarianttranches/main.nf index 05489e179b9..2730938769e 100644 --- a/modules/nf-core/gatk4/filtervarianttranches/main.nf +++ b/modules/nf-core/gatk4/filtervarianttranches/main.nf @@ -4,8 +4,8 @@ process GATK4_FILTERVARIANTTRANCHES { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/gatk4:4.5.0.0--py36hdfd78af_0': - 'biocontainers/gatk4:4.5.0.0--py36hdfd78af_0' }" + 'https://depot.galaxyproject.org/singularity/gatk4:4.6.1.0--py310hdfd78af_0': + 'biocontainers/gatk4:4.6.1.0--py310hdfd78af_0' }" input: tuple val(meta), path(vcf), path(tbi), path(intervals) diff --git a/modules/nf-core/gatk4/gatherbqsrreports/environment.yml b/modules/nf-core/gatk4/gatherbqsrreports/environment.yml index 55993f440cd..e93eac37506 100644 --- a/modules/nf-core/gatk4/gatherbqsrreports/environment.yml +++ b/modules/nf-core/gatk4/gatherbqsrreports/environment.yml @@ -2,4 +2,4 @@ channels: - conda-forge - bioconda dependencies: - - bioconda::gatk4=4.5.0.0 + - bioconda::gatk4=4.6.1.0 diff --git a/modules/nf-core/gatk4/gatherbqsrreports/main.nf b/modules/nf-core/gatk4/gatherbqsrreports/main.nf index 79667a29948..98a71473c2c 100644 --- a/modules/nf-core/gatk4/gatherbqsrreports/main.nf +++ b/modules/nf-core/gatk4/gatherbqsrreports/main.nf @@ -4,8 +4,8 @@ process GATK4_GATHERBQSRREPORTS { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/gatk4:4.5.0.0--py36hdfd78af_0': - 'biocontainers/gatk4:4.5.0.0--py36hdfd78af_0' }" + 'https://depot.galaxyproject.org/singularity/gatk4:4.6.1.0--py310hdfd78af_0': + 'biocontainers/gatk4:4.6.1.0--py310hdfd78af_0' }" input: tuple val(meta), path(table) diff --git a/modules/nf-core/gatk4/gatherpileupsummaries/environment.yml b/modules/nf-core/gatk4/gatherpileupsummaries/environment.yml index 55993f440cd..e93eac37506 100644 --- a/modules/nf-core/gatk4/gatherpileupsummaries/environment.yml +++ b/modules/nf-core/gatk4/gatherpileupsummaries/environment.yml @@ -2,4 +2,4 @@ channels: - conda-forge - bioconda dependencies: - - bioconda::gatk4=4.5.0.0 + - bioconda::gatk4=4.6.1.0 diff --git a/modules/nf-core/gatk4/gatherpileupsummaries/main.nf b/modules/nf-core/gatk4/gatherpileupsummaries/main.nf index bcafd544b43..36f1a4123d8 100644 --- a/modules/nf-core/gatk4/gatherpileupsummaries/main.nf +++ b/modules/nf-core/gatk4/gatherpileupsummaries/main.nf @@ -4,8 +4,8 @@ process GATK4_GATHERPILEUPSUMMARIES { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/gatk4:4.5.0.0--py36hdfd78af_0': - 'biocontainers/gatk4:4.5.0.0--py36hdfd78af_0' }" + 'https://depot.galaxyproject.org/singularity/gatk4:4.6.1.0--py310hdfd78af_0': + 'biocontainers/gatk4:4.6.1.0--py310hdfd78af_0' }" input: diff --git a/modules/nf-core/gatk4/genomicsdbimport/environment.yml b/modules/nf-core/gatk4/genomicsdbimport/environment.yml index 55993f440cd..e93eac37506 100644 --- a/modules/nf-core/gatk4/genomicsdbimport/environment.yml +++ b/modules/nf-core/gatk4/genomicsdbimport/environment.yml @@ -2,4 +2,4 @@ channels: - conda-forge - bioconda dependencies: - - bioconda::gatk4=4.5.0.0 + - bioconda::gatk4=4.6.1.0 diff --git a/modules/nf-core/gatk4/genomicsdbimport/main.nf b/modules/nf-core/gatk4/genomicsdbimport/main.nf index 6f1d4c53709..ce9a7042378 100644 --- a/modules/nf-core/gatk4/genomicsdbimport/main.nf +++ b/modules/nf-core/gatk4/genomicsdbimport/main.nf @@ -4,8 +4,8 @@ process GATK4_GENOMICSDBIMPORT { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/gatk4:4.5.0.0--py36hdfd78af_0': - 'biocontainers/gatk4:4.5.0.0--py36hdfd78af_0' }" + 'https://depot.galaxyproject.org/singularity/gatk4:4.6.1.0--py310hdfd78af_0': + 'biocontainers/gatk4:4.6.1.0--py310hdfd78af_0' }" input: tuple val(meta), path(vcf), path(tbi), path(interval_file), val(interval_value), path(wspace) diff --git a/modules/nf-core/gatk4/genotypegvcfs/environment.yml b/modules/nf-core/gatk4/genotypegvcfs/environment.yml index 55993f440cd..e93eac37506 100644 --- a/modules/nf-core/gatk4/genotypegvcfs/environment.yml +++ b/modules/nf-core/gatk4/genotypegvcfs/environment.yml @@ -2,4 +2,4 @@ channels: - conda-forge - bioconda dependencies: - - bioconda::gatk4=4.5.0.0 + - bioconda::gatk4=4.6.1.0 diff --git a/modules/nf-core/gatk4/genotypegvcfs/main.nf b/modules/nf-core/gatk4/genotypegvcfs/main.nf index f180f74975c..a0fed0699ac 100644 --- a/modules/nf-core/gatk4/genotypegvcfs/main.nf +++ b/modules/nf-core/gatk4/genotypegvcfs/main.nf @@ -4,8 +4,8 @@ process GATK4_GENOTYPEGVCFS { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/gatk4:4.5.0.0--py36hdfd78af_0': - 'biocontainers/gatk4:4.5.0.0--py36hdfd78af_0' }" + 'https://depot.galaxyproject.org/singularity/gatk4:4.6.1.0--py310hdfd78af_0': + 'biocontainers/gatk4:4.6.1.0--py310hdfd78af_0' }" input: tuple val(meta), path(input), path(gvcf_index), path(intervals), path(intervals_index) diff --git a/modules/nf-core/gatk4/germlinecnvcaller/environment.yml b/modules/nf-core/gatk4/germlinecnvcaller/environment.yml new file mode 100644 index 00000000000..e93eac37506 --- /dev/null +++ b/modules/nf-core/gatk4/germlinecnvcaller/environment.yml @@ -0,0 +1,5 @@ +channels: + - conda-forge + - bioconda +dependencies: + - bioconda::gatk4=4.6.1.0 diff --git a/modules/nf-core/gatk4/germlinecnvcaller/main.nf b/modules/nf-core/gatk4/germlinecnvcaller/main.nf index cd1916ec439..180c0a940f9 100644 --- a/modules/nf-core/gatk4/germlinecnvcaller/main.nf +++ b/modules/nf-core/gatk4/germlinecnvcaller/main.nf @@ -2,8 +2,10 @@ process GATK4_GERMLINECNVCALLER { tag "$meta.id" label 'process_single' - //Conda is not supported at the moment: https://github.com/broadinstitute/gatk/issues/7811 - container "nf-core/gatk:4.5.0.0" //Biocontainers is missing a package + conda "${moduleDir}/environment.yml" + container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + 'https://depot.galaxyproject.org/singularity/gatk4:4.6.1.0--py310hdfd78af_0': + 'biocontainers/gatk4:4.6.1.0--py310hdfd78af_0' }" input: tuple val(meta), path(tsv), path(intervals), path(ploidy), path(model) diff --git a/modules/nf-core/gatk4/getpileupsummaries/environment.yml b/modules/nf-core/gatk4/getpileupsummaries/environment.yml index 55993f440cd..e93eac37506 100644 --- a/modules/nf-core/gatk4/getpileupsummaries/environment.yml +++ b/modules/nf-core/gatk4/getpileupsummaries/environment.yml @@ -2,4 +2,4 @@ channels: - conda-forge - bioconda dependencies: - - bioconda::gatk4=4.5.0.0 + - bioconda::gatk4=4.6.1.0 diff --git a/modules/nf-core/gatk4/getpileupsummaries/main.nf b/modules/nf-core/gatk4/getpileupsummaries/main.nf index 43611271e01..af477f818e7 100644 --- a/modules/nf-core/gatk4/getpileupsummaries/main.nf +++ b/modules/nf-core/gatk4/getpileupsummaries/main.nf @@ -4,8 +4,8 @@ process GATK4_GETPILEUPSUMMARIES { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/gatk4:4.5.0.0--py36hdfd78af_0': - 'biocontainers/gatk4:4.5.0.0--py36hdfd78af_0' }" + 'https://depot.galaxyproject.org/singularity/gatk4:4.6.1.0--py310hdfd78af_0': + 'biocontainers/gatk4:4.6.1.0--py310hdfd78af_0' }" input: tuple val(meta), path(input), path(index), path(intervals) diff --git a/modules/nf-core/gatk4/haplotypecaller/environment.yml b/modules/nf-core/gatk4/haplotypecaller/environment.yml index 55993f440cd..e93eac37506 100644 --- a/modules/nf-core/gatk4/haplotypecaller/environment.yml +++ b/modules/nf-core/gatk4/haplotypecaller/environment.yml @@ -2,4 +2,4 @@ channels: - conda-forge - bioconda dependencies: - - bioconda::gatk4=4.5.0.0 + - bioconda::gatk4=4.6.1.0 diff --git a/modules/nf-core/gatk4/haplotypecaller/main.nf b/modules/nf-core/gatk4/haplotypecaller/main.nf index b2aff48969e..097626064ce 100644 --- a/modules/nf-core/gatk4/haplotypecaller/main.nf +++ b/modules/nf-core/gatk4/haplotypecaller/main.nf @@ -4,8 +4,8 @@ process GATK4_HAPLOTYPECALLER { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/gatk4:4.5.0.0--py36hdfd78af_0': - 'biocontainers/gatk4:4.5.0.0--py36hdfd78af_0' }" + 'https://depot.galaxyproject.org/singularity/gatk4:4.6.1.0--py310hdfd78af_0': + 'biocontainers/gatk4:4.6.1.0--py310hdfd78af_0' }" input: tuple val(meta), path(input), path(input_index), path(intervals), path(dragstr_model) diff --git a/modules/nf-core/gatk4/indexfeaturefile/environment.yml b/modules/nf-core/gatk4/indexfeaturefile/environment.yml index 55993f440cd..e93eac37506 100644 --- a/modules/nf-core/gatk4/indexfeaturefile/environment.yml +++ b/modules/nf-core/gatk4/indexfeaturefile/environment.yml @@ -2,4 +2,4 @@ channels: - conda-forge - bioconda dependencies: - - bioconda::gatk4=4.5.0.0 + - bioconda::gatk4=4.6.1.0 diff --git a/modules/nf-core/gatk4/indexfeaturefile/main.nf b/modules/nf-core/gatk4/indexfeaturefile/main.nf index b1a2698c263..dddb2c111fc 100644 --- a/modules/nf-core/gatk4/indexfeaturefile/main.nf +++ b/modules/nf-core/gatk4/indexfeaturefile/main.nf @@ -4,8 +4,8 @@ process GATK4_INDEXFEATUREFILE { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/gatk4:4.5.0.0--py36hdfd78af_0': - 'biocontainers/gatk4:4.5.0.0--py36hdfd78af_0' }" + 'https://depot.galaxyproject.org/singularity/gatk4:4.6.1.0--py310hdfd78af_0': + 'biocontainers/gatk4:4.6.1.0--py310hdfd78af_0' }" input: tuple val(meta), path(feature_file) diff --git a/modules/nf-core/gatk4/intervallisttobed/environment.yml b/modules/nf-core/gatk4/intervallisttobed/environment.yml index 55993f440cd..e93eac37506 100644 --- a/modules/nf-core/gatk4/intervallisttobed/environment.yml +++ b/modules/nf-core/gatk4/intervallisttobed/environment.yml @@ -2,4 +2,4 @@ channels: - conda-forge - bioconda dependencies: - - bioconda::gatk4=4.5.0.0 + - bioconda::gatk4=4.6.1.0 diff --git a/modules/nf-core/gatk4/intervallisttobed/main.nf b/modules/nf-core/gatk4/intervallisttobed/main.nf index 2f6893c0caf..61f68a68dcf 100644 --- a/modules/nf-core/gatk4/intervallisttobed/main.nf +++ b/modules/nf-core/gatk4/intervallisttobed/main.nf @@ -4,8 +4,8 @@ process GATK4_INTERVALLISTTOBED { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/gatk4:4.5.0.0--py36hdfd78af_0': - 'biocontainers/gatk4:4.5.0.0--py36hdfd78af_0' }" + 'https://depot.galaxyproject.org/singularity/gatk4:4.6.1.0--py310hdfd78af_0': + 'biocontainers/gatk4:4.6.1.0--py310hdfd78af_0' }" input: tuple val(meta), path(intervals) diff --git a/modules/nf-core/gatk4/intervallisttools/environment.yml b/modules/nf-core/gatk4/intervallisttools/environment.yml index 55993f440cd..e93eac37506 100644 --- a/modules/nf-core/gatk4/intervallisttools/environment.yml +++ b/modules/nf-core/gatk4/intervallisttools/environment.yml @@ -2,4 +2,4 @@ channels: - conda-forge - bioconda dependencies: - - bioconda::gatk4=4.5.0.0 + - bioconda::gatk4=4.6.1.0 diff --git a/modules/nf-core/gatk4/intervallisttools/main.nf b/modules/nf-core/gatk4/intervallisttools/main.nf index 400fa0380e7..5bf38ab8aad 100644 --- a/modules/nf-core/gatk4/intervallisttools/main.nf +++ b/modules/nf-core/gatk4/intervallisttools/main.nf @@ -4,8 +4,8 @@ process GATK4_INTERVALLISTTOOLS { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/gatk4:4.5.0.0--py36hdfd78af_0': - 'biocontainers/gatk4:4.5.0.0--py36hdfd78af_0' }" + 'https://depot.galaxyproject.org/singularity/gatk4:4.6.1.0--py310hdfd78af_0': + 'biocontainers/gatk4:4.6.1.0--py310hdfd78af_0' }" input: tuple val(meta), path(intervals) diff --git a/modules/nf-core/gatk4/learnreadorientationmodel/environment.yml b/modules/nf-core/gatk4/learnreadorientationmodel/environment.yml index 55993f440cd..e93eac37506 100644 --- a/modules/nf-core/gatk4/learnreadorientationmodel/environment.yml +++ b/modules/nf-core/gatk4/learnreadorientationmodel/environment.yml @@ -2,4 +2,4 @@ channels: - conda-forge - bioconda dependencies: - - bioconda::gatk4=4.5.0.0 + - bioconda::gatk4=4.6.1.0 diff --git a/modules/nf-core/gatk4/learnreadorientationmodel/main.nf b/modules/nf-core/gatk4/learnreadorientationmodel/main.nf index a61b292812e..2d15b176023 100644 --- a/modules/nf-core/gatk4/learnreadorientationmodel/main.nf +++ b/modules/nf-core/gatk4/learnreadorientationmodel/main.nf @@ -4,8 +4,8 @@ process GATK4_LEARNREADORIENTATIONMODEL { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/gatk4:4.5.0.0--py36hdfd78af_0': - 'biocontainers/gatk4:4.5.0.0--py36hdfd78af_0' }" + 'https://depot.galaxyproject.org/singularity/gatk4:4.6.1.0--py310hdfd78af_0': + 'biocontainers/gatk4:4.6.1.0--py310hdfd78af_0' }" input: tuple val(meta), path(f1r2) diff --git a/modules/nf-core/gatk4/leftalignandtrimvariants/environment.yml b/modules/nf-core/gatk4/leftalignandtrimvariants/environment.yml index 55993f440cd..e93eac37506 100644 --- a/modules/nf-core/gatk4/leftalignandtrimvariants/environment.yml +++ b/modules/nf-core/gatk4/leftalignandtrimvariants/environment.yml @@ -2,4 +2,4 @@ channels: - conda-forge - bioconda dependencies: - - bioconda::gatk4=4.5.0.0 + - bioconda::gatk4=4.6.1.0 diff --git a/modules/nf-core/gatk4/leftalignandtrimvariants/main.nf b/modules/nf-core/gatk4/leftalignandtrimvariants/main.nf index b0bede7093d..0fbccc1a5b3 100644 --- a/modules/nf-core/gatk4/leftalignandtrimvariants/main.nf +++ b/modules/nf-core/gatk4/leftalignandtrimvariants/main.nf @@ -4,8 +4,8 @@ process GATK4_LEFTALIGNANDTRIMVARIANTS { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/gatk4:4.5.0.0--py36hdfd78af_0': - 'biocontainers/gatk4:4.5.0.0--py36hdfd78af_0' }" + 'https://depot.galaxyproject.org/singularity/gatk4:4.6.1.0--py310hdfd78af_0': + 'biocontainers/gatk4:4.6.1.0--py310hdfd78af_0' }" input: tuple val(meta), path(vcf), path(tbi), path(intervals) diff --git a/modules/nf-core/gatk4/markduplicates/environment.yml b/modules/nf-core/gatk4/markduplicates/environment.yml index 3c73c17e433..8a70182eac7 100644 --- a/modules/nf-core/gatk4/markduplicates/environment.yml +++ b/modules/nf-core/gatk4/markduplicates/environment.yml @@ -3,6 +3,6 @@ channels: - bioconda dependencies: - - bioconda::gatk4=4.5.0.0 + - bioconda::gatk4=4.6.1.0 - bioconda::htslib=1.19.1 - bioconda::samtools=1.19.2 diff --git a/modules/nf-core/gatk4/mergebamalignment/environment.yml b/modules/nf-core/gatk4/mergebamalignment/environment.yml index 55993f440cd..e93eac37506 100644 --- a/modules/nf-core/gatk4/mergebamalignment/environment.yml +++ b/modules/nf-core/gatk4/mergebamalignment/environment.yml @@ -2,4 +2,4 @@ channels: - conda-forge - bioconda dependencies: - - bioconda::gatk4=4.5.0.0 + - bioconda::gatk4=4.6.1.0 diff --git a/modules/nf-core/gatk4/mergebamalignment/main.nf b/modules/nf-core/gatk4/mergebamalignment/main.nf index 0085026c8e5..f390eda2317 100644 --- a/modules/nf-core/gatk4/mergebamalignment/main.nf +++ b/modules/nf-core/gatk4/mergebamalignment/main.nf @@ -4,8 +4,8 @@ process GATK4_MERGEBAMALIGNMENT { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/gatk4:4.5.0.0--py36hdfd78af_0': - 'biocontainers/gatk4:4.5.0.0--py36hdfd78af_0' }" + 'https://depot.galaxyproject.org/singularity/gatk4:4.6.1.0--py310hdfd78af_0': + 'biocontainers/gatk4:4.6.1.0--py310hdfd78af_0' }" input: tuple val(meta), path(aligned), path(unmapped) diff --git a/modules/nf-core/gatk4/mergemutectstats/environment.yml b/modules/nf-core/gatk4/mergemutectstats/environment.yml index 55993f440cd..e93eac37506 100644 --- a/modules/nf-core/gatk4/mergemutectstats/environment.yml +++ b/modules/nf-core/gatk4/mergemutectstats/environment.yml @@ -2,4 +2,4 @@ channels: - conda-forge - bioconda dependencies: - - bioconda::gatk4=4.5.0.0 + - bioconda::gatk4=4.6.1.0 diff --git a/modules/nf-core/gatk4/mergemutectstats/main.nf b/modules/nf-core/gatk4/mergemutectstats/main.nf index 06bce31e31b..1a500fc1f88 100644 --- a/modules/nf-core/gatk4/mergemutectstats/main.nf +++ b/modules/nf-core/gatk4/mergemutectstats/main.nf @@ -4,8 +4,8 @@ process GATK4_MERGEMUTECTSTATS { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/gatk4:4.5.0.0--py36hdfd78af_0': - 'biocontainers/gatk4:4.5.0.0--py36hdfd78af_0' }" + 'https://depot.galaxyproject.org/singularity/gatk4:4.6.1.0--py310hdfd78af_0': + 'biocontainers/gatk4:4.6.1.0--py310hdfd78af_0' }" input: tuple val(meta), path(stats) diff --git a/modules/nf-core/gatk4/mergevcfs/environment.yml b/modules/nf-core/gatk4/mergevcfs/environment.yml index 55993f440cd..e93eac37506 100644 --- a/modules/nf-core/gatk4/mergevcfs/environment.yml +++ b/modules/nf-core/gatk4/mergevcfs/environment.yml @@ -2,4 +2,4 @@ channels: - conda-forge - bioconda dependencies: - - bioconda::gatk4=4.5.0.0 + - bioconda::gatk4=4.6.1.0 diff --git a/modules/nf-core/gatk4/mergevcfs/main.nf b/modules/nf-core/gatk4/mergevcfs/main.nf index 9e8d43915cc..d9ae935d5f8 100644 --- a/modules/nf-core/gatk4/mergevcfs/main.nf +++ b/modules/nf-core/gatk4/mergevcfs/main.nf @@ -4,8 +4,8 @@ process GATK4_MERGEVCFS { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/gatk4:4.5.0.0--py36hdfd78af_0': - 'biocontainers/gatk4:4.5.0.0--py36hdfd78af_0' }" + 'https://depot.galaxyproject.org/singularity/gatk4:4.6.1.0--py310hdfd78af_0': + 'biocontainers/gatk4:4.6.1.0--py310hdfd78af_0' }" input: tuple val(meta), path(vcf) diff --git a/modules/nf-core/gatk4/mutect2/environment.yml b/modules/nf-core/gatk4/mutect2/environment.yml index 55993f440cd..e93eac37506 100644 --- a/modules/nf-core/gatk4/mutect2/environment.yml +++ b/modules/nf-core/gatk4/mutect2/environment.yml @@ -2,4 +2,4 @@ channels: - conda-forge - bioconda dependencies: - - bioconda::gatk4=4.5.0.0 + - bioconda::gatk4=4.6.1.0 diff --git a/modules/nf-core/gatk4/mutect2/main.nf b/modules/nf-core/gatk4/mutect2/main.nf index 79d8d2826ca..044da1822f9 100644 --- a/modules/nf-core/gatk4/mutect2/main.nf +++ b/modules/nf-core/gatk4/mutect2/main.nf @@ -4,8 +4,8 @@ process GATK4_MUTECT2 { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/gatk4:4.5.0.0--py36hdfd78af_0': - 'biocontainers/gatk4:4.5.0.0--py36hdfd78af_0' }" + 'https://depot.galaxyproject.org/singularity/gatk4:4.6.1.0--py310hdfd78af_0': + 'biocontainers/gatk4:4.6.1.0--py310hdfd78af_0' }" input: tuple val(meta), path(input), path(input_index), path(intervals) diff --git a/modules/nf-core/gatk4/preprocessintervals/environment.yml b/modules/nf-core/gatk4/preprocessintervals/environment.yml index 55993f440cd..e93eac37506 100644 --- a/modules/nf-core/gatk4/preprocessintervals/environment.yml +++ b/modules/nf-core/gatk4/preprocessintervals/environment.yml @@ -2,4 +2,4 @@ channels: - conda-forge - bioconda dependencies: - - bioconda::gatk4=4.5.0.0 + - bioconda::gatk4=4.6.1.0 diff --git a/modules/nf-core/gatk4/preprocessintervals/main.nf b/modules/nf-core/gatk4/preprocessintervals/main.nf index dffc4bb1df8..0a606275e77 100644 --- a/modules/nf-core/gatk4/preprocessintervals/main.nf +++ b/modules/nf-core/gatk4/preprocessintervals/main.nf @@ -4,8 +4,8 @@ process GATK4_PREPROCESSINTERVALS { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/gatk4:4.5.0.0--py36hdfd78af_0': - 'biocontainers/gatk4:4.5.0.0--py36hdfd78af_0' }" + 'https://depot.galaxyproject.org/singularity/gatk4:4.6.1.0--py310hdfd78af_0': + 'biocontainers/gatk4:4.6.1.0--py310hdfd78af_0' }" input: tuple val(meta), path(fasta) diff --git a/modules/nf-core/gatk4/printreads/environment.yml b/modules/nf-core/gatk4/printreads/environment.yml index 55993f440cd..e93eac37506 100644 --- a/modules/nf-core/gatk4/printreads/environment.yml +++ b/modules/nf-core/gatk4/printreads/environment.yml @@ -2,4 +2,4 @@ channels: - conda-forge - bioconda dependencies: - - bioconda::gatk4=4.5.0.0 + - bioconda::gatk4=4.6.1.0 diff --git a/modules/nf-core/gatk4/printreads/main.nf b/modules/nf-core/gatk4/printreads/main.nf index f97180adc24..e24cfa49fb7 100644 --- a/modules/nf-core/gatk4/printreads/main.nf +++ b/modules/nf-core/gatk4/printreads/main.nf @@ -4,8 +4,8 @@ process GATK4_PRINTREADS { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/gatk4:4.5.0.0--py36hdfd78af_0': - 'biocontainers/gatk4:4.5.0.0--py36hdfd78af_0' }" + 'https://depot.galaxyproject.org/singularity/gatk4:4.6.1.0--py310hdfd78af_0': + 'biocontainers/gatk4:4.6.1.0--py310hdfd78af_0' }" input: tuple val(meta), path(input), path(index) diff --git a/modules/nf-core/gatk4/printsvevidence/environment.yml b/modules/nf-core/gatk4/printsvevidence/environment.yml index 55993f440cd..e93eac37506 100644 --- a/modules/nf-core/gatk4/printsvevidence/environment.yml +++ b/modules/nf-core/gatk4/printsvevidence/environment.yml @@ -2,4 +2,4 @@ channels: - conda-forge - bioconda dependencies: - - bioconda::gatk4=4.5.0.0 + - bioconda::gatk4=4.6.1.0 diff --git a/modules/nf-core/gatk4/printsvevidence/main.nf b/modules/nf-core/gatk4/printsvevidence/main.nf index 5cf5b05affc..c4e42bbc5eb 100644 --- a/modules/nf-core/gatk4/printsvevidence/main.nf +++ b/modules/nf-core/gatk4/printsvevidence/main.nf @@ -4,8 +4,8 @@ process GATK4_PRINTSVEVIDENCE { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/gatk4:4.5.0.0--py36hdfd78af_0': - 'biocontainers/gatk4:4.5.0.0--py36hdfd78af_0' }" + 'https://depot.galaxyproject.org/singularity/gatk4:4.6.1.0--py310hdfd78af_0': + 'biocontainers/gatk4:4.6.1.0--py310hdfd78af_0' }" input: tuple val(meta), path(evidence_files), path(evidence_indices) diff --git a/modules/nf-core/gatk4/reblockgvcf/environment.yml b/modules/nf-core/gatk4/reblockgvcf/environment.yml index 55993f440cd..e93eac37506 100644 --- a/modules/nf-core/gatk4/reblockgvcf/environment.yml +++ b/modules/nf-core/gatk4/reblockgvcf/environment.yml @@ -2,4 +2,4 @@ channels: - conda-forge - bioconda dependencies: - - bioconda::gatk4=4.5.0.0 + - bioconda::gatk4=4.6.1.0 diff --git a/modules/nf-core/gatk4/reblockgvcf/main.nf b/modules/nf-core/gatk4/reblockgvcf/main.nf index 4b58bec7788..43376050cb6 100644 --- a/modules/nf-core/gatk4/reblockgvcf/main.nf +++ b/modules/nf-core/gatk4/reblockgvcf/main.nf @@ -4,8 +4,8 @@ process GATK4_REBLOCKGVCF { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/gatk4:4.5.0.0--py36hdfd78af_0': - 'biocontainers/gatk4:4.5.0.0--py36hdfd78af_0' }" + 'https://depot.galaxyproject.org/singularity/gatk4:4.6.1.0--py310hdfd78af_0': + 'biocontainers/gatk4:4.6.1.0--py310hdfd78af_0' }" input: tuple val(meta), path(gvcf), path(tbi), path(intervals) diff --git a/modules/nf-core/gatk4/revertsam/environment.yml b/modules/nf-core/gatk4/revertsam/environment.yml index 55993f440cd..e93eac37506 100644 --- a/modules/nf-core/gatk4/revertsam/environment.yml +++ b/modules/nf-core/gatk4/revertsam/environment.yml @@ -2,4 +2,4 @@ channels: - conda-forge - bioconda dependencies: - - bioconda::gatk4=4.5.0.0 + - bioconda::gatk4=4.6.1.0 diff --git a/modules/nf-core/gatk4/revertsam/main.nf b/modules/nf-core/gatk4/revertsam/main.nf index 635784ab29f..5ce72543e21 100644 --- a/modules/nf-core/gatk4/revertsam/main.nf +++ b/modules/nf-core/gatk4/revertsam/main.nf @@ -4,8 +4,8 @@ process GATK4_REVERTSAM { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/gatk4:4.5.0.0--py36hdfd78af_0': - 'biocontainers/gatk4:4.5.0.0--py36hdfd78af_0' }" + 'https://depot.galaxyproject.org/singularity/gatk4:4.6.1.0--py310hdfd78af_0': + 'biocontainers/gatk4:4.6.1.0--py310hdfd78af_0' }" input: tuple val(meta), path(bam) diff --git a/modules/nf-core/gatk4/samtofastq/environment.yml b/modules/nf-core/gatk4/samtofastq/environment.yml index 55993f440cd..e93eac37506 100644 --- a/modules/nf-core/gatk4/samtofastq/environment.yml +++ b/modules/nf-core/gatk4/samtofastq/environment.yml @@ -2,4 +2,4 @@ channels: - conda-forge - bioconda dependencies: - - bioconda::gatk4=4.5.0.0 + - bioconda::gatk4=4.6.1.0 diff --git a/modules/nf-core/gatk4/samtofastq/main.nf b/modules/nf-core/gatk4/samtofastq/main.nf index 35b9b76db4c..2b1484e7da5 100644 --- a/modules/nf-core/gatk4/samtofastq/main.nf +++ b/modules/nf-core/gatk4/samtofastq/main.nf @@ -4,8 +4,8 @@ process GATK4_SAMTOFASTQ { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/gatk4:4.5.0.0--py36hdfd78af_0': - 'biocontainers/gatk4:4.5.0.0--py36hdfd78af_0' }" + 'https://depot.galaxyproject.org/singularity/gatk4:4.6.1.0--py310hdfd78af_0': + 'biocontainers/gatk4:4.6.1.0--py310hdfd78af_0' }" input: tuple val(meta), path(bam) diff --git a/modules/nf-core/gatk4/selectvariants/environment.yml b/modules/nf-core/gatk4/selectvariants/environment.yml index 55993f440cd..e93eac37506 100644 --- a/modules/nf-core/gatk4/selectvariants/environment.yml +++ b/modules/nf-core/gatk4/selectvariants/environment.yml @@ -2,4 +2,4 @@ channels: - conda-forge - bioconda dependencies: - - bioconda::gatk4=4.5.0.0 + - bioconda::gatk4=4.6.1.0 diff --git a/modules/nf-core/gatk4/selectvariants/main.nf b/modules/nf-core/gatk4/selectvariants/main.nf index c342ee93996..4e59b3ef9cb 100644 --- a/modules/nf-core/gatk4/selectvariants/main.nf +++ b/modules/nf-core/gatk4/selectvariants/main.nf @@ -4,8 +4,8 @@ process GATK4_SELECTVARIANTS { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/gatk4:4.5.0.0--py36hdfd78af_0': - 'biocontainers/gatk4:4.5.0.0--py36hdfd78af_0' }" + 'https://depot.galaxyproject.org/singularity/gatk4:4.6.1.0--py310hdfd78af_0': + 'biocontainers/gatk4:4.6.1.0--py310hdfd78af_0' }" input: tuple val(meta), path(vcf), path(vcf_idx), path (intervals) diff --git a/modules/nf-core/gatk4/shiftfasta/environment.yml b/modules/nf-core/gatk4/shiftfasta/environment.yml index 55993f440cd..e93eac37506 100644 --- a/modules/nf-core/gatk4/shiftfasta/environment.yml +++ b/modules/nf-core/gatk4/shiftfasta/environment.yml @@ -2,4 +2,4 @@ channels: - conda-forge - bioconda dependencies: - - bioconda::gatk4=4.5.0.0 + - bioconda::gatk4=4.6.1.0 diff --git a/modules/nf-core/gatk4/shiftfasta/main.nf b/modules/nf-core/gatk4/shiftfasta/main.nf