From 857da545e480c8a2e081d257e489ccdb25a1a20c Mon Sep 17 00:00:00 2001 From: Greg Date: Tue, 20 Aug 2024 15:16:12 -0700 Subject: [PATCH 1/3] bumped MultiQC version for dumpsoftwareversions --- modules/nf-core/custom/dumpsoftwareversions/environment.yml | 2 +- modules/nf-core/custom/dumpsoftwareversions/main.nf | 4 ++-- 2 files changed, 3 insertions(+), 3 deletions(-) diff --git a/modules/nf-core/custom/dumpsoftwareversions/environment.yml b/modules/nf-core/custom/dumpsoftwareversions/environment.yml index b48ced2690f..cd1839fa058 100644 --- a/modules/nf-core/custom/dumpsoftwareversions/environment.yml +++ b/modules/nf-core/custom/dumpsoftwareversions/environment.yml @@ -4,4 +4,4 @@ channels: - bioconda - defaults dependencies: - - bioconda::multiqc=1.20 + - bioconda::multiqc=1.24 diff --git a/modules/nf-core/custom/dumpsoftwareversions/main.nf b/modules/nf-core/custom/dumpsoftwareversions/main.nf index 105f9265a8d..d14f549d8c6 100644 --- a/modules/nf-core/custom/dumpsoftwareversions/main.nf +++ b/modules/nf-core/custom/dumpsoftwareversions/main.nf @@ -4,8 +4,8 @@ process CUSTOM_DUMPSOFTWAREVERSIONS { // Requires `pyyaml` which does not have a dedicated container but is in the MultiQC container conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/multiqc:1.20--pyhdfd78af_0' : - 'biocontainers/multiqc:1.20--pyhdfd78af_0' }" + 'https://depot.galaxyproject.org/singularity/multiqc:1.24--pyhdfd78af_0' : + 'biocontainers/multiqc:1.24--pyhdfd78af_0' }" input: path versions From 7fc734531a31f5f4cd49f5056ec9126ec5fe43a1 Mon Sep 17 00:00:00 2001 From: Greg Date: Wed, 21 Aug 2024 09:12:44 -0700 Subject: [PATCH 2/3] bump to 1.24.1 --- modules/nf-core/custom/dumpsoftwareversions/environment.yml | 2 +- modules/nf-core/custom/dumpsoftwareversions/main.nf | 4 ++-- 2 files changed, 3 insertions(+), 3 deletions(-) diff --git a/modules/nf-core/custom/dumpsoftwareversions/environment.yml b/modules/nf-core/custom/dumpsoftwareversions/environment.yml index cd1839fa058..324fa8f787b 100644 --- a/modules/nf-core/custom/dumpsoftwareversions/environment.yml +++ b/modules/nf-core/custom/dumpsoftwareversions/environment.yml @@ -4,4 +4,4 @@ channels: - bioconda - defaults dependencies: - - bioconda::multiqc=1.24 + - bioconda::multiqc=1.24.1 diff --git a/modules/nf-core/custom/dumpsoftwareversions/main.nf b/modules/nf-core/custom/dumpsoftwareversions/main.nf index d14f549d8c6..ffb2577fa8b 100644 --- a/modules/nf-core/custom/dumpsoftwareversions/main.nf +++ b/modules/nf-core/custom/dumpsoftwareversions/main.nf @@ -4,8 +4,8 @@ process CUSTOM_DUMPSOFTWAREVERSIONS { // Requires `pyyaml` which does not have a dedicated container but is in the MultiQC container conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/multiqc:1.24--pyhdfd78af_0' : - 'biocontainers/multiqc:1.24--pyhdfd78af_0' }" + 'https://depot.galaxyproject.org/singularity/multiqc:1.24.1--pyhdfd78af_0' : + 'biocontainers/multiqc:1.24.1--pyhdfd78af_0' }" input: path versions From b9d5449808fc00b98296ae11840a0fc26b2b54a9 Mon Sep 17 00:00:00 2001 From: Simon Pearce <24893913+SPPearce@users.noreply.github.com> Date: Wed, 18 Sep 2024 08:26:26 +0000 Subject: [PATCH 3/3] Add deprecation message --- modules/nf-core/custom/dumpsoftwareversions/main.nf | 9 +++++++++ 1 file changed, 9 insertions(+) diff --git a/modules/nf-core/custom/dumpsoftwareversions/main.nf b/modules/nf-core/custom/dumpsoftwareversions/main.nf index ffb2577fa8b..65c3c59fcbd 100644 --- a/modules/nf-core/custom/dumpsoftwareversions/main.nf +++ b/modules/nf-core/custom/dumpsoftwareversions/main.nf @@ -1,3 +1,11 @@ +def deprecation_message = """ +WARNING: This module has been deprecated. + +Reason: +This module is no longer recommended for use, as it is replaced by the function softwareVersionsToYAML +in the utils_nfcore_pipeline subworkflow that is included in the nf-core template. + +""" process CUSTOM_DUMPSOFTWAREVERSIONS { label 'process_single' @@ -19,6 +27,7 @@ process CUSTOM_DUMPSOFTWAREVERSIONS { task.ext.when == null || task.ext.when script: + assert true: deprecation_message def args = task.ext.args ?: '' template 'dumpsoftwareversions.py' }