From 2d8f8fd533fc945358ce11eede8c5e2c86c36e8d Mon Sep 17 00:00:00 2001 From: Simon Heumos Date: Mon, 4 Sep 2023 13:15:24 +0200 Subject: [PATCH] bump odgi modules to v0.8.3 (#3805) * bump odgi modules v0.8.3 * fix linting error * fix galaxy container --- modules/nf-core/odgi/build/main.nf | 6 +++--- modules/nf-core/odgi/draw/main.nf | 6 +++--- modules/nf-core/odgi/layout/main.nf | 6 +++--- modules/nf-core/odgi/sort/main.nf | 6 +++--- modules/nf-core/odgi/squeeze/main.nf | 6 +++--- modules/nf-core/odgi/squeeze/meta.yml | 2 +- modules/nf-core/odgi/stats/main.nf | 6 +++--- modules/nf-core/odgi/unchop/main.nf | 6 +++--- modules/nf-core/odgi/view/main.nf | 6 +++--- modules/nf-core/odgi/viz/main.nf | 6 +++--- 10 files changed, 28 insertions(+), 28 deletions(-) diff --git a/modules/nf-core/odgi/build/main.nf b/modules/nf-core/odgi/build/main.nf index 6e7f20e7706..938c16bb4b0 100644 --- a/modules/nf-core/odgi/build/main.nf +++ b/modules/nf-core/odgi/build/main.nf @@ -2,10 +2,10 @@ process ODGI_BUILD { tag "$meta.id" label 'process_medium' - conda "bioconda::odgi=0.8.2" + conda "bioconda::odgi=0.8.3" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/odgi:0.8.2--py310hc8f18ef_0': - 'biocontainers/odgi:0.8.2--py310hc8f18ef_0' }" + 'https://depot.galaxyproject.org/singularity/odgi:0.8.3--py310h6cc9453_0': + 'biocontainers/odgi:0.8.3--py310h6cc9453_0' }" input: tuple val(meta), path(graph) diff --git a/modules/nf-core/odgi/draw/main.nf b/modules/nf-core/odgi/draw/main.nf index 61ad082650a..426c258e7cf 100644 --- a/modules/nf-core/odgi/draw/main.nf +++ b/modules/nf-core/odgi/draw/main.nf @@ -2,10 +2,10 @@ process ODGI_DRAW { tag "$meta.id" label 'process_single' - conda "bioconda::odgi=0.8.2" + conda "bioconda::odgi=0.8.3" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/odgi:0.8.2--py310hc8f18ef_0': - 'biocontainers/odgi:0.8.2--py310hc8f18ef_0' }" + 'https://depot.galaxyproject.org/singularity/odgi:0.8.3--py310h6cc9453_0': + 'biocontainers/odgi:0.8.3--py310h6cc9453_0' }" input: tuple val(meta), path(graph), path(lay) diff --git a/modules/nf-core/odgi/layout/main.nf b/modules/nf-core/odgi/layout/main.nf index 2edfda2da06..22e7c438cfa 100644 --- a/modules/nf-core/odgi/layout/main.nf +++ b/modules/nf-core/odgi/layout/main.nf @@ -2,10 +2,10 @@ process ODGI_LAYOUT { tag "$meta.id" label 'process_medium' - conda "bioconda::odgi=0.8.2" + conda "bioconda::odgi=0.8.3" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/odgi:0.8.2--py310hc8f18ef_0': - 'biocontainers/odgi:0.8.2--py310hc8f18ef_0' }" + 'https://depot.galaxyproject.org/singularity/odgi:0.8.3--py310h6cc9453_0': + 'biocontainers/odgi:0.8.3--py310h6cc9453_0' }" input: tuple val(meta), path(graph) diff --git a/modules/nf-core/odgi/sort/main.nf b/modules/nf-core/odgi/sort/main.nf index 9b6ac30fdcf..d57cc04ad70 100644 --- a/modules/nf-core/odgi/sort/main.nf +++ b/modules/nf-core/odgi/sort/main.nf @@ -2,10 +2,10 @@ process ODGI_SORT { tag "$meta.id" label 'process_high' - conda "bioconda::odgi=0.8.2" + conda "bioconda::odgi=0.8.3" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/odgi:0.8.2--py310hc8f18ef_0': - 'biocontainers/odgi:0.8.2--py310hc8f18ef_0' }" + 'https://depot.galaxyproject.org/singularity/odgi:0.8.3--py310h6cc9453_0': + 'biocontainers/odgi:0.8.3--py310h6cc9453_0' }" input: tuple val(meta), path(graph) diff --git a/modules/nf-core/odgi/squeeze/main.nf b/modules/nf-core/odgi/squeeze/main.nf index 3b31df88e49..a2e187febab 100644 --- a/modules/nf-core/odgi/squeeze/main.nf +++ b/modules/nf-core/odgi/squeeze/main.nf @@ -2,10 +2,10 @@ process ODGI_SQUEEZE { tag "$meta.id" label 'process_medium' - conda "bioconda::odgi=0.8.2" + conda "bioconda::odgi=0.8.3" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/odgi:0.8.2--py310hc8f18ef_0': - 'biocontainers/odgi:0.8.2--py310hc8f18ef_0' }" + 'https://depot.galaxyproject.org/singularity/odgi:0.8.3--py310h6cc9453_0': + 'biocontainers/odgi:0.8.3--py310h6cc9453_0' }" input: tuple val(meta), path(graphs) diff --git a/modules/nf-core/odgi/squeeze/meta.yml b/modules/nf-core/odgi/squeeze/meta.yml index 89acd892e46..4b6181d3850 100644 --- a/modules/nf-core/odgi/squeeze/meta.yml +++ b/modules/nf-core/odgi/squeeze/meta.yml @@ -21,7 +21,7 @@ input: Groovy Map containing sample information e.g. [ id:'test', single_end:false ] - graphs: - type: files + type: file description: Pangenome graph files in ODGI format. pattern: "*.{og}" diff --git a/modules/nf-core/odgi/stats/main.nf b/modules/nf-core/odgi/stats/main.nf index 7600ae1a43c..99409f65613 100644 --- a/modules/nf-core/odgi/stats/main.nf +++ b/modules/nf-core/odgi/stats/main.nf @@ -2,10 +2,10 @@ process ODGI_STATS { tag "$meta.id" label 'process_single' - conda "bioconda::odgi=0.8.2" + conda "bioconda::odgi=0.8.3" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/odgi:0.8.2--py310hc8f18ef_0': - 'biocontainers/odgi:0.8.2--py310hc8f18ef_0' }" + 'https://depot.galaxyproject.org/singularity/odgi:0.8.3--py310h6cc9453_0': + 'biocontainers/odgi:0.8.3--py310h6cc9453_0' }" input: tuple val(meta), path(graph) diff --git a/modules/nf-core/odgi/unchop/main.nf b/modules/nf-core/odgi/unchop/main.nf index a55d99d7e04..50cbfde27d7 100644 --- a/modules/nf-core/odgi/unchop/main.nf +++ b/modules/nf-core/odgi/unchop/main.nf @@ -2,10 +2,10 @@ process ODGI_UNCHOP { tag "$meta.id" label 'process_medium' - conda "bioconda::odgi=0.8.2" + conda "bioconda::odgi=0.8.3" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/odgi:0.8.2--py310hc8f18ef_0': - 'biocontainers/odgi:0.8.2--py310hc8f18ef_0' }" + 'https://depot.galaxyproject.org/singularity/odgi:0.8.3--py310h6cc9453_0': + 'biocontainers/odgi:0.8.3--py310h6cc9453_0' }" input: tuple val(meta), path(graph) diff --git a/modules/nf-core/odgi/view/main.nf b/modules/nf-core/odgi/view/main.nf index 4c1de756ec2..cecfe454fc9 100644 --- a/modules/nf-core/odgi/view/main.nf +++ b/modules/nf-core/odgi/view/main.nf @@ -2,10 +2,10 @@ process ODGI_VIEW { tag "$meta.id" label 'process_single' - conda "bioconda::odgi=0.8.2" + conda "bioconda::odgi=0.8.3" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/odgi:0.8.2--py310hc8f18ef_0': - 'biocontainers/odgi:0.8.2--py310hc8f18ef_0' }" + 'https://depot.galaxyproject.org/singularity/odgi:0.8.3--py310h6cc9453_0': + 'biocontainers/odgi:0.8.3--py310h6cc9453_0' }" input: tuple val(meta), path(graph) diff --git a/modules/nf-core/odgi/viz/main.nf b/modules/nf-core/odgi/viz/main.nf index 81da80f1644..feef5be2b93 100644 --- a/modules/nf-core/odgi/viz/main.nf +++ b/modules/nf-core/odgi/viz/main.nf @@ -2,10 +2,10 @@ process ODGI_VIZ { tag "$meta.id" label 'process_single' - conda "bioconda::odgi=0.8.2" + conda "bioconda::odgi=0.8.3" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/odgi:0.8.2--py39h2add14b_0': - 'biocontainers/odgi:0.8.2--py310hc8f18ef_0' }" + 'https://depot.galaxyproject.org/singularity/odgi:0.8.3--py310h6cc9453_0': + 'biocontainers/odgi:0.8.3--py310h6cc9453_0' }" input: tuple val(meta), path(graph)