index 350ff8d3366..8d6874ff6aa 100644 --- a/modules/nf-core/gatk4/shiftfasta/main.nf +++ b/modules/nf-core/gatk4/shiftfasta/main.nf @@ -4,8 +4,8 @@ process GATK4_SHIFTFASTA { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/gatk4:4.5.0.0--py36hdfd78af_0': - 'biocontainers/gatk4:4.5.0.0--py36hdfd78af_0' }" + 'https://depot.galaxyproject.org/singularity/gatk4:4.6.1.0--py310hdfd78af_0': + 'biocontainers/gatk4:4.6.1.0--py310hdfd78af_0' }" input: tuple val(meta), path(fasta) diff --git a/modules/nf-core/gatk4/sitedepthtobaf/environment.yml b/modules/nf-core/gatk4/sitedepthtobaf/environment.yml index 55993f440cd..e93eac37506 100644 --- a/modules/nf-core/gatk4/sitedepthtobaf/environment.yml +++ b/modules/nf-core/gatk4/sitedepthtobaf/environment.yml @@ -2,4 +2,4 @@ channels: - conda-forge - bioconda dependencies: - - bioconda::gatk4=4.5.0.0 + - bioconda::gatk4=4.6.1.0 diff --git a/modules/nf-core/gatk4/sitedepthtobaf/main.nf b/modules/nf-core/gatk4/sitedepthtobaf/main.nf index 514096cac47..b7d7c9eac61 100644 --- a/modules/nf-core/gatk4/sitedepthtobaf/main.nf +++ b/modules/nf-core/gatk4/sitedepthtobaf/main.nf @@ -4,8 +4,8 @@ process GATK4_SITEDEPTHTOBAF { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/gatk4:4.5.0.0--py36hdfd78af_0': - 'biocontainers/gatk4:4.5.0.0--py36hdfd78af_0' }" + 'https://depot.galaxyproject.org/singularity/gatk4:4.6.1.0--py310hdfd78af_0': + 'biocontainers/gatk4:4.6.1.0--py310hdfd78af_0' }" input: tuple val(meta), path(site_depths), path(site_depths_indices) diff --git a/modules/nf-core/gatk4/splitcram/environment.yml b/modules/nf-core/gatk4/splitcram/environment.yml index 55993f440cd..e93eac37506 100644 --- a/modules/nf-core/gatk4/splitcram/environment.yml +++ b/modules/nf-core/gatk4/splitcram/environment.yml @@ -2,4 +2,4 @@ channels: - conda-forge - bioconda dependencies: - - bioconda::gatk4=4.5.0.0 + - bioconda::gatk4=4.6.1.0 diff --git a/modules/nf-core/gatk4/splitcram/main.nf b/modules/nf-core/gatk4/splitcram/main.nf index 1e635cd4926..48544298ab8 100644 --- a/modules/nf-core/gatk4/splitcram/main.nf +++ b/modules/nf-core/gatk4/splitcram/main.nf @@ -4,8 +4,8 @@ process GATK4_SPLITCRAM { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/gatk4:4.5.0.0--py36hdfd78af_0': - 'biocontainers/gatk4:4.5.0.0--py36hdfd78af_0' }" + 'https://depot.galaxyproject.org/singularity/gatk4:4.6.1.0--py310hdfd78af_0': + 'biocontainers/gatk4:4.6.1.0--py310hdfd78af_0' }" input: tuple val(meta), path(cram) diff --git a/modules/nf-core/gatk4/splitintervals/environment.yml b/modules/nf-core/gatk4/splitintervals/environment.yml index 55993f440cd..e93eac37506 100644 --- a/modules/nf-core/gatk4/splitintervals/environment.yml +++ b/modules/nf-core/gatk4/splitintervals/environment.yml @@ -2,4 +2,4 @@ channels: - conda-forge - bioconda dependencies: - - bioconda::gatk4=4.5.0.0 + - bioconda::gatk4=4.6.1.0 diff --git a/modules/nf-core/gatk4/splitintervals/main.nf b/modules/nf-core/gatk4/splitintervals/main.nf index d59b6afb1d7..db43dfa19c9 100644 --- a/modules/nf-core/gatk4/splitintervals/main.nf +++ b/modules/nf-core/gatk4/splitintervals/main.nf @@ -4,8 +4,8 @@ process GATK4_SPLITINTERVALS { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/gatk4:4.5.0.0--py36hdfd78af_0': - 'biocontainers/gatk4:4.5.0.0--py36hdfd78af_0' }" + 'https://depot.galaxyproject.org/singularity/gatk4:4.6.1.0--py310hdfd78af_0': + 'biocontainers/gatk4:4.6.1.0--py310hdfd78af_0' }" input: tuple val(meta), path(intervals) diff --git a/modules/nf-core/gatk4/splitncigarreads/environment.yml b/modules/nf-core/gatk4/splitncigarreads/environment.yml index 55993f440cd..e93eac37506 100644 --- a/modules/nf-core/gatk4/splitncigarreads/environment.yml +++ b/modules/nf-core/gatk4/splitncigarreads/environment.yml @@ -2,4 +2,4 @@ channels: - conda-forge - bioconda dependencies: - - bioconda::gatk4=4.5.0.0 + - bioconda::gatk4=4.6.1.0 diff --git a/modules/nf-core/gatk4/splitncigarreads/main.nf b/modules/nf-core/gatk4/splitncigarreads/main.nf index e2c287a02b1..b5552391ea4 100644 --- a/modules/nf-core/gatk4/splitncigarreads/main.nf +++ b/modules/nf-core/gatk4/splitncigarreads/main.nf @@ -4,8 +4,8 @@ process GATK4_SPLITNCIGARREADS { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/gatk4:4.5.0.0--py36hdfd78af_0': - 'biocontainers/gatk4:4.5.0.0--py36hdfd78af_0' }" + 'https://depot.galaxyproject.org/singularity/gatk4:4.6.1.0--py310hdfd78af_0': + 'biocontainers/gatk4:4.6.1.0--py310hdfd78af_0' }" input: tuple val(meta), path(bam), path(bai), path(intervals) diff --git a/modules/nf-core/gatk4/svannotate/environment.yml b/modules/nf-core/gatk4/svannotate/environment.yml index 55993f440cd..e93eac37506 100644 --- a/modules/nf-core/gatk4/svannotate/environment.yml +++ b/modules/nf-core/gatk4/svannotate/environment.yml @@ -2,4 +2,4 @@ channels: - conda-forge - bioconda dependencies: - - bioconda::gatk4=4.5.0.0 + - bioconda::gatk4=4.6.1.0 diff --git a/modules/nf-core/gatk4/svannotate/main.nf b/modules/nf-core/gatk4/svannotate/main.nf index e5cf874a2b9..e76d81c16a7 100644 --- a/modules/nf-core/gatk4/svannotate/main.nf +++ b/modules/nf-core/gatk4/svannotate/main.nf @@ -4,8 +4,8 @@ process GATK4_SVANNOTATE { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/gatk4:4.5.0.0--py36hdfd78af_0': - 'biocontainers/gatk4:4.5.0.0--py36hdfd78af_0' }" + 'https://depot.galaxyproject.org/singularity/gatk4:4.6.1.0--py310hdfd78af_0': + 'biocontainers/gatk4:4.6.1.0--py310hdfd78af_0' }" input: tuple val(meta), path(vcf), path(tbi), path(bed) diff --git a/modules/nf-core/gatk4/svcluster/environment.yml b/modules/nf-core/gatk4/svcluster/environment.yml index 55993f440cd..e93eac37506 100644 --- a/modules/nf-core/gatk4/svcluster/environment.yml +++ b/modules/nf-core/gatk4/svcluster/environment.yml @@ -2,4 +2,4 @@ channels: - conda-forge - bioconda dependencies: - - bioconda::gatk4=4.5.0.0 + - bioconda::gatk4=4.6.1.0 diff --git a/modules/nf-core/gatk4/svcluster/main.nf b/modules/nf-core/gatk4/svcluster/main.nf index 855dd700f89..19bd55c63be 100644 --- a/modules/nf-core/gatk4/svcluster/main.nf +++ b/modules/nf-core/gatk4/svcluster/main.nf @@ -4,8 +4,8 @@ process GATK4_SVCLUSTER { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/gatk4:4.5.0.0--py36hdfd78af_0': - 'biocontainers/gatk4:4.5.0.0--py36hdfd78af_0' }" + 'https://depot.galaxyproject.org/singularity/gatk4:4.6.1.0--py310hdfd78af_0': + 'biocontainers/gatk4:4.6.1.0--py310hdfd78af_0' }" input: tuple val(meta), path(vcfs), path(indices) diff --git a/modules/nf-core/gatk4/variantfiltration/environment.yml b/modules/nf-core/gatk4/variantfiltration/environment.yml index 55993f440cd..e93eac37506 100644 --- a/modules/nf-core/gatk4/variantfiltration/environment.yml +++ b/modules/nf-core/gatk4/variantfiltration/environment.yml @@ -2,4 +2,4 @@ channels: - conda-forge - bioconda dependencies: - - bioconda::gatk4=4.5.0.0 + - bioconda::gatk4=4.6.1.0 diff --git a/modules/nf-core/gatk4/variantfiltration/main.nf b/modules/nf-core/gatk4/variantfiltration/main.nf index 388c60abf0e..b23f6cf4e9d 100644 --- a/modules/nf-core/gatk4/variantfiltration/main.nf +++ b/modules/nf-core/gatk4/variantfiltration/main.nf @@ -4,8 +4,8 @@ process GATK4_VARIANTFILTRATION { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/gatk4:4.5.0.0--py36hdfd78af_0': - 'biocontainers/gatk4:4.5.0.0--py36hdfd78af_0' }" + 'https://depot.galaxyproject.org/singularity/gatk4:4.6.1.0--py310hdfd78af_0': + 'biocontainers/gatk4:4.6.1.0--py310hdfd78af_0' }" input: tuple val(meta), path(vcf), path(tbi) diff --git a/modules/nf-core/gatk4/variantrecalibrator/environment.yml b/modules/nf-core/gatk4/variantrecalibrator/environment.yml index 55993f440cd..e93eac37506 100644 --- a/modules/nf-core/gatk4/variantrecalibrator/environment.yml +++ b/modules/nf-core/gatk4/variantrecalibrator/environment.yml @@ -2,4 +2,4 @@ channels: - conda-forge - bioconda dependencies: - - bioconda::gatk4=4.5.0.0 + - bioconda::gatk4=4.6.1.0 diff --git a/modules/nf-core/gatk4/variantrecalibrator/main.nf b/modules/nf-core/gatk4/variantrecalibrator/main.nf index 24844ce0c95..317b83ce60a 100644 --- a/modules/nf-core/gatk4/variantrecalibrator/main.nf +++ b/modules/nf-core/gatk4/variantrecalibrator/main.nf @@ -4,8 +4,8 @@ process GATK4_VARIANTRECALIBRATOR { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/gatk4:4.5.0.0--py36hdfd78af_0': - 'biocontainers/gatk4:4.5.0.0--py36hdfd78af_0' }" + 'https://depot.galaxyproject.org/singularity/gatk4:4.6.1.0--py310hdfd78af_0': + 'biocontainers/gatk4:4.6.1.0--py310hdfd78af_0' }" input: tuple val(meta), path(vcf), path(tbi) // input vcf and tbi of variants to recalibrate diff --git a/modules/nf-core/gatk4/variantstotable/environment.yml b/modules/nf-core/gatk4/variantstotable/environment.yml index aa7d804d4ad..03610def61e 100644 --- a/modules/nf-core/gatk4/variantstotable/environment.yml +++ b/modules/nf-core/gatk4/variantstotable/environment.yml @@ -3,4 +3,4 @@ channels: - conda-forge - bioconda dependencies: - - bioconda::gatk4=4.5.0.0 + - bioconda::gatk4=4.6.1.0 diff --git a/modules/nf-core/gatk4/variantstotable/main.nf b/modules/nf-core/gatk4/variantstotable/main.nf index 5a189beed61..b61040aac48 100644 --- a/modules/nf-core/gatk4/variantstotable/main.nf +++ b/modules/nf-core/gatk4/variantstotable/main.nf @@ -4,8 +4,8 @@ process GATK4_VARIANTSTOTABLE { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/gatk4:4.5.0.0--py36hdfd78af_0': - 'biocontainers/gatk4:4.5.0.0--py36hdfd78af_0' }" + 'https://depot.galaxyproject.org/singularity/gatk4:4.6.1.0--py310hdfd78af_0': + 'biocontainers/gatk4:4.6.1.0--py310hdfd78af_0' }" input: tuple val(meta), path(vcf), path(tbi), path(arguments_file), path(include_intervals), path(exclude_intervals) From c581acf54846673c6951c38f1320de06a85335bc Mon Sep 17 00:00:00 2001 From: Matthias De Smet Date: Thu, 31 Oct 2024 10:46:00 +0000 Subject: [PATCH 2/4] fix some tests --- .../tests/main.nf.test.snap | 18 +++--- .../annotateintervals/tests/main.nf.test.snap | 58 +++++++++---------- .../gatk4/applybqsr/tests/main.nf.test.snap | 56 +++++++++--------- .../gatk4/applyvqsr/tests/main.nf.test.snap | 26 ++++----- .../gatk4/asereadcounter/main.nf.test.snap | 10 ++-- .../baserecalibrator/tests/main.nf.test.snap | 50 ++++++++-------- .../bedtointervallist/tests/main.nf.test.snap | 10 ++-- .../tests/main.nf.test.snap | 34 +++++------ .../tests/main.nf.test.snap | 32 +++++----- .../collectreadcounts/tests/main.nf.test.snap | 20 +++---- .../denoisereadcounts/tests/main.nf.test.snap | 8 +-- .../intervallisttools/tests/main.nf.test.snap | 20 +++---- 12 files changed, 171 insertions(+), 171 deletions(-) diff --git a/modules/nf-core/gatk4/addorreplacereadgroups/tests/main.nf.test.snap b/modules/nf-core/gatk4/addorreplacereadgroups/tests/main.nf.test.snap index 93a87cc39eb..07101dc9bfd 100644 --- a/modules/nf-core/gatk4/addorreplacereadgroups/tests/main.nf.test.snap +++ b/modules/nf-core/gatk4/addorreplacereadgroups/tests/main.nf.test.snap @@ -32,7 +32,7 @@ ], "3": [ - "versions.yml:md5,da55295b55986cfcf65d41745c7bda4c" + "versions.yml:md5,09f498302943b70029a56ddf65522814" ], "bai": [ [ @@ -54,27 +54,27 @@ ], "versions": [ - "versions.yml:md5,da55295b55986cfcf65d41745c7bda4c" + "versions.yml:md5,09f498302943b70029a56ddf65522814" ] } ], "meta": { - "nf-test": "0.8.4", - "nextflow": "23.10.1" + "nf-test": "0.9.1", + "nextflow": "24.10.0" }, - "timestamp": "2024-03-20T13:19:33.815262" + "timestamp": "2024-10-31T10:28:22.832793576" }, "versions": { "content": [ [ - "versions.yml:md5,da55295b55986cfcf65d41745c7bda4c" + "versions.yml:md5,09f498302943b70029a56ddf65522814" ] ], "meta": { - "nf-test": "0.8.4", - "nextflow": "23.10.1" + "nf-test": "0.9.1", + "nextflow": "24.10.0" }, - "timestamp": "2024-03-20T13:19:18.103325" + "timestamp": "2024-10-31T10:28:10.146204216" }, "cram_name": { "content": [ diff --git a/modules/nf-core/gatk4/annotateintervals/tests/main.nf.test.snap b/modules/nf-core/gatk4/annotateintervals/tests/main.nf.test.snap index 749f6fb6f13..3b06f09771a 100644 --- a/modules/nf-core/gatk4/annotateintervals/tests/main.nf.test.snap +++ b/modules/nf-core/gatk4/annotateintervals/tests/main.nf.test.snap @@ -12,7 +12,7 @@ ] ], "1": [ - "versions.yml:md5,599cde136feb5d60b2d01b5fbd252fa0" + "versions.yml:md5,6e1e1caad2a19737e858bc743284cbb2" ], "annotated_intervals": [ [ @@ -24,15 +24,15 @@ ] ], "versions": [ - "versions.yml:md5,599cde136feb5d60b2d01b5fbd252fa0" + "versions.yml:md5,6e1e1caad2a19737e858bc743284cbb2" ] } ], "meta": { - "nf-test": "0.8.4", - "nextflow": "23.10.0" + "nf-test": "0.9.1", + "nextflow": "24.10.0" }, - "timestamp": "2024-02-13T16:07:36.32193" + "timestamp": "2024-10-31T10:29:29.006068994" }, "homo_sapiens