From 8295f1ee248f662fef70d47149e1774d1fdedfd0 Mon Sep 17 00:00:00 2001 From: Stephen Watts Date: Tue, 28 May 2024 09:50:15 +1000 Subject: [PATCH] Bump SvPrep to 1.2.4 --- modules/local/svprep/assemble/environment.yml | 2 +- modules/local/svprep/assemble/main.nf | 4 ++-- modules/local/svprep/call/environment.yml | 2 +- modules/local/svprep/call/main.nf | 4 ++-- modules/local/svprep/depth_annotator/environment.yml | 2 +- modules/local/svprep/depth_annotator/main.nf | 4 ++-- modules/local/svprep/preprocess/environment.yml | 2 +- modules/local/svprep/preprocess/main.nf | 4 ++-- modules/local/svprep/svprep/environment.yml | 2 +- modules/local/svprep/svprep/main.nf | 4 ++-- 10 files changed, 15 insertions(+), 15 deletions(-) diff --git a/modules/local/svprep/assemble/environment.yml b/modules/local/svprep/assemble/environment.yml index 744167d9..ff1c9e1a 100644 --- a/modules/local/svprep/assemble/environment.yml +++ b/modules/local/svprep/assemble/environment.yml @@ -4,4 +4,4 @@ channels: - bioconda - defaults dependencies: - - bioconda::hmftools-sv-prep=1.2.3=hdfd78af_1 + - bioconda::hmftools-sv-prep=1.2.4 diff --git a/modules/local/svprep/assemble/main.nf b/modules/local/svprep/assemble/main.nf index 1f9a3957..d205b09f 100644 --- a/modules/local/svprep/assemble/main.nf +++ b/modules/local/svprep/assemble/main.nf @@ -4,8 +4,8 @@ process GRIDSS_ASSEMBLE { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/hmftools-sv-prep:1.2.3--hdfd78af_1' : - 'biocontainers/hmftools-sv-prep:1.2.3--hdfd78af_1' }" + 'https://depot.galaxyproject.org/singularity/hmftools-sv-prep:1.2.4--hdfd78af_0' : + 'biocontainers/hmftools-sv-prep:1.2.4--hdfd78af_0' }" input: tuple val(meta), path(bams), path(bams_filtered), path(preprocess_dirs), val(labels) diff --git a/modules/local/svprep/call/environment.yml b/modules/local/svprep/call/environment.yml index 8961a674..90d888f4 100644 --- a/modules/local/svprep/call/environment.yml +++ b/modules/local/svprep/call/environment.yml @@ -4,4 +4,4 @@ channels: - bioconda - defaults dependencies: - - bioconda::hmftools-sv-prep=1.2.3=hdfd78af_1 + - bioconda::hmftools-sv-prep=1.2.4 diff --git a/modules/local/svprep/call/main.nf b/modules/local/svprep/call/main.nf index ef5243b9..ef28f83a 100644 --- a/modules/local/svprep/call/main.nf +++ b/modules/local/svprep/call/main.nf @@ -4,8 +4,8 @@ process GRIDSS_CALL { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/hmftools-sv-prep:1.2.3--hdfd78af_1' : - 'biocontainers/hmftools-sv-prep:1.2.3--hdfd78af_1' }" + 'https://depot.galaxyproject.org/singularity/hmftools-sv-prep:1.2.4--hdfd78af_0' : + 'biocontainers/hmftools-sv-prep:1.2.4--hdfd78af_0' }" input: tuple val(meta), path(bams), path(bams_filtered), path(assemble_dir), val(labels) diff --git a/modules/local/svprep/depth_annotator/environment.yml b/modules/local/svprep/depth_annotator/environment.yml index c715d41a..dc6c4f3c 100644 --- a/modules/local/svprep/depth_annotator/environment.yml +++ b/modules/local/svprep/depth_annotator/environment.yml @@ -4,4 +4,4 @@ channels: - bioconda - defaults dependencies: - - bioconda::hmftools-sv-prep=1.2.3=hdfd78af_1 + - bioconda::hmftools-sv-prep=1.2.4 diff --git a/modules/local/svprep/depth_annotator/main.nf b/modules/local/svprep/depth_annotator/main.nf index 2d7cb3be..0a75529e 100644 --- a/modules/local/svprep/depth_annotator/main.nf +++ b/modules/local/svprep/depth_annotator/main.nf @@ -4,8 +4,8 @@ process SVPREP_DEPTH_ANNOTATOR { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/hmftools-sv-prep:1.2.3--hdfd78af_1' : - 'biocontainers/hmftools-sv-prep:1.2.3--hdfd78af_1' }" + 'https://depot.galaxyproject.org/singularity/hmftools-sv-prep:1.2.4--hdfd78af_0' : + 'biocontainers/hmftools-sv-prep:1.2.4--hdfd78af_0' }" input: tuple val(meta), path(bams), path(bais), path(vcf), val(labels) diff --git a/modules/local/svprep/preprocess/environment.yml b/modules/local/svprep/preprocess/environment.yml index 6a1e5fd0..6414c016 100644 --- a/modules/local/svprep/preprocess/environment.yml +++ b/modules/local/svprep/preprocess/environment.yml @@ -4,4 +4,4 @@ channels: - bioconda - defaults dependencies: - - bioconda::hmftools-sv-prep=1.2.3=hdfd78af_1 + - bioconda::hmftools-sv-prep=1.2.4 diff --git a/modules/local/svprep/preprocess/main.nf b/modules/local/svprep/preprocess/main.nf index 4fa37b05..ed3f3430 100644 --- a/modules/local/svprep/preprocess/main.nf +++ b/modules/local/svprep/preprocess/main.nf @@ -4,8 +4,8 @@ process GRIDSS_PREPROCESS { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/hmftools-sv-prep:1.2.3--hdfd78af_1' : - 'biocontainers/hmftools-sv-prep:1.2.3--hdfd78af_1' }" + 'https://depot.galaxyproject.org/singularity/hmftools-sv-prep:1.2.4--hdfd78af_0' : + 'biocontainers/hmftools-sv-prep:1.2.4--hdfd78af_0' }" input: tuple val(meta), path(bam), path(bam_filtered) diff --git a/modules/local/svprep/svprep/environment.yml b/modules/local/svprep/svprep/environment.yml index 5fb5d9c9..9435340f 100644 --- a/modules/local/svprep/svprep/environment.yml +++ b/modules/local/svprep/svprep/environment.yml @@ -4,4 +4,4 @@ channels: - bioconda - defaults dependencies: - - bioconda::hmftools-sv-prep=1.2.3=hdfd78af_1 + - bioconda::hmftools-sv-prep=1.2.4 diff --git a/modules/local/svprep/svprep/main.nf b/modules/local/svprep/svprep/main.nf index 3b4477bd..bba5bc5a 100644 --- a/modules/local/svprep/svprep/main.nf +++ b/modules/local/svprep/svprep/main.nf @@ -4,8 +4,8 @@ process SVPREP { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/hmftools-sv-prep:1.2.3--hdfd78af_1' : - 'biocontainers/hmftools-sv-prep:1.2.3--hdfd78af_1' }" + 'https://depot.galaxyproject.org/singularity/hmftools-sv-prep:1.2.4--hdfd78af_0' : + 'biocontainers/hmftools-sv-prep:1.2.4--hdfd78af_0' }" input: tuple val(meta), path(bam), path(bai), path(junctions)