genome [interval_list]": { "content": [ @@ -47,7 +47,7 @@ ] ], "1": [ - "versions.yml:md5,599cde136feb5d60b2d01b5fbd252fa0" + "versions.yml:md5,6e1e1caad2a19737e858bc743284cbb2" ], "annotated_intervals": [ [ @@ -59,15 +59,15 @@ ] ], "versions": [ - "versions.yml:md5,599cde136feb5d60b2d01b5fbd252fa0" + "versions.yml:md5,6e1e1caad2a19737e858bc743284cbb2" ] } ], "meta": { - "nf-test": "0.8.4", - "nextflow": "23.10.0" + "nf-test": "0.9.1", + "nextflow": "24.10.0" }, - "timestamp": "2024-02-13T16:08:12.533176" + "timestamp": "2024-10-31T10:30:08.763305448" }, "homo_sapiens genome multi-interval [bed]": { "content": [ @@ -82,7 +82,7 @@ ] ], "1": [ - "versions.yml:md5,599cde136feb5d60b2d01b5fbd252fa0" + "versions.yml:md5,6e1e1caad2a19737e858bc743284cbb2" ], "annotated_intervals": [ [ @@ -94,15 +94,15 @@ ] ], "versions": [ - "versions.yml:md5,599cde136feb5d60b2d01b5fbd252fa0" + "versions.yml:md5,6e1e1caad2a19737e858bc743284cbb2" ] } ], "meta": { - "nf-test": "0.8.4", - "nextflow": "23.10.0" + "nf-test": "0.9.1", + "nextflow": "24.10.0" }, - "timestamp": "2024-02-13T16:07:54.643276" + "timestamp": "2024-10-31T10:29:48.403638052" }, "homo_sapiens genome [interval_list] mappable_regions": { "content": [ @@ -117,7 +117,7 @@ ] ], "1": [ - "versions.yml:md5,599cde136feb5d60b2d01b5fbd252fa0" + "versions.yml:md5,6e1e1caad2a19737e858bc743284cbb2" ], "annotated_intervals": [ [ @@ -129,28 +129,28 @@ ] ], "versions": [ - "versions.yml:md5,599cde136feb5d60b2d01b5fbd252fa0" + "versions.yml:md5,6e1e1caad2a19737e858bc743284cbb2" ] } ], "meta": { - "nf-test": "0.8.4", - "nextflow": "23.10.0" + "nf-test": "0.9.1", + "nextflow": "24.10.0" }, - "timestamp": "2024-02-13T16:08:31.311782" + "timestamp": "2024-10-31T10:30:23.256626974" }, "homo_sapiens genome [bed] - stub": { "content": [ [ "test.tsv", - "versions.yml:md5,599cde136feb5d60b2d01b5fbd252fa0" + "versions.yml:md5,6e1e1caad2a19737e858bc743284cbb2" ] ], "meta": { - "nf-test": "0.8.4", - "nextflow": "23.10.0" + "nf-test": "0.9.1", + "nextflow": "24.10.0" }, - "timestamp": "2024-02-13T16:09:04.54745" + "timestamp": "2024-10-31T10:30:52.179735439" }, "homo_sapiens genome [interval_list] duplication_regions": { "content": [ @@ -165,7 +165,7 @@ ] ], "1": [ - "versions.yml:md5,599cde136feb5d60b2d01b5fbd252fa0" + "versions.yml:md5,6e1e1caad2a19737e858bc743284cbb2" ], "annotated_intervals": [ [ @@ -177,14 +177,14 @@ ] ], "versions": [ - "versions.yml:md5,599cde136feb5d60b2d01b5fbd252fa0" + "versions.yml:md5,6e1e1caad2a19737e858bc743284cbb2" ] } ], "meta": { - "nf-test": "0.8.4", - "nextflow": "23.10.0" + "nf-test": "0.9.1", + "nextflow": "24.10.0" }, - "timestamp": "2024-02-13T16:08:49.684766" + "timestamp": "2024-10-31T10:30:37.398809104" } } \ No newline at end of file diff --git a/modules/nf-core/gatk4/applybqsr/tests/main.nf.test.snap b/modules/nf-core/gatk4/applybqsr/tests/main.nf.test.snap index 19b37d0636d..427cbddb8d0 100644 --- a/modules/nf-core/gatk4/applybqsr/tests/main.nf.test.snap +++ b/modules/nf-core/gatk4/applybqsr/tests/main.nf.test.snap @@ -14,7 +14,7 @@ ], "2": [ - "versions.yml:md5,bb2a060a0280c812fba3c74b1707b350" + "versions.yml:md5,91928754768510a59bde637403ee6a94" ], "bam": [ [ @@ -28,15 +28,15 @@ ], "versions": [ - "versions.yml:md5,bb2a060a0280c812fba3c74b1707b350" + "versions.yml:md5,91928754768510a59bde637403ee6a94" ] } ], "meta": { - "nf-test": "0.9.0", - "nextflow": "24.04.4" + "nf-test": "0.9.1", + "nextflow": "24.10.0" }, - "timestamp": "2024-09-20T10:25:00.314573" + "timestamp": "2024-10-31T10:32:45.888751339" }, "sarscov2 - bam - intervals": { "content": [ @@ -46,48 +46,48 @@ { "id": "test" }, - "test.bam:md5,096d269e17f4ae53f765013479240db8" + "test.bam:md5,51259943bca01c92b20fb5b7ac09a246" ] ], "1": [ ], "2": [ - "versions.yml:md5,bb2a060a0280c812fba3c74b1707b350" + "versions.yml:md5,91928754768510a59bde637403ee6a94" ], "bam": [ [ { "id": "test" }, - "test.bam:md5,096d269e17f4ae53f765013479240db8" + "test.bam:md5,51259943bca01c92b20fb5b7ac09a246" ] ], "cram": [ ], "versions": [ - "versions.yml:md5,bb2a060a0280c812fba3c74b1707b350" + "versions.yml:md5,91928754768510a59bde637403ee6a94" ] } ], "meta": { - "nf-test": "0.8.4", - "nextflow": "23.10.0" + "nf-test": "0.9.1", + "nextflow": "24.10.0" }, - "timestamp": "2024-02-13T16:21:48.144461" + "timestamp": "2024-10-31T10:31:59.340916681" }, "sarscov2 - cram": { "content": [ [ - "versions.yml:md5,bb2a060a0280c812fba3c74b1707b350" + "versions.yml:md5,91928754768510a59bde637403ee6a94" ] ], "meta": { - "nf-test": "0.8.4", - "nextflow": "23.10.0" + "nf-test": "0.9.1", + "nextflow": "24.10.0" }, - "timestamp": "2024-02-13T16:22:09.308602" + "timestamp": "2024-10-31T10:32:16.162569909" }, "test.cram": { "content": [ @@ -114,7 +114,7 @@ ] ], "2": [ - "versions.yml:md5,bb2a060a0280c812fba3c74b1707b350" + "versions.yml:md5,91928754768510a59bde637403ee6a94" ], "bam": [ @@ -128,15 +128,15 @@ ] ], "versions": [ - "versions.yml:md5,bb2a060a0280c812fba3c74b1707b350" + "versions.yml:md5,91928754768510a59bde637403ee6a94" ] } ], "meta": { - "nf-test": "0.9.0", - "nextflow": "24.04.4" + "nf-test": "0.9.1", + "nextflow": "24.10.0" }, - "timestamp": "2024-09-20T10:24:52.761169" + "timestamp": "2024-10-31T10:32:34.223186142" }, "sarscov2 - bam": { "content": [ @@ -146,35 +146,35 @@ { "id": "test" }, - "test.bam:md5,022271b9ce0a07579282a2a5c1186513" + "test.bam:md5,213acb451007a0098a6a6a360fa68d72" ] ], "1": [ ], "2": [ - "versions.yml:md5,bb2a060a0280c812fba3c74b1707b350" + "versions.yml:md5,91928754768510a59bde637403ee6a94" ], "bam": [ [ { "id": "test" }, - "test.bam:md5,022271b9ce0a07579282a2a5c1186513" + "test.bam:md5,213acb451007a0098a6a6a360fa68d72" ] ], "cram": [ ], "versions": [ - "versions.yml:md5,bb2a060a0280c812fba3c74b1707b350" + "versions.yml:md5,91928754768510a59bde637403ee6a94" ] } ], "meta": { - "nf-test": "0.8.4", - "nextflow": "23.10.0" + "nf-test": "0.9.1", + "nextflow": "24.10.0" }, - "timestamp": "2024-02-13T16:21:28.719225" + "timestamp": "2024-10-31T10:31:44.601557038" } } \ No newline at end of file diff --git a/modules/nf-core/gatk4/applyvqsr/tests/main.nf.test.snap b/modules/nf-core/gatk4/applyvqsr/tests/main.nf.test.snap index ad2fe8be65a..1f3e97cbfdc 100644 --- a/modules/nf-core/gatk4/applyvqsr/tests/main.nf.test.snap +++ b/modules/nf-core/gatk4/applyvqsr/tests/main.nf.test.snap @@ -22,14 +22,14 @@ "versions": { "content": [ [ - "versions.yml:md5,4a6890d486a62ce6f2edfd2f8961da4f" + "versions.yml:md5,198986205018e3e6cdd651680a5e8cdd" ] ], "meta": { - "nf-test": "0.8.4", - "nextflow": "23.10.0" + "nf-test": "0.9.1", + "nextflow": "24.10.0" }, - "timestamp": "2024-05-15T13:00:49.353138" + "timestamp": "2024-10-31T10:33:41.980566137" }, "human - vcf - stub": { "content": [ @@ -51,7 +51,7 @@ ] ], "2": [ - "versions.yml:md5,4a6890d486a62ce6f2edfd2f8961da4f" + "versions.yml:md5,198986205018e3e6cdd651680a5e8cdd" ], "tbi": [ [ @@ -70,26 +70,26 @@ ] ], "versions": [ - "versions.yml:md5,4a6890d486a62ce6f2edfd2f8961da4f" + "versions.yml:md5,198986205018e3e6cdd651680a5e8cdd" ] } ], "meta": { - "nf-test": "0.8.4", - "nextflow": "23.10.0" + "nf-test": "0.9.1", + "nextflow": "24.10.0" }, - "timestamp": "2024-05-15T13:01:24.370421" + "timestamp": "2024-10-31T10:34:08.561335315" }, "versions_allelspecific": { "content": [ [ - "versions.yml:md5,4a6890d486a62ce6f2edfd2f8961da4f" + "versions.yml:md5,198986205018e3e6cdd651680a5e8cdd" ] ], "meta": { - "nf-test": "0.8.4", - "nextflow": "23.10.0" + "nf-test": "0.9.1", + "nextflow": "24.10.0" }, - "timestamp": "2024-05-15T13:01:08.104194" + "timestamp": "2024-10-31T10:33:56.418381574" } } \ No newline at end of file diff --git a/modules/nf-core/gatk4/asereadcounter/main.nf.test.snap b/modules/nf-core/gatk4/asereadcounter/main.nf.test.snap index cb2740864b2..afaec52efe4 100644 --- a/modules/nf-core/gatk4/asereadcounter/main.nf.test.snap +++ b/modules/nf-core/gatk4/asereadcounter/main.nf.test.snap @@ -11,7 +11,7 @@ ] ], "1": [ - "versions.yml:md5,d567b20620f5adf0829cc4b4adb9f6ff" + "versions.yml:md5,64995de5e01e2d49fccd2b97df276d01" ], "csv": [ [ @@ -22,14 +22,14 @@ ] ], "versions": [ - "versions.yml:md5,d567b20620f5adf0829cc4b4adb9f6ff" + "versions.yml:md5,64995de5e01e2d49fccd2b97df276d01" ] } ], "meta": { - "nf-test": "0.8.4", - "nextflow": "23.10.1" + "nf-test": "0.9.1", + "nextflow": "24.10.0" }, - "timestamp": "2024-03-19T10:03:42.158801" + "timestamp": "2024-10-31T10:35:00.386844997" } } \ No newline at end of file diff --git a/modules/nf-core/gatk4/baserecalibrator/tests/main.nf.test.snap b/modules/nf-core/gatk4/baserecalibrator/tests/main.nf.test.snap index 8291304ba87..c3fca758eb8 100644 --- a/modules/nf-core/gatk4/baserecalibrator/tests/main.nf.test.snap +++ b/modules/nf-core/gatk4/baserecalibrator/tests/main.nf.test.snap @@ -11,7 +11,7 @@ ] ], "1": [ - "versions.yml:md5,4ff697a3a05bb4d30701e6750c246ed2" + "versions.yml:md5,1150a8b62c614926eeedda9d4bc8f651" ], "table": [ [ @@ -22,15 +22,15 @@ ] ], "versions": [ - "versions.yml:md5,4ff697a3a05bb4d30701e6750c246ed2" + "versions.yml:md5,1150a8b62c614926eeedda9d4bc8f651" ] } ], "meta": { - "nf-test": "0.8.4", - "nextflow": "23.10.0" + "nf-test": "0.9.1", + "nextflow": "24.10.0" }, - "timestamp": "2024-02-13T16:16:00.04396" + "timestamp": "2024-10-31T10:36:20.634357503" }, "sarscov2 - bam - intervals": { "content": [ @@ -44,7 +44,7 @@ ] ], "1": [ - "versions.yml:md5,4ff697a3a05bb4d30701e6750c246ed2" + "versions.yml:md5,1150a8b62c614926eeedda9d4bc8f651" ], "table": [ [ @@ -55,15 +55,15 @@ ] ], "versions": [ - "versions.yml:md5,4ff697a3a05bb4d30701e6750c246ed2" + "versions.yml:md5,1150a8b62c614926eeedda9d4bc8f651" ] } ], "meta": { - "nf-test": "0.8.4", - "nextflow": "23.10.0" + "nf-test": "0.9.1", + "nextflow": "24.10.0" }, - "timestamp": "2024-02-13T16:15:17.899391" + "timestamp": "2024-10-31T10:35:55.223087741" }, "sarscov2 - bam - multiple sites": { "content": [ @@ -77,7 +77,7 @@ ] ], "1": [ - "versions.yml:md5,4ff697a3a05bb4d30701e6750c246ed2" + "versions.yml:md5,1150a8b62c614926eeedda9d4bc8f651" ], "table": [ [ @@ -88,15 +88,15 @@ ] ], "versions": [ - "versions.yml:md5,4ff697a3a05bb4d30701e6750c246ed2" + "versions.yml:md5,1150a8b62c614926eeedda9d4bc8f651" ] } ], "meta": { - "nf-test": "0.8.4", - "nextflow": "23.10.0" + "nf-test": "0.9.1", + "nextflow": "24.10.0" }, - "timestamp": "2024-02-13T16:15:47.770383" + "timestamp": "2024-10-31T10:36:10.08523788" }, "homo_sapiens - cram ": { "content": [ @@ -110,7 +110,7 @@ ] ], "1": [ - "versions.yml:md5,4ff697a3a05bb4d30701e6750c246ed2" + "versions.yml:md5,1150a8b62c614926eeedda9d4bc8f651" ], "table": [ [ @@ -121,15 +121,15 @@ ] ], "versions": [ - "versions.yml:md5,4ff697a3a05bb4d30701e6750c246ed2" + "versions.yml:md5,1150a8b62c614926eeedda9d4bc8f651" ] } ], "meta": { - "nf-test": "0.8.4", - "nextflow": "23.10.0" + "nf-test": "0.9.1", + "nextflow": "24.10.0" }, - "timestamp": "2024-02-13T16:16:42.135898" + "timestamp": "2024-10-31T10:36:42.285370441" }, "sarscov2 - bam": { "content": [ @@ -143,7 +143,7 @@ ] ], "1": [ - "versions.yml:md5,4ff697a3a05bb4d30701e6750c246ed2" + "versions.yml:md5,1150a8b62c614926eeedda9d4bc8f651" ], "table": [ [ @@ -154,14 +154,14 @@ ] ], "versions": [ - "versions.yml:md5,4ff697a3a05bb4d30701e6750c246ed2" + "versions.yml:md5,1150a8b62c614926eeedda9d4bc8f651" ] } ], "meta": { - "nf-test": "0.8.4", - "nextflow": "23.10.0" + "nf-test": "0.9.1", + "nextflow": "24.10.0" }, - "timestamp": "2024-02-13T16:14:57.629443" + "timestamp": "2024-10-31T10:35:41.89476551" } } \ No newline at end of file diff --git a/modules/nf-core/gatk4/bedtointervallist/tests/main.nf.test.snap b/modules/nf-core/gatk4/bedtointervallist/tests/main.nf.test.snap index 48c322fd001..6936cf97175 100644 --- a/modules/nf-core/gatk4/bedtointervallist/tests/main.nf.test.snap +++ b/modules/nf-core/gatk4/bedtointervallist/tests/main.nf.test.snap @@ -11,7 +11,7 @@ ] ], "1": [ - "versions.yml:md5,29a18c36f27584eb5a5f2f5457088b3b" + "versions.yml:md5,6b3aa4d49cc3ba433ecf92e31f155d00" ], "interval_list": [ [ @@ -22,14 +22,14 @@ ] ], "versions": [ - "versions.yml:md5,29a18c36f27584eb5a5f2f5457088b3b" + "versions.yml:md5,6b3aa4d49cc3ba433ecf92e31f155d00" ] } ], "meta": { - "nf-test": "0.8.4", - "nextflow": "23.10.1" + "nf-test": "0.9.1", + "nextflow": "24.10.0" }, - "timestamp": "2024-03-19T14:20:12.168775" + "timestamp": "2024-10-31T10:37:25.720782902" } } \ No newline at end of file diff --git a/modules/nf-core/gatk4/calculatecontamination/tests/main.nf.test.snap b/modules/nf-core/gatk4/calculatecontamination/tests/main.nf.test.snap index 5c2930f948f..756c2452f8a 100644 --- a/modules/nf-core/gatk4/calculatecontamination/tests/main.nf.test.snap +++ b/modules/nf-core/gatk4/calculatecontamination/tests/main.nf.test.snap @@ -2,38 +2,38 @@ "versions_pair": { "content": [ [ - "versions.yml:md5,4a72b1da18f7045d470225881e7266a6" + "versions.yml:md5,05685d2e6a839916a120c07b4db98914" ] ], "meta": { - "nf-test": "0.8.4", - "nextflow": "23.10.0" + "nf-test": "0.9.1", + "nextflow": "24.10.0" }, - "timestamp": "2024-05-15T11:08:17.057861" + "timestamp": "2024-10-31T10:39:04.844937172" }, "versions": { "content": [ [ - "versions.yml:md5,4a72b1da18f7045d470225881e7266a6" + "versions.yml:md5,05685d2e6a839916a120c07b4db98914" ] ], "meta": { - "nf-test": "0.8.4", - "nextflow": "23.10.0" + "nf-test": "0.9.1", + "nextflow": "24.10.0" }, - "timestamp": "2024-05-15T11:08:07.193762" + "timestamp": "2024-10-31T10:38:50.36175509" }, "versions_segmentation": { "content": [ [ - "versions.yml:md5,4a72b1da18f7045d470225881e7266a6" + "versions.yml:md5,05685d2e6a839916a120c07b4db98914" ] ], "meta": { - "nf-test": "0.8.4", - "nextflow": "23.10.0" + "nf-test": "0.9.1", + "nextflow": "24.10.0" }, - "timestamp": "2024-05-15T11:08:26.99069" + "timestamp": "2024-10-31T10:39:22.516513354" }, "segmentation": { "content": [ @@ -75,7 +75,7 @@ ] ], "2": [ - "versions.yml:md5,4a72b1da18f7045d470225881e7266a6" + "versions.yml:md5,05685d2e6a839916a120c07b4db98914" ], "contamination": [ [ @@ -94,15 +94,15 @@ ] ], "versions": [ - "versions.yml:md5,4a72b1da18f7045d470225881e7266a6" + "versions.yml:md5,05685d2e6a839916a120c07b4db98914" ] } ], "meta": { - "nf-test": "0.8.4", - "nextflow": "23.10.0" + "nf-test": "0.9.1", + "nextflow": "24.10.0" }, - "timestamp": "2024-05-15T12:56:14.817045" + "timestamp": "2024-10-31T10:39:40.353818746" }, "human - pileup-table - matched-pair": { "content": [ diff --git a/modules/nf-core/gatk4/calibratedragstrmodel/tests/main.nf.test.snap b/modules/nf-core/gatk4/calibratedragstrmodel/tests/main.nf.test.snap index d0d7b8b9dce..2ece2ae6151 100644 --- a/modules/nf-core/gatk4/calibratedragstrmodel/tests/main.nf.test.snap +++ b/modules/nf-core/gatk4/calibratedragstrmodel/tests/main.nf.test.snap @@ -9,14 +9,14 @@ "############################################################################################" ], [ - "versions.yml:md5,3a652afb9cc9fca4e162ec205406b368" + "versions.yml:md5,10b807dc7c15142d4e2486e20ea622ee" ] ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.4" + "nf-test": "0.9.1", + "nextflow": "24.10.0" }, - "timestamp": "2024-08-26T13:22:17.584362" + "timestamp": "2024-10-31T10:40:49.021126898" }, "test-gatk4-calibratedragstrmodel-cram": { "content": [ @@ -28,14 +28,14 @@ "############################################################################################" ], [ - "versions.yml:md5,3a652afb9cc9fca4e162ec205406b368" + "versions.yml:md5,10b807dc7c15142d4e2486e20ea622ee" ] ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.4" + "nf-test": "0.9.1", + "nextflow": "24.10.0" }, - "timestamp": "2024-08-26T13:22:30.21551" + "timestamp": "2024-10-31T10:41:19.764355383" }, "test-gatk4-calibratedragstrmodel-gzipped-beds": { "content": [ @@ -47,14 +47,14 @@ "############################################################################################" ], [ - "versions.yml:md5,3a652afb9cc9fca4e162ec205406b368" + "versions.yml:md5,10b807dc7c15142d4e2486e20ea622ee" ] ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.4" + "nf-test": "0.9.1", + "nextflow": "24.10.0" }, - "timestamp": "2024-08-26T13:22:53.619871" + "timestamp": "2024-10-31T10:42:13.527330586" }, "test-gatk4-calibratedragstrmodel-beds": { "content": [ @@ -66,13 +66,13 @@ "############################################################################################" ], [ - "versions.yml:md5,3a652afb9cc9fca4e162ec205406b368" + "versions.yml:md5,10b807dc7c15142d4e2486e20ea622ee" ] ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.4" + "nf-test": "0.9.1", + "nextflow": "24.10.0" }, - "timestamp": "2024-08-26T13:22:41.938548" + "timestamp": "2024-10-31T10:41:47.344014169" } } \ No newline at end of file diff --git a/modules/nf-core/gatk4/collectreadcounts/tests/main.nf.test.snap b/modules/nf-core/gatk4/collectreadcounts/tests/main.nf.test.snap index 28a3a6e151b..212f950d28a 100644 --- a/modules/nf-core/gatk4/collectreadcounts/tests/main.nf.test.snap +++ b/modules/nf-core/gatk4/collectreadcounts/tests/main.nf.test.snap @@ -15,7 +15,7 @@ ] ], "2": [ - "versions.yml:md5,ebf23f4ab63948ba97df07035f8d2659" + "versions.yml:md5,5d92970288bee9ff45551e783f7058fb" ], "hdf5": [ @@ -30,15 +30,15 @@ ] ], "versions": [ - "versions.yml:md5,ebf23f4ab63948ba97df07035f8d2659" + "versions.yml:md5,5d92970288bee9ff45551e783f7058fb" ] } ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.4" + "nf-test": "0.9.1", + "nextflow": "24.10.0" }, - "timestamp": "2024-08-26T12:58:19.610687" + "timestamp": "2024-10-31T10:44:48.133712731" }, "test-gatk4-collectreadcounts-hdf5": { "content": [ @@ -69,7 +69,7 @@ ] ], "2": [ - "versions.yml:md5,ebf23f4ab63948ba97df07035f8d2659" + "versions.yml:md5,5d92970288bee9ff45551e783f7058fb" ], "hdf5": [ @@ -84,14 +84,14 @@ ] ], "versions": [ - "versions.yml:md5,ebf23f4ab63948ba97df07035f8d2659" + "versions.yml:md5,5d92970288bee9ff45551e783f7058fb" ] } ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.4" + "nf-test": "0.9.1", + "nextflow": "24.10.0" }, - "timestamp": "2024-08-26T12:58:07.500024" + "timestamp": "2024-10-31T10:44:24.624195466" } } \ No newline at end of file diff --git a/modules/nf-core/gatk4/denoisereadcounts/tests/main.nf.test.snap b/modules/nf-core/gatk4/denoisereadcounts/tests/main.nf.test.snap index f35eb283db4..541e6c61216 100644 --- a/modules/nf-core/gatk4/denoisereadcounts/tests/main.nf.test.snap +++ b/modules/nf-core/gatk4/denoisereadcounts/tests/main.nf.test.snap @@ -20,13 +20,13 @@ ] ], [ - "versions.yml:md5,140780e1af7318cc9259b8970bc70c81" + "versions.yml:md5,2e89249bc2ef4e86a3fc59f0913c5525" ] ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.4" + "nf-test": "0.9.1", + "nextflow": "24.10.0" }, - "timestamp": "2024-08-16T12:34:12.568925" + "timestamp": "2024-10-31T10:45:25.930205969" } } \ No newline at end of file diff --git a/modules/nf-core/gatk4/intervallisttools/tests/main.nf.test.snap b/modules/nf-core/gatk4/intervallisttools/tests/main.nf.test.snap index 7718ed00382..3be7acaa3ea 100644 --- a/modules/nf-core/gatk4/intervallisttools/tests/main.nf.test.snap +++ b/modules/nf-core/gatk4/intervallisttools/tests/main.nf.test.snap @@ -16,7 +16,7 @@ ] ], "1": [ - "versions.yml:md5,ff682cc9ad70d65a80280df57b316b03" + "versions.yml:md5,a2a074f61ecf1e0a21d1aeefd139125f" ], "interval_list": [ [ @@ -32,15 +32,15 @@ ] ], "versions": [ - "versions.yml:md5,ff682cc9ad70d65a80280df57b316b03" + "versions.yml:md5,a2a074f61ecf1e0a21d1aeefd139125f" ] } ], "meta": { - "nf-test": "0.8.4", - "nextflow": "23.04.2" + "nf-test": "0.9.1", + "nextflow": "24.10.0" }, - "timestamp": "2024-05-22T21:26:22.252885" + "timestamp": "2024-10-31T10:37:46.848386632" }, "test_gatk4_intervallisttools -stub": { "content": [ @@ -59,7 +59,7 @@ ] ], "1": [ - "versions.yml:md5,ff682cc9ad70d65a80280df57b316b03" + "versions.yml:md5,a2a074f61ecf1e0a21d1aeefd139125f" ], "interval_list": [ [ @@ -75,14 +75,14 @@ ] ], "versions": [ - "versions.yml:md5,ff682cc9ad70d65a80280df57b316b03" + "versions.yml:md5,a2a074f61ecf1e0a21d1aeefd139125f" ] } ], "meta": { - "nf-test": "0.8.4", - "nextflow": "23.04.2" + "nf-test": "0.9.1", + "nextflow": "24.10.0" }, - "timestamp": "2024-05-22T22:15:11.772344" + "timestamp": "2024-10-31T10:38:00.631338482" } } \ No newline at end of file From 4cc9150dc0edc6caf95dd29d24046b7591743ac3 Mon Sep 17 00:00:00 2001 From: Matthias De Smet Date: Thu, 31 Oct 2024 10:48:19 +0000 Subject: [PATCH 3/4] more tests --- .../collectsvevidence/tests/main.nf.test.snap | 44 +++++++++---------- .../combinegvcfs/tests/main.nf.test.snap | 18 ++++---- 2 files changed, 31 insertions(+), 31 deletions(-) diff --git a/modules/nf-core/gatk4/collectsvevidence/tests/main.nf.test.snap b/modules/nf-core/gatk4/collectsvevidence/tests/main.nf.test.snap index 1f6992b8c64..cca8eea4c05 100644 --- a/modules/nf-core/gatk4/collectsvevidence/tests/main.nf.test.snap +++ b/modules/nf-core/gatk4/collectsvevidence/tests/main.nf.test.snap @@ -6,14 +6,14 @@ "chr22\t3320\t+\tchr22\t3482\t-\tnormal", "test.pe.txt.gz.tbi", [ - "versions.yml:md5,eb641a78898f7bfe135ef01b77647079" + "versions.yml:md5,3fe376f43b4993a9edd5fa5f147f2bfe" ] ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.4" + "nf-test": "0.9.1", + "nextflow": "24.10.0" }, - "timestamp": "2024-08-26T12:51:11.44656" + "timestamp": "2024-10-31T10:46:15.558451518" }, "test-gatk4-collectsvevidence-cram - stub": { "content": [ @@ -61,7 +61,7 @@ ], "6": [ - "versions.yml:md5,eb641a78898f7bfe135ef01b77647079" + "versions.yml:md5,3fe376f43b4993a9edd5fa5f147f2bfe" ], "paired_end_evidence": [ [ @@ -106,15 +106,15 @@ ] ], "versions": [ - "versions.yml:md5,eb641a78898f7bfe135ef01b77647079" + "versions.yml:md5,3fe376f43b4993a9edd5fa5f147f2bfe" ] } ], "meta": { - "nf-test": "0.9.0", - "nextflow": "24.04.4" + "nf-test": "0.9.1", + "nextflow": "24.10.0" }, - "timestamp": "2024-09-20T10:36:35.045647" + "timestamp": "2024-10-31T10:46:54.409850619" }, "test-gatk4-collectsvevidence-allele-count": { "content": [ @@ -125,14 +125,14 @@ "chr22\t1981\tnormal\t235\t0\t48\t0", "test.sd.txt.gz.tbi", [ - "versions.yml:md5,eb641a78898f7bfe135ef01b77647079" + "versions.yml:md5,3fe376f43b4993a9edd5fa5f147f2bfe" ] ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.4" + "nf-test": "0.9.1", + "nextflow": "24.10.0" }, - "timestamp": "2024-08-26T12:48:13.663238" + "timestamp": "2024-10-31T10:46:42.62581769" }, "test-gatk4-collectsvevidence-allele-count - stub": { "content": [ @@ -192,7 +192,7 @@ ] ], "6": [ - "versions.yml:md5,eb641a78898f7bfe135ef01b77647079" + "versions.yml:md5,3fe376f43b4993a9edd5fa5f147f2bfe" ], "paired_end_evidence": [ [ @@ -249,15 +249,15 @@ ] ], "versions": [ - "versions.yml:md5,eb641a78898f7bfe135ef01b77647079" + "versions.yml:md5,3fe376f43b4993a9edd5fa5f147f2bfe" ] } ], "meta": { - "nf-test": "0.9.0", - "nextflow": "24.04.4" + "nf-test": "0.9.1", + "nextflow": "24.10.0" }, - "timestamp": "2024-09-20T10:36:43.992644" + "timestamp": "2024-10-31T10:47:05.276032478" }, "test-gatk4-collectsvevidence-bam": { "content": [ @@ -266,13 +266,13 @@ "chr22\t3320\t+\tchr22\t3482\t-\tnormal", "test.pe.txt.gz.tbi", [ - "versions.yml:md5,eb641a78898f7bfe135ef01b77647079" + "versions.yml:md5,3fe376f43b4993a9edd5fa5f147f2bfe" ] ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.4" + "nf-test": "0.9.1", + "nextflow": "24.10.0" }, - "timestamp": "2024-08-26T12:51:22.087808" + "timestamp": "2024-10-31T10:46:29.443818792" } } \ No newline at end of file diff --git a/modules/nf-core/gatk4/combinegvcfs/tests/main.nf.test.snap b/modules/nf-core/gatk4/combinegvcfs/tests/main.nf.test.snap index dfbd1ac1ef7..00aea2bdcca 100644 --- a/modules/nf-core/gatk4/combinegvcfs/tests/main.nf.test.snap +++ b/modules/nf-core/gatk4/combinegvcfs/tests/main.nf.test.snap @@ -12,7 +12,7 @@ ] ], "1": [ - "versions.yml:md5,d6331ea8e97541d1d439707fe3dd41b2" + "versions.yml:md5,aca96fc758ea3451abf185e1470788b5" ], "combined_gvcf": [ [ @@ -24,15 +24,15 @@ ] ], "versions": [ - "versions.yml:md5,d6331ea8e97541d1d439707fe3dd41b2" + "versions.yml:md5,aca96fc758ea3451abf185e1470788b5" ] } ], "meta": { - "nf-test": "0.9.0", - "nextflow": "24.04.4" + "nf-test": "0.9.1", + "nextflow": "24.10.0" }, - "timestamp": "2024-09-20T10:35:25.18434" + "timestamp": "2024-10-31T10:47:56.847188152" }, "test_gatk4_combinegvcfs": { "content": [ @@ -169,13 +169,13 @@ "chr22\t4608\t.\tA\t\t.\t.\tEND=40001\tGT:DP:GQ:MIN_DP:PL\t./.:0:0:0:0,0,0" ], [ - "versions.yml:md5,d6331ea8e97541d1d439707fe3dd41b2" + "versions.yml:md5,aca96fc758ea3451abf185e1470788b5" ] ], "meta": { - "nf-test": "0.8.4", - "nextflow": "23.10.1" + "nf-test": "0.9.1", + "nextflow": "24.10.0" }, - "timestamp": "2024-03-20T15:41:25.316932" + "timestamp": "2024-10-31T10:47:45.34645647" } } \ No newline at end of file From 9ddb1a29183b6f56cc3709516d4154799b70f6dd Mon Sep 17 00:00:00 2001 From: Matthias De Smet Date: Thu, 31 Oct 2024 12:12:04 +0000 Subject: [PATCH 4/4] more tests --- .../tests/main.nf.test.snap | 8 +- .../tests/main.nf.test.snap | 18 ++-- .../tests/main.nf.test.snap | 20 ++-- .../tests/main.nf.test.snap | 16 +-- .../gatk4/fastqtosam/tests/main.nf.test.snap | 26 ++--- .../filterintervals/tests/main.nf.test.snap | 10 +- .../filtermutectcalls/tests/main.nf.test.snap | 34 +++---- .../gatherbqsrreports/tests/main.nf.test.snap | 20 ++-- .../tests/main.nf.test.snap | 20 ++-- .../genomicsdbimport/tests/main.nf.test.snap | 34 +++---- .../genotypegvcfs/tests/main.nf.test.snap | 50 +++++----- .../tests/main.nf.test.snap | 38 +++---- .../haplotypecaller/tests/main.nf.test.snap | 32 +++--- .../indexfeaturefile/tests/main.nf.test.snap | 36 +++---- .../tests/main.nf.test.snap | 8 +- .../tests/main.nf.test.snap | 16 +-- .../mergebamalignment/tests/main.nf.test.snap | 18 ++-- .../mergemutectstats/tests/main.nf.test.snap | 18 ++-- .../gatk4/mutect2/tests/main.nf.test.snap | 56 +++++------ .../tests/main.nf.test.snap | 10 +- .../gatk4/printreads/tests/main.nf.test.snap | 18 ++-- .../gatk4/reblockgvcf/tests/main.nf.test.snap | 24 ++--- .../gatk4/revertsam/tests/main.nf.test.snap | 18 ++-- .../gatk4/samtofastq/tests/main.nf.test.snap | 24 ++--- .../gatk4/shiftfasta/tests/main.nf.test.snap | 10 +- .../gatk4/splitcram/tests/main.nf.test.snap | 18 ++-- .../splitintervals/tests/main.nf.test.snap | 30 +++--- .../splitncigarreads/tests/main.nf.test.snap | 16 +-- .../gatk4/svannotate/tests/main.nf.test.snap | 24 ++--- .../gatk4/svcluster/tests/main.nf.test.snap | 8 +- .../variantfiltration/tests/main.nf.test.snap | 16 +-- .../variantstotable/tests/main.nf.test.snap | 99 +++++++++---------- 32 files changed, 396 insertions(+), 397 deletions(-) diff --git a/modules/nf-core/gatk4/composestrtablefile/tests/main.nf.test.snap b/modules/nf-core/gatk4/composestrtablefile/tests/main.nf.test.snap index 02136a8b365..4a62f028b5d 100644 --- a/modules/nf-core/gatk4/composestrtablefile/tests/main.nf.test.snap +++ b/modules/nf-core/gatk4/composestrtablefile/tests/main.nf.test.snap @@ -3,13 +3,13 @@ "content": [ "genome.zip", [ - "versions.yml:md5,755f9a44a99148151b624d70eb6ce260" + "versions.yml:md5,b70639968daefca28136a26156170e29" ] ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.4" + "nf-test": "0.9.1", + "nextflow": "24.10.0" }, - "timestamp": "2024-08-26T13:37:10.366333" + "timestamp": "2024-10-31T10:48:46.420056406" } } \ No newline at end of file diff --git a/modules/nf-core/gatk4/condensedepthevidence/tests/main.nf.test.snap b/modules/nf-core/gatk4/condensedepthevidence/tests/main.nf.test.snap index b9dddfbb989..ac0a8fa58fd 100644 --- a/modules/nf-core/gatk4/condensedepthevidence/tests/main.nf.test.snap +++ b/modules/nf-core/gatk4/condensedepthevidence/tests/main.nf.test.snap @@ -21,7 +21,7 @@ ] ], "2": [ - "versions.yml:md5,d1d29007b92a10b3e50bdd25335013a8" + "versions.yml:md5,f1e49a983c12aa65895e70405a9dfc14" ], "condensed_evidence": [ [ @@ -42,15 +42,15 @@ ] ], "versions": [ - "versions.yml:md5,d1d29007b92a10b3e50bdd25335013a8" + "versions.yml:md5,f1e49a983c12aa65895e70405a9dfc14" ] } ], "meta": { - "nf-test": "0.9.0", - "nextflow": "24.04.4" + "nf-test": "0.9.1", + "nextflow": "24.10.0" }, - "timestamp": "2024-09-20T10:42:07.848497" + "timestamp": "2024-10-31T10:49:51.212441436" }, "test-gatk4-condensdepthevidence": { "content": [ @@ -60,13 +60,13 @@ ], "test.rd.txt.gz.tbi", [ - "versions.yml:md5,d1d29007b92a10b3e50bdd25335013a8" + "versions.yml:md5,f1e49a983c12aa65895e70405a9dfc14" ] ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.4" + "nf-test": "0.9.1", + "nextflow": "24.10.0" }, - "timestamp": "2024-08-26T12:33:21.910858" + "timestamp": "2024-10-31T10:49:37.340222412" } } \ No newline at end of file diff --git a/modules/nf-core/gatk4/createsequencedictionary/tests/main.nf.test.snap b/modules/nf-core/gatk4/createsequencedictionary/tests/main.nf.test.snap index 16735f9549a..e8a600fd114 100644 --- a/modules/nf-core/gatk4/createsequencedictionary/tests/main.nf.test.snap +++ b/modules/nf-core/gatk4/createsequencedictionary/tests/main.nf.test.snap @@ -11,7 +11,7 @@ ] ], "1": [ - "versions.yml:md5,e60dd34a71fc2029d81dc67ccb5d6be6" + "versions.yml:md5,e993b2c99f7f6b0fcd8428de15c61439" ], "dict": [ [ @@ -22,15 +22,15 @@ ] ], "versions": [ - "versions.yml:md5,e60dd34a71fc2029d81dc67ccb5d6be6" + "versions.yml:md5,e993b2c99f7f6b0fcd8428de15c61439" ] } ], "meta": { - "nf-test": "0.8.4", - "nextflow": "23.10.0" + "nf-test": "0.9.1", + "nextflow": "24.10.0" }, - "timestamp": "2024-05-16T10:16:16.34453" + "timestamp": "2024-10-31T10:51:56.155954077" }, "sarscov2 - fasta": { "content": [ @@ -44,7 +44,7 @@ ] ], "1": [ - "versions.yml:md5,e60dd34a71fc2029d81dc67ccb5d6be6" + "versions.yml:md5,e993b2c99f7f6b0fcd8428de15c61439" ], "dict": [ [ @@ -55,14 +55,14 @@ ] ], "versions": [ - "versions.yml:md5,e60dd34a71fc2029d81dc67ccb5d6be6" + "versions.yml:md5,e993b2c99f7f6b0fcd8428de15c61439" ] } ], "meta": { - "nf-test": "0.8.4", - "nextflow": "23.10.0" + "nf-test": "0.9.1", + "nextflow": "24.10.0" }, - "timestamp": "2024-05-16T13:58:25.822068" + "timestamp": "2024-10-31T10:51:45.562993875" } } \ No newline at end of file diff --git a/modules/nf-core/gatk4/estimatelibrarycomplexity/tests/main.nf.test.snap b/modules/nf-core/gatk4/estimatelibrarycomplexity/tests/main.nf.test.snap index bbcef1471e0..fa478ca8f7a 100644 --- a/modules/nf-core/gatk4/estimatelibrarycomplexity/tests/main.nf.test.snap +++ b/modules/nf-core/gatk4/estimatelibrarycomplexity/tests/main.nf.test.snap @@ -3,14 +3,14 @@ "content": [ "test.metrics", [ - "versions.yml:md5,1d9c175d88b6c50c7dc999c1f70261a8" + "versions.yml:md5,a7b6a9d538151a577da5f5727ace31e6" ] ], "meta": { - "nf-test": "0.8.4", - "nextflow": "23.10.1" + "nf-test": "0.9.1", + "nextflow": "24.10.0" }, - "timestamp": "2024-03-20T14:41:39.857566" + "timestamp": "2024-10-31T11:01:20.304274717" }, "sarscov2 - bam - stub": { "content": [ @@ -29,13 +29,13 @@ "content": [ "test.metrics", [ - "versions.yml:md5,1d9c175d88b6c50c7dc999c1f70261a8" + "versions.yml:md5,a7b6a9d538151a577da5f5727ace31e6" ] ], "meta": { - "nf-test": "0.8.4", - "nextflow": "23.10.1" + "nf-test": "0.9.1", + "nextflow": "24.10.0" }, - "timestamp": "2024-03-20T14:24:41.460191" + "timestamp": "2024-10-31T11:00:54.378191881" } } \ No newline at end of file diff --git a/modules/nf-core/gatk4/fastqtosam/tests/main.nf.test.snap b/modules/nf-core/gatk4/fastqtosam/tests/main.nf.test.snap index a4b44520dc5..5c575866db7 100644 --- a/modules/nf-core/gatk4/fastqtosam/tests/main.nf.test.snap +++ b/modules/nf-core/gatk4/fastqtosam/tests/main.nf.test.snap @@ -12,7 +12,7 @@ ] ], "1": [ - "versions.yml:md5,ac3f2cf1b686e56d72f1dd4a5977f7ab" + "versions.yml:md5,1d5e403a0c261ca92954dd22455adf47" ], "bam": [ [ @@ -24,40 +24,40 @@ ] ], "versions": [ - "versions.yml:md5,ac3f2cf1b686e56d72f1dd4a5977f7ab" + "versions.yml:md5,1d5e403a0c261ca92954dd22455adf47" ] } ], "meta": { - "nf-test": "0.9.0", - "nextflow": "24.04.4" + "nf-test": "0.9.1", + "nextflow": "24.10.0" }, - "timestamp": "2024-09-20T10:43:37.316141" + "timestamp": "2024-10-31T11:02:58.024964061" }, "test-gatk4-fastqtosam-single-end": { "content": [ "e6a4aa204d980e177a0458596f0a70ac", [ - "versions.yml:md5,ac3f2cf1b686e56d72f1dd4a5977f7ab" + "versions.yml:md5,1d5e403a0c261ca92954dd22455adf47" ] ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.4" + "nf-test": "0.9.1", + "nextflow": "24.10.0" }, - "timestamp": "2024-08-26T12:29:12.362942" + "timestamp": "2024-10-31T11:02:34.422399439" }, "test-gatk4-fastqtosam-paired-end": { "content": [ "e6a4aa204d980e177a0458596f0a70ac", [ - "versions.yml:md5,ac3f2cf1b686e56d72f1dd4a5977f7ab" + "versions.yml:md5,1d5e403a0c261ca92954dd22455adf47" ] ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.4" + "nf-test": "0.9.1", + "nextflow": "24.10.0" }, - "timestamp": "2024-08-26T12:29:22.385798" + "timestamp": "2024-10-31T11:02:47.309600742" } } \ No newline at end of file diff --git a/modules/nf-core/gatk4/filterintervals/tests/main.nf.test.snap b/modules/nf-core/gatk4/filterintervals/tests/main.nf.test.snap index c9626666948..add6095b313 100644 --- a/modules/nf-core/gatk4/filterintervals/tests/main.nf.test.snap +++ b/modules/nf-core/gatk4/filterintervals/tests/main.nf.test.snap @@ -11,7 +11,7 @@ ] ], "1": [ - "versions.yml:md5,9a445090a815c06982d5deb5ed7d5e30" + "versions.yml:md5,6fbacd816f4d48eae20f1fd423cb4e56" ], "interval_list": [ [ @@ -22,14 +22,14 @@ ] ], "versions": [ - "versions.yml:md5,9a445090a815c06982d5deb5ed7d5e30" + "versions.yml:md5,6fbacd816f4d48eae20f1fd423cb4e56" ] } ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.4" + "nf-test": "0.9.1", + "nextflow": "24.10.0" }, - "timestamp": "2024-08-26T12:25:35.933532" + "timestamp": "2024-10-31T11:03:52.645895175" } } \ No newline at end of file diff --git a/modules/nf-core/gatk4/filtermutectcalls/tests/main.nf.test.snap b/modules/nf-core/gatk4/filtermutectcalls/tests/main.nf.test.snap index 1c39e3b5d7c..28a63357e7f 100644 --- a/modules/nf-core/gatk4/filtermutectcalls/tests/main.nf.test.snap +++ b/modules/nf-core/gatk4/filtermutectcalls/tests/main.nf.test.snap @@ -12,14 +12,14 @@ "versions_with-files": { "content": [ [ - "versions.yml:md5,1e86368bd682668a6777ccf2cfd90689" + "versions.yml:md5,029e46832ac21665f3ba027974061ed0" ] ], "meta": { - "nf-test": "0.8.4", - "nextflow": "23.10.0" + "nf-test": "0.9.1", + "nextflow": "24.10.0" }, - "timestamp": "2024-05-15T12:45:43.679571" + "timestamp": "2024-10-31T11:04:55.625468064" }, "human - vcf - stub": { "content": [ @@ -49,7 +49,7 @@ ] ], "3": [ - "versions.yml:md5,1e86368bd682668a6777ccf2cfd90689" + "versions.yml:md5,029e46832ac21665f3ba027974061ed0" ], "stats": [ [ @@ -76,39 +76,39 @@ ] ], "versions": [ - "versions.yml:md5,1e86368bd682668a6777ccf2cfd90689" + "versions.yml:md5,029e46832ac21665f3ba027974061ed0" ] } ], "meta": { - "nf-test": "0.8.4", - "nextflow": "23.10.0" + "nf-test": "0.9.1", + "nextflow": "24.10.0" }, - "timestamp": "2024-05-15T12:46:32.666273" + "timestamp": "2024-10-31T11:05:33.111919824" }, "versions_use-val": { "content": [ [ - "versions.yml:md5,1e86368bd682668a6777ccf2cfd90689" + "versions.yml:md5,029e46832ac21665f3ba027974061ed0" ] ], "meta": { - "nf-test": "0.8.4", - "nextflow": "23.10.0" + "nf-test": "0.9.1", + "nextflow": "24.10.0" }, - "timestamp": "2024-05-15T12:46:03.876073" + "timestamp": "2024-10-31T11:05:19.277193087" }, "versions_base": { "content": [ [ - "versions.yml:md5,1e86368bd682668a6777ccf2cfd90689" + "versions.yml:md5,029e46832ac21665f3ba027974061ed0" ] ], "meta": { - "nf-test": "0.8.4", - "nextflow": "23.10.0" + "nf-test": "0.9.1", + "nextflow": "24.10.0" }, - "timestamp": "2024-05-15T12:47:39.930795" + "timestamp": "2024-10-31T11:04:36.657284567" }, "human - vcf - with-files": { "content": [ diff --git a/modules/nf-core/gatk4/gatherbqsrreports/tests/main.nf.test.snap b/modules/nf-core/gatk4/gatherbqsrreports/tests/main.nf.test.snap index bc5d4bd1332..e792d07ec56 100644 --- a/modules/nf-core/gatk4/gatherbqsrreports/tests/main.nf.test.snap +++ b/modules/nf-core/gatk4/gatherbqsrreports/tests/main.nf.test.snap @@ -12,7 +12,7 @@ ] ], "1": [ - "versions.yml:md5,413fc0014d5dc41ab67d65f59f61a4a0" + "versions.yml:md5,f7d3164566a7377bf766fb8b3933a34f" ], "table": [ [ @@ -24,15 +24,15 @@ ] ], "versions": [ - "versions.yml:md5,413fc0014d5dc41ab67d65f59f61a4a0" + "versions.yml:md5,f7d3164566a7377bf766fb8b3933a34f" ] } ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.4" + "nf-test": "0.9.1", + "nextflow": "24.10.0" }, - "timestamp": "2024-08-26T12:22:34.490694" + "timestamp": "2024-10-31T11:07:33.025431761" }, "test-gatk4-gatherbqsrreports": { "content": [ @@ -47,7 +47,7 @@ ] ], "1": [ - "versions.yml:md5,413fc0014d5dc41ab67d65f59f61a4a0" + "versions.yml:md5,f7d3164566a7377bf766fb8b3933a34f" ], "table": [ [ @@ -59,14 +59,14 @@ ] ], "versions": [ - "versions.yml:md5,413fc0014d5dc41ab67d65f59f61a4a0" + "versions.yml:md5,f7d3164566a7377bf766fb8b3933a34f" ] } ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.4" + "nf-test": "0.9.1", + "nextflow": "24.10.0" }, - "timestamp": "2024-08-26T12:22:10.552951" + "timestamp": "2024-10-31T11:07:09.791064374" } } \ No newline at end of file diff --git a/modules/nf-core/gatk4/gatherpileupsummaries/tests/main.nf.test.snap b/modules/nf-core/gatk4/gatherpileupsummaries/tests/main.nf.test.snap index fd9f2583440..e7094d73f4b 100644 --- a/modules/nf-core/gatk4/gatherpileupsummaries/tests/main.nf.test.snap +++ b/modules/nf-core/gatk4/gatherpileupsummaries/tests/main.nf.test.snap @@ -12,7 +12,7 @@ ] ], "1": [ - "versions.yml:md5,d3772ab0d5963a88a2748fd83af76c02" + "versions.yml:md5,585747d3136a5bf0563bbbe229690526" ], "table": [ [ @@ -24,15 +24,15 @@ ] ], "versions": [ - "versions.yml:md5,d3772ab0d5963a88a2748fd83af76c02" + "versions.yml:md5,585747d3136a5bf0563bbbe229690526" ] } ], "meta": { - "nf-test": "0.9.0", - "nextflow": "24.04.4" + "nf-test": "0.9.1", + "nextflow": "24.10.0" }, - "timestamp": "2024-09-20T10:44:42.759098" + "timestamp": "2024-10-31T11:08:38.118444526" }, "test-gatk4-gatherpileupsummaries": { "content": [ @@ -47,7 +47,7 @@ ] ], "1": [ - "versions.yml:md5,d3772ab0d5963a88a2748fd83af76c02" + "versions.yml:md5,585747d3136a5bf0563bbbe229690526" ], "table": [ [ @@ -59,14 +59,14 @@ ] ], "versions": [ - "versions.yml:md5,d3772ab0d5963a88a2748fd83af76c02" + "versions.yml:md5,585747d3136a5bf0563bbbe229690526" ] } ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.4" + "nf-test": "0.9.1", + "nextflow": "24.10.0" }, - "timestamp": "2024-08-26T12:18:40.835226" + "timestamp": "2024-10-31T11:08:17.759423015" } } \ No newline at end of file diff --git a/modules/nf-core/gatk4/genomicsdbimport/tests/main.nf.test.snap b/modules/nf-core/gatk4/genomicsdbimport/tests/main.nf.test.snap index 55ced0d8802..cb47a432c9e 100644 --- a/modules/nf-core/gatk4/genomicsdbimport/tests/main.nf.test.snap +++ b/modules/nf-core/gatk4/genomicsdbimport/tests/main.nf.test.snap @@ -3,14 +3,14 @@ "content": [ "test.interval_list:md5,4c85812ac15fc1cd29711a851d23c0bf", [ - "versions.yml:md5,c1233a04213021aa66599a36e0fb28cc" + "versions.yml:md5,5e722d5d01b9b1a0076ce80d0199b157" ] ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.2" + "nf-test": "0.9.1", + "nextflow": "24.10.0" }, - "timestamp": "2024-07-09T10:42:51.836379" + "timestamp": "2024-10-31T11:09:55.9195126" }, "test_gatk4_genomicsdbimport_create_genomicsdb": { "content": [ @@ -22,14 +22,14 @@ "vidmap.json" ], [ - "versions.yml:md5,c1233a04213021aa66599a36e0fb28cc" + "versions.yml:md5,5e722d5d01b9b1a0076ce80d0199b157" ] ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.2" + "nf-test": "0.9.1", + "nextflow": "24.10.0" }, - "timestamp": "2024-07-09T10:42:36.846239" + "timestamp": "2024-10-31T11:09:25.302350893" }, "test_gatk4_genomicsdbimport_update_genomicsdb": { "content": [ @@ -41,14 +41,14 @@ "vidmap.json" ], [ - "versions.yml:md5,c1233a04213021aa66599a36e0fb28cc" + "versions.yml:md5,5e722d5d01b9b1a0076ce80d0199b157" ] ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.2" + "nf-test": "0.9.1", + "nextflow": "24.10.0" }, - "timestamp": "2024-07-09T10:43:09.00769" + "timestamp": "2024-10-31T11:10:13.206208761" }, "test_gatk4_genomicsdbimport_stub": { "content": [ @@ -68,7 +68,7 @@ ], "3": [ - "versions.yml:md5,c1233a04213021aa66599a36e0fb28cc" + "versions.yml:md5,5e722d5d01b9b1a0076ce80d0199b157" ], "genomicsdb": [ [ @@ -85,14 +85,14 @@ ], "versions": [ - "versions.yml:md5,c1233a04213021aa66599a36e0fb28cc" + "versions.yml:md5,5e722d5d01b9b1a0076ce80d0199b157" ] } ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.2" + "nf-test": "0.9.1", + "nextflow": "24.10.0" }, - "timestamp": "2024-07-09T10:43:20.921712" + "timestamp": "2024-10-31T11:10:36.510210505" } } \ No newline at end of file diff --git a/modules/nf-core/gatk4/genotypegvcfs/tests/main.nf.test.snap b/modules/nf-core/gatk4/genotypegvcfs/tests/main.nf.test.snap index 1621618e7a9..30e2dc1cc6a 100644 --- a/modules/nf-core/gatk4/genotypegvcfs/tests/main.nf.test.snap +++ b/modules/nf-core/gatk4/genotypegvcfs/tests/main.nf.test.snap @@ -18,14 +18,14 @@ ] ], [ - "versions.yml:md5,3c16cbf71737813609ad10d901d92ab3" + "versions.yml:md5,fb1ca56ba52eb3fcda70dbef401f06b9" ] ], "meta": { - "nf-test": "0.9.0", - "nextflow": "24.04.4" + "nf-test": "0.9.1", + "nextflow": "24.10.0" }, - "timestamp": "2024-09-04T14:27:24.926097884" + "timestamp": "2024-10-31T11:16:45.625453031" }, "homo_sapiens - [gvcf, idx, [], []], fasta, fai, dict, [], []": { "content": [ @@ -46,14 +46,14 @@ ] ], [ - "versions.yml:md5,3c16cbf71737813609ad10d901d92ab3" + "versions.yml:md5,fb1ca56ba52eb3fcda70dbef401f06b9" ] ], "meta": { - "nf-test": "0.9.0", - "nextflow": "24.04.4" + "nf-test": "0.9.1", + "nextflow": "24.10.0" }, - "timestamp": "2024-09-04T14:26:24.426228557" + "timestamp": "2024-10-31T11:15:55.296562046" }, "homo_sapiens - [gvcf_gz, tbi, bed, []], fasta, fai, dict, [], []": { "content": [ @@ -74,14 +74,14 @@ ] ], [ - "versions.yml:md5,3c16cbf71737813609ad10d901d92ab3" + "versions.yml:md5,fb1ca56ba52eb3fcda70dbef401f06b9" ] ], "meta": { - "nf-test": "0.9.0", - "nextflow": "24.04.4" + "nf-test": "0.9.1", + "nextflow": "24.10.0" }, - "timestamp": "2024-09-04T14:27:04.179308513" + "timestamp": "2024-10-31T11:16:30.471742609" }, "homo_sapiens - [gvcf_gz, tbi, [], []], fasta, fai, dict, dbsnp, dbsnp_tbi": { "content": [ @@ -102,14 +102,14 @@ ] ], [ - "versions.yml:md5,3c16cbf71737813609ad10d901d92ab3" + "versions.yml:md5,fb1ca56ba52eb3fcda70dbef401f06b9" ] ], "meta": { - "nf-test": "0.9.0", - "nextflow": "24.04.4" + "nf-test": "0.9.1", + "nextflow": "24.10.0" }, - "timestamp": "2024-09-04T14:26:43.9088684" + "timestamp": "2024-10-31T11:16:13.266019505" }, "homo_sapiens - [gvcf, idx, [], []], fasta, fai, dict, [], [] - stub": { "content": [ @@ -131,7 +131,7 @@ ] ], "2": [ - "versions.yml:md5,3c16cbf71737813609ad10d901d92ab3" + "versions.yml:md5,fb1ca56ba52eb3fcda70dbef401f06b9" ], "tbi": [ [ @@ -150,15 +150,15 @@ ] ], "versions": [ - "versions.yml:md5,3c16cbf71737813609ad10d901d92ab3" + "versions.yml:md5,fb1ca56ba52eb3fcda70dbef401f06b9" ] } ], "meta": { - "nf-test": "0.9.0", - "nextflow": "24.04.4" + "nf-test": "0.9.1", + "nextflow": "24.10.0" }, - "timestamp": "2024-09-04T14:19:57.615552867" + "timestamp": "2024-10-31T11:17:19.342242664" }, "homo_sapiens - [gendb, bed, [], []], fasta, fai, dict, [], []": { "content": [ @@ -179,13 +179,13 @@ ] ], [ - "versions.yml:md5,3c16cbf71737813609ad10d901d92ab3" + "versions.yml:md5,fb1ca56ba52eb3fcda70dbef401f06b9" ] ], "meta": { - "nf-test": "0.9.0", - "nextflow": "24.04.4" + "nf-test": "0.9.1", + "nextflow": "24.10.0" }, - "timestamp": "2024-09-04T14:27:46.189794941" + "timestamp": "2024-10-31T11:17:01.475664058" } } \ No newline at end of file diff --git a/modules/nf-core/gatk4/getpileupsummaries/tests/main.nf.test.snap b/modules/nf-core/gatk4/getpileupsummaries/tests/main.nf.test.snap index d9304bcdc5c..e44c13bad89 100644 --- a/modules/nf-core/gatk4/getpileupsummaries/tests/main.nf.test.snap +++ b/modules/nf-core/gatk4/getpileupsummaries/tests/main.nf.test.snap @@ -11,7 +11,7 @@ ] ], "1": [ - "versions.yml:md5,a243840d67560fd6de1209a0aa99401a" + "versions.yml:md5,eb6e918939c8daf7ba3b4b65169ea98a" ], "table": [ [ @@ -22,15 +22,15 @@ ] ], "versions": [ - "versions.yml:md5,a243840d67560fd6de1209a0aa99401a" + "versions.yml:md5,eb6e918939c8daf7ba3b4b65169ea98a" ] } ], "meta": { - "nf-test": "0.8.4", - "nextflow": "23.10.0" + "nf-test": "0.9.1", + "nextflow": "24.10.0" }, - "timestamp": "2024-05-16T10:18:25.186463" + "timestamp": "2024-10-31T11:19:28.038865911" }, "human - bam": { "content": [ @@ -40,30 +40,30 @@ { "id": "test" }, - "test.pileups.table:md5,8e0ca6f66e112bd2f7ec1d31a2d62469" + "test.pileups.table:md5,2d7ce4a54df6b9249e12d60737a67dac" ] ], "1": [ - "versions.yml:md5,a243840d67560fd6de1209a0aa99401a" + "versions.yml:md5,eb6e918939c8daf7ba3b4b65169ea98a" ], "table": [ [ { "id": "test" }, - "test.pileups.table:md5,8e0ca6f66e112bd2f7ec1d31a2d62469" + "test.pileups.table:md5,2d7ce4a54df6b9249e12d60737a67dac" ] ], "versions": [ - "versions.yml:md5,a243840d67560fd6de1209a0aa99401a" + "versions.yml:md5,eb6e918939c8daf7ba3b4b65169ea98a" ] } ], "meta": { - "nf-test": "0.8.4", - "nextflow": "23.10.0" + "nf-test": "0.9.1", + "nextflow": "24.10.0" }, - "timestamp": "2024-05-16T14:14:59.7414" + "timestamp": "2024-10-31T11:18:47.633313304" }, "human - cram": { "content": [ @@ -73,29 +73,29 @@ { "id": "test" }, - "test.pileups.table:md5,8e0ca6f66e112bd2f7ec1d31a2d62469" + "test.pileups.table:md5,2d7ce4a54df6b9249e12d60737a67dac" ] ], "1": [ - "versions.yml:md5,a243840d67560fd6de1209a0aa99401a" + "versions.yml:md5,eb6e918939c8daf7ba3b4b65169ea98a" ], "table": [ [ { "id": "test" }, - "test.pileups.table:md5,8e0ca6f66e112bd2f7ec1d31a2d62469" + "test.pileups.table:md5,2d7ce4a54df6b9249e12d60737a67dac" ] ], "versions": [ - "versions.yml:md5,a243840d67560fd6de1209a0aa99401a" + "versions.yml:md5,eb6e918939c8daf7ba3b4b65169ea98a" ] } ], "meta": { - "nf-test": "0.8.4", - "nextflow": "23.10.0" + "nf-test": "0.9.1", + "nextflow": "24.10.0" }, - "timestamp": "2024-05-16T14:15:25.680928" + "timestamp": "2024-10-31T11:19:14.207172594" } } \ No newline at end of file diff --git a/modules/nf-core/gatk4/haplotypecaller/tests/main.nf.test.snap b/modules/nf-core/gatk4/haplotypecaller/tests/main.nf.test.snap index 0203fcfcf48..e3ba2bdfa96 100644 --- a/modules/nf-core/gatk4/haplotypecaller/tests/main.nf.test.snap +++ b/modules/nf-core/gatk4/haplotypecaller/tests/main.nf.test.snap @@ -4,55 +4,55 @@ "test_cram.vcf.gz", "test_cram.vcf.gz.tbi", [ - "versions.yml:md5,05431a0ab28c85412c8b3582e863a7ab" + "versions.yml:md5,2528212fed975c92514cf6641379e878" ] ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.4" + "nf-test": "0.9.1", + "nextflow": "24.10.0" }, - "timestamp": "2024-08-14T09:36:54.158605" + "timestamp": "2024-10-31T11:20:32.392608448" }, "homo_sapiens - [cram, crai] - fasta - fai - dict - sites - sites_tbi": { "content": [ "test_cram_sites.vcf.gz", "test_cram_sites.vcf.gz.tbi", [ - "versions.yml:md5,05431a0ab28c85412c8b3582e863a7ab" + "versions.yml:md5,2528212fed975c92514cf6641379e878" ] ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.4" + "nf-test": "0.9.1", + "nextflow": "24.10.0" }, - "timestamp": "2024-08-14T09:37:13.77024" + "timestamp": "2024-10-31T11:20:49.012555768" }, "homo_sapiens - [bam, bai] - fasta - fai - dict": { "content": [ "test_bam.vcf.gz", "test_bam.vcf.gz.tbi", [ - "versions.yml:md5,05431a0ab28c85412c8b3582e863a7ab" + "versions.yml:md5,2528212fed975c92514cf6641379e878" ] ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.4" + "nf-test": "0.9.1", + "nextflow": "24.10.0" }, - "timestamp": "2024-08-14T09:36:34.77631" + "timestamp": "2024-10-31T11:20:09.342159899" }, "homo_sapiens - [cram, crai, dragstr_model] - fasta - fai - dict - sites - sites_tbi": { "content": [ "test_cram_sites_dragstr.vcf.gz", "test_cram_sites_dragstr.vcf.gz.tbi", [ - "versions.yml:md5,05431a0ab28c85412c8b3582e863a7ab" + "versions.yml:md5,2528212fed975c92514cf6641379e878" ] ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.4" + "nf-test": "0.9.1", + "nextflow": "24.10.0" }, - "timestamp": "2024-08-14T09:37:32.967085" + "timestamp": "2024-10-31T11:21:06.551678783" } } \ No newline at end of file diff --git a/modules/nf-core/gatk4/indexfeaturefile/tests/main.nf.test.snap b/modules/nf-core/gatk4/indexfeaturefile/tests/main.nf.test.snap index fc19333634f..788b9290b87 100644 --- a/modules/nf-core/gatk4/indexfeaturefile/tests/main.nf.test.snap +++ b/modules/nf-core/gatk4/indexfeaturefile/tests/main.nf.test.snap @@ -12,14 +12,14 @@ "test_gatk4_indexfeaturefile_vcf": { "content": [ [ - "versions.yml:md5,e01e4575236d930ace929eec9c4c80dd" + "versions.yml:md5,3a4023239bad8505fdf37002915f8a7f" ] ], "meta": { - "nf-test": "0.8.4", - "nextflow": "23.04.2" + "nf-test": "0.9.1", + "nextflow": "24.10.0" }, - "timestamp": "2024-05-22T18:57:20.602472" + "timestamp": "2024-10-31T11:22:21.619530121" }, "geneome.bed.idx": { "content": [ @@ -53,7 +53,7 @@ ] ], "1": [ - "versions.yml:md5,e01e4575236d930ace929eec9c4c80dd" + "versions.yml:md5,3a4023239bad8505fdf37002915f8a7f" ], "index": [ [ @@ -64,15 +64,15 @@ ] ], "versions": [ - "versions.yml:md5,e01e4575236d930ace929eec9c4c80dd" + "versions.yml:md5,3a4023239bad8505fdf37002915f8a7f" ] } ], "meta": { - "nf-test": "0.8.4", - "nextflow": "23.04.2" + "nf-test": "0.9.1", + "nextflow": "24.10.0" }, - "timestamp": "2024-05-22T18:57:03.058351" + "timestamp": "2024-10-31T11:22:06.537858152" }, "test_gatk4_indexfeaturefile_vcf_gz": { "content": [ @@ -86,7 +86,7 @@ ] ], "1": [ - "versions.yml:md5,e01e4575236d930ace929eec9c4c80dd" + "versions.yml:md5,3a4023239bad8505fdf37002915f8a7f" ], "index": [ [ @@ -97,15 +97,15 @@ ] ], "versions": [ - "versions.yml:md5,e01e4575236d930ace929eec9c4c80dd" + "versions.yml:md5,3a4023239bad8505fdf37002915f8a7f" ] } ], "meta": { - "nf-test": "0.8.4", - "nextflow": "23.04.2" + "nf-test": "0.9.1", + "nextflow": "24.10.0" }, - "timestamp": "2024-05-22T18:57:51.861697" + "timestamp": "2024-10-31T11:22:37.41693965" }, "test.genome.vcf.idx": { "content": [ @@ -120,13 +120,13 @@ "test_gatk4_indexfeaturefile_bed": { "content": [ [ - "versions.yml:md5,e01e4575236d930ace929eec9c4c80dd" + "versions.yml:md5,3a4023239bad8505fdf37002915f8a7f" ] ], "meta": { - "nf-test": "0.8.4", - "nextflow": "23.04.2" + "nf-test": "0.9.1", + "nextflow": "24.10.0" }, - "timestamp": "2024-05-22T18:56:46.885162" + "timestamp": "2024-10-31T11:21:52.805375486" } } \ No newline at end of file diff --git a/modules/nf-core/gatk4/learnreadorientationmodel/tests/main.nf.test.snap b/modules/nf-core/gatk4/learnreadorientationmodel/tests/main.nf.test.snap index b829bd9c4aa..638e058359c 100644 --- a/modules/nf-core/gatk4/learnreadorientationmodel/tests/main.nf.test.snap +++ b/modules/nf-core/gatk4/learnreadorientationmodel/tests/main.nf.test.snap @@ -9,13 +9,13 @@ "CAA\tTTG\t0.0\t3.4445551925564533E-6\t3.435193155024585E-6\t5.139879646597498E-6\t0.0\t3.4674461103560476E-6\t3.428570449688764E-6\t6.343168047383713E-6\t0.9945238954147358\t1.3629167993931722E-4\t0.0052793454402581125\t3.5208652465150646E-5\t29263\t197" ], [ - "versions.yml:md5,88928ff140a0967e574e66944fd2a2f2" + "versions.yml:md5,e8e087001bd49c02f325e90b1fbeb44d" ] ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.4" + "nf-test": "0.9.1", + "nextflow": "24.10.0" }, - "timestamp": "2024-08-26T12:16:08.296564" + "timestamp": "2024-10-31T11:24:53.596350009" } } \ No newline at end of file diff --git a/modules/nf-core/gatk4/leftalignandtrimvariants/tests/main.nf.test.snap b/modules/nf-core/gatk4/leftalignandtrimvariants/tests/main.nf.test.snap index f500c0dcc08..e28a7be77b0 100644 --- a/modules/nf-core/gatk4/leftalignandtrimvariants/tests/main.nf.test.snap +++ b/modules/nf-core/gatk4/leftalignandtrimvariants/tests/main.nf.test.snap @@ -4,27 +4,27 @@ "85745045e9c55d3846d80bfde08a7d34", "test.normalised.vcf.gz.tbi", [ - "versions.yml:md5,2c2a0a8745e7517e028d257d39b07d61" + "versions.yml:md5,b8e7f53a1e802cf29ff86c9d1aaae5da" ] ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.4" + "nf-test": "0.9.1", + "nextflow": "24.10.0" }, - "timestamp": "2024-08-26T12:09:35.03744" + "timestamp": "2024-10-31T11:25:49.57287314" }, "test-gatk4-leftalignandtrimvariants-interval": { "content": [ "VcfFile [chromosomes=[], sampleCount=1, variantCount=0, phased=true, phasedAutodetect=true]", "test.normalised.vcf.gz.tbi", [ - "versions.yml:md5,2c2a0a8745e7517e028d257d39b07d61" + "versions.yml:md5,b8e7f53a1e802cf29ff86c9d1aaae5da" ] ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.4" + "nf-test": "0.9.1", + "nextflow": "24.10.0" }, - "timestamp": "2024-08-26T12:11:42.893725" + "timestamp": "2024-10-31T11:25:35.479943622" } } \ No newline at end of file diff --git a/modules/nf-core/gatk4/mergebamalignment/tests/main.nf.test.snap b/modules/nf-core/gatk4/mergebamalignment/tests/main.nf.test.snap index 719a7bb3311..476eecdfd08 100644 --- a/modules/nf-core/gatk4/mergebamalignment/tests/main.nf.test.snap +++ b/modules/nf-core/gatk4/mergebamalignment/tests/main.nf.test.snap @@ -11,7 +11,7 @@ ] ], "1": [ - "versions.yml:md5,a72cfce8c9d171260cbb82b492be4372" + "versions.yml:md5,19f0b1268d925943a61f6f686061d519" ], "bam": [ [ @@ -22,27 +22,27 @@ ] ], "versions": [ - "versions.yml:md5,a72cfce8c9d171260cbb82b492be4372" + "versions.yml:md5,19f0b1268d925943a61f6f686061d519" ] } ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.4" + "nf-test": "0.9.1", + "nextflow": "24.10.0" }, - "timestamp": "2024-08-26T12:02:15.41024" + "timestamp": "2024-10-31T11:29:07.319519362" }, "test-gatk4-mergebamalignment": { "content": [ "30c325e1e032eb1782a280d34c0fb1c7", [ - "versions.yml:md5,a72cfce8c9d171260cbb82b492be4372" + "versions.yml:md5,19f0b1268d925943a61f6f686061d519" ] ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.4" + "nf-test": "0.9.1", + "nextflow": "24.10.0" }, - "timestamp": "2024-08-26T12:02:08.379035" + "timestamp": "2024-10-31T11:28:55.287907787" } } \ No newline at end of file diff --git a/modules/nf-core/gatk4/mergemutectstats/tests/main.nf.test.snap b/modules/nf-core/gatk4/mergemutectstats/tests/main.nf.test.snap index d0279f272e4..77da5d78203 100644 --- a/modules/nf-core/gatk4/mergemutectstats/tests/main.nf.test.snap +++ b/modules/nf-core/gatk4/mergemutectstats/tests/main.nf.test.snap @@ -2,14 +2,14 @@ "versions": { "content": [ [ - "versions.yml:md5,7298d6e6e18024f7c2ed0fe38d259a52" + "versions.yml:md5,2b6e8361dd6734be029e7480dbcb7794" ] ], "meta": { - "nf-test": "0.8.4", - "nextflow": "23.10.0" + "nf-test": "0.9.1", + "nextflow": "24.10.0" }, - "timestamp": "2024-05-16T10:13:56.2195" + "timestamp": "2024-10-31T11:29:44.84165293" }, "human - stats,tsv - stub": { "content": [ @@ -24,7 +24,7 @@ ] ], "1": [ - "versions.yml:md5,7298d6e6e18024f7c2ed0fe38d259a52" + "versions.yml:md5,2b6e8361dd6734be029e7480dbcb7794" ], "stats": [ [ @@ -36,15 +36,15 @@ ] ], "versions": [ - "versions.yml:md5,7298d6e6e18024f7c2ed0fe38d259a52" + "versions.yml:md5,2b6e8361dd6734be029e7480dbcb7794" ] } ], "meta": { - "nf-test": "0.8.4", - "nextflow": "23.10.0" + "nf-test": "0.9.1", + "nextflow": "24.10.0" }, - "timestamp": "2024-05-16T10:14:10.058769" + "timestamp": "2024-10-31T11:29:54.48600467" }, "human - stats, tsv": { "content": [ diff --git a/modules/nf-core/gatk4/mutect2/tests/main.nf.test.snap b/modules/nf-core/gatk4/mutect2/tests/main.nf.test.snap index f047af19dd9..b37450f4f47 100644 --- a/modules/nf-core/gatk4/mutect2/tests/main.nf.test.snap +++ b/modules/nf-core/gatk4/mutect2/tests/main.nf.test.snap @@ -14,14 +14,14 @@ "test.f1r2.tar.gz" ], [ - "h" + "w" ] ], "meta": { - "nf-test": "0.8.4", - "nextflow": "23.04.2" + "nf-test": "0.9.1", + "nextflow": "24.10.0" }, - "timestamp": "2024-03-21T10:14:45.599103891" + "timestamp": "2024-10-31T11:49:16.64829295" }, "generate_pon": { "content": [ @@ -43,14 +43,14 @@ ], [ - "versions.yml:md5,d94731c50c20569fe9896235a843f382" + "versions.yml:md5,8b99605d0a404d9ccbf8628ca881a8a4" ] ], "meta": { - "nf-test": "0.8.4", - "nextflow": "23.04.2" + "nf-test": "0.9.1", + "nextflow": "24.10.0" }, - "timestamp": "2024-03-20T15:57:18.264453766" + "timestamp": "2024-10-31T11:48:44.796786166" }, "mitochondria": { "content": [ @@ -72,14 +72,14 @@ ], [ - "versions.yml:md5,d94731c50c20569fe9896235a843f382" + "versions.yml:md5,8b99605d0a404d9ccbf8628ca881a8a4" ] ], "meta": { - "nf-test": "0.8.4", - "nextflow": "23.04.2" + "nf-test": "0.9.1", + "nextflow": "24.10.0" }, - "timestamp": "2024-03-20T16:05:47.668766905" + "timestamp": "2024-10-31T11:49:03.399442766" }, "cram_input": { "content": [ @@ -101,14 +101,14 @@ ], [ - "versions.yml:md5,d94731c50c20569fe9896235a843f382" + "versions.yml:md5,8b99605d0a404d9ccbf8628ca881a8a4" ] ], "meta": { - "nf-test": "0.8.4", - "nextflow": "23.04.2" + "nf-test": "0.9.1", + "nextflow": "24.10.0" }, - "timestamp": "2024-03-20T15:52:27.894730554" + "timestamp": "2024-10-31T11:45:49.212101867" }, "tumor_single": { "content": [ @@ -130,14 +130,14 @@ ], [ - "versions.yml:md5,d94731c50c20569fe9896235a843f382" + "versions.yml:md5,8b99605d0a404d9ccbf8628ca881a8a4" ] ], "meta": { - "nf-test": "0.8.4", - "nextflow": "23.04.2" + "nf-test": "0.9.1", + "nextflow": "24.10.0" }, - "timestamp": "2024-03-20T15:43:28.935723443" + "timestamp": "2024-10-31T11:42:47.335589964" }, "tumor_normal_pair": { "content": [ @@ -161,14 +161,14 @@ ], [ - "versions.yml:md5,d94731c50c20569fe9896235a843f382" + "versions.yml:md5,8b99605d0a404d9ccbf8628ca881a8a4" ] ], "meta": { - "nf-test": "0.8.4", - "nextflow": "23.04.2" + "nf-test": "0.9.1", + "nextflow": "24.10.0" }, - "timestamp": "2024-03-20T15:31:31.913366311" + "timestamp": "2024-10-31T11:36:10.506528759" }, "tumor_normal_pair_f1r2": { "content": [ @@ -192,13 +192,13 @@ "test.f1r2.tar.gz" ], [ - "versions.yml:md5,d94731c50c20569fe9896235a843f382" + "versions.yml:md5,8b99605d0a404d9ccbf8628ca881a8a4" ] ], "meta": { - "nf-test": "0.8.4", - "nextflow": "23.04.2" + "nf-test": "0.9.1", + "nextflow": "24.10.0" }, - "timestamp": "2024-03-21T09:45:52.321385704" + "timestamp": "2024-10-31T11:39:21.909639821" } } \ No newline at end of file diff --git a/modules/nf-core/gatk4/preprocessintervals/tests/main.nf.test.snap b/modules/nf-core/gatk4/preprocessintervals/tests/main.nf.test.snap index 5365291dab8..127164975e3 100644 --- a/modules/nf-core/gatk4/preprocessintervals/tests/main.nf.test.snap +++ b/modules/nf-core/gatk4/preprocessintervals/tests/main.nf.test.snap @@ -11,7 +11,7 @@ ] ], "1": [ - "versions.yml:md5,fc3037804d90d3d3424047cfac85d5e4" + "versions.yml:md5,275510c640bbc3050a257bece1e51f85" ], "interval_list": [ [ @@ -22,14 +22,14 @@ ] ], "versions": [ - "versions.yml:md5,fc3037804d90d3d3424047cfac85d5e4" + "versions.yml:md5,275510c640bbc3050a257bece1e51f85" ] } ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.4" + "nf-test": "0.9.1", + "nextflow": "24.10.0" }, - "timestamp": "2024-08-26T11:58:51.314382" + "timestamp": "2024-10-31T11:55:38.222687003" } } \ No newline at end of file diff --git a/modules/nf-core/gatk4/printreads/tests/main.nf.test.snap b/modules/nf-core/gatk4/printreads/tests/main.nf.test.snap index 7f1266f2641..b847f44a910 100644 --- a/modules/nf-core/gatk4/printreads/tests/main.nf.test.snap +++ b/modules/nf-core/gatk4/printreads/tests/main.nf.test.snap @@ -9,32 +9,32 @@ ], [ - "versions.yml:md5,9b368270d802ed95c530a7f0105f6453" + "versions.yml:md5,b14bcdd8d9bfcf5b7e8f1f58b79fd179" ] ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.4" + "nf-test": "0.9.1", + "nextflow": "24.10.0" }, - "timestamp": "2024-08-26T11:48:53.871683" + "timestamp": "2024-10-31T11:56:25.490158526" }, "test-gatk4-printreads-cram": { "content": [ [ ], - "591299d00e262474250c5ccc241bba59", + "d105c4aee01f68ada72b288b1fd72f35", [ ], [ - "versions.yml:md5,9b368270d802ed95c530a7f0105f6453" + "versions.yml:md5,b14bcdd8d9bfcf5b7e8f1f58b79fd179" ] ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.4" + "nf-test": "0.9.1", + "nextflow": "24.10.0" }, - "timestamp": "2024-08-26T13:42:29.968056" + "timestamp": "2024-10-31T11:56:39.698048025" } } \ No newline at end of file diff --git a/modules/nf-core/gatk4/reblockgvcf/tests/main.nf.test.snap b/modules/nf-core/gatk4/reblockgvcf/tests/main.nf.test.snap index 6121c3d208a..df58a6495e8 100644 --- a/modules/nf-core/gatk4/reblockgvcf/tests/main.nf.test.snap +++ b/modules/nf-core/gatk4/reblockgvcf/tests/main.nf.test.snap @@ -4,41 +4,41 @@ "test.rb.g.vcf.gz", "test.rb.g.vcf.gz.tbi", [ - "versions.yml:md5,31df4173620cc2fbcca52d71f554015b" + "versions.yml:md5,29d0014d4e4858fac9d984ed0d6d7dd2" ] ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.4" + "nf-test": "0.9.1", + "nextflow": "24.10.0" }, - "timestamp": "2024-08-16T12:32:19.353113" + "timestamp": "2024-10-31T11:58:15.459756351" }, "test_gatk4_reblockgvcf_intervals": { "content": [ "test.rb.g.vcf.gz", "test.rb.g.vcf.gz.tbi", [ - "versions.yml:md5,31df4173620cc2fbcca52d71f554015b" + "versions.yml:md5,29d0014d4e4858fac9d984ed0d6d7dd2" ] ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.4" + "nf-test": "0.9.1", + "nextflow": "24.10.0" }, - "timestamp": "2024-08-16T12:32:11.896391" + "timestamp": "2024-10-31T11:58:04.712624842" }, "test_gatk4_reblockgvcf": { "content": [ "test.rb.g.vcf.gz", "test.rb.g.vcf.gz.tbi", [ - "versions.yml:md5,31df4173620cc2fbcca52d71f554015b" + "versions.yml:md5,29d0014d4e4858fac9d984ed0d6d7dd2" ] ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.4" + "nf-test": "0.9.1", + "nextflow": "24.10.0" }, - "timestamp": "2024-08-16T12:32:00.687676" + "timestamp": "2024-10-31T11:57:51.607837498" } } \ No newline at end of file diff --git a/modules/nf-core/gatk4/revertsam/tests/main.nf.test.snap b/modules/nf-core/gatk4/revertsam/tests/main.nf.test.snap index 1cbb5ce6e79..72fda7af8e4 100644 --- a/modules/nf-core/gatk4/revertsam/tests/main.nf.test.snap +++ b/modules/nf-core/gatk4/revertsam/tests/main.nf.test.snap @@ -3,14 +3,14 @@ "content": [ "e3cfa46b13cc4fc425cccae944f43b10", [ - "versions.yml:md5,ee8dfa21abb49349e4865984cc122b9e" + "versions.yml:md5,ef0c48b3a3499410f2ed092a3e9814b4" ] ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.4" + "nf-test": "0.9.1", + "nextflow": "24.10.0" }, - "timestamp": "2024-08-26T11:45:39.712635" + "timestamp": "2024-10-31T11:58:52.167057245" }, "test-gatk4-revertsam-stubs": { "content": [ @@ -24,7 +24,7 @@ ] ], "1": [ - "versions.yml:md5,ee8dfa21abb49349e4865984cc122b9e" + "versions.yml:md5,ef0c48b3a3499410f2ed092a3e9814b4" ], "bam": [ [ @@ -35,14 +35,14 @@ ] ], "versions": [ - "versions.yml:md5,ee8dfa21abb49349e4865984cc122b9e" + "versions.yml:md5,ef0c48b3a3499410f2ed092a3e9814b4" ] } ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.4" + "nf-test": "0.9.1", + "nextflow": "24.10.0" }, - "timestamp": "2024-08-26T11:45:46.856318" + "timestamp": "2024-10-31T11:59:02.762117999" } } \ No newline at end of file diff --git a/modules/nf-core/gatk4/samtofastq/tests/main.nf.test.snap b/modules/nf-core/gatk4/samtofastq/tests/main.nf.test.snap index 0e1ec4b79d4..38040db0ee4 100644 --- a/modules/nf-core/gatk4/samtofastq/tests/main.nf.test.snap +++ b/modules/nf-core/gatk4/samtofastq/tests/main.nf.test.snap @@ -9,14 +9,14 @@ "AAA6AEEEEEEEEEAEEE/6EEAEEEAEEEEEAEEEEEEEEEEEEEEEEEEEEE