From 0cee76b37170ea163b2e5196bd18fee6116f964d Mon Sep 17 00:00:00 2001 From: ypriverol Date: Fri, 28 Jan 2022 18:36:27 +0000 Subject: [PATCH 1/2] sdrf -> 0.0.20 idmapper moved to precursor --- modules/local/openms/idmapper/main.nf | 1 + modules/local/samplesheet_check.nf | 6 +++--- modules/local/sdrfparsing/main.nf | 8 ++++---- 3 files changed, 8 insertions(+), 7 deletions(-) diff --git a/modules/local/openms/idmapper/main.nf b/modules/local/openms/idmapper/main.nf index 5128dc5a..93aefa47 100644 --- a/modules/local/openms/idmapper/main.nf +++ b/modules/local/openms/idmapper/main.nf @@ -38,6 +38,7 @@ process IDMAPPER { -mz_tolerance $params.mz_tolerance \\ -mz_measure $params.mz_measure \\ -mz_reference $params.mz_reference \\ + -mz_reference 'precursor' -debug 100 \\ -out ${id_file.baseName}_map.consensusXML \\ > ${id_file.baseName}_map.log diff --git a/modules/local/samplesheet_check.nf b/modules/local/samplesheet_check.nf index d4d41bba..3d9d33f2 100644 --- a/modules/local/samplesheet_check.nf +++ b/modules/local/samplesheet_check.nf @@ -12,11 +12,11 @@ process SAMPLESHEET_CHECK { mode: params.publish_dir_mode, saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:'pipeline_info', meta:[:], publish_by_meta:[]) } - conda (params.enable_conda ? "conda-forge::pandas_schema bioconda::sdrf-pipelines=0.0.19" : null) + conda (params.enable_conda ? "conda-forge::pandas_schema bioconda::sdrf-pipelines=0.0.20" : null) if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) { - container "https://depot.galaxyproject.org/singularity/sdrf-pipelines:0.0.18--pyhdfd78af_0" + container "https://depot.galaxyproject.org/singularity/sdrf-pipelines:0.0.20--pyhdfd78af_0" } else { - container "quay.io/biocontainers/sdrf-pipelines:0.0.18--pyhdfd78af_0" + container "quay.io/biocontainers/sdrf-pipelines:0.0.20--pyhdfd78af_0" } input: diff --git a/modules/local/sdrfparsing/main.nf b/modules/local/sdrfparsing/main.nf index 514da03d..7c7f2a46 100644 --- a/modules/local/sdrfparsing/main.nf +++ b/modules/local/sdrfparsing/main.nf @@ -10,11 +10,11 @@ process SDRFPARSING { mode: params.publish_dir_mode, saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:[:], publish_by_meta:[]) } - conda (params.enable_conda ? "conda-forge::pandas_schema bioconda::sdrf-pipelines=0.0.19" : null) + conda (params.enable_conda ? "conda-forge::pandas_schema bioconda::sdrf-pipelines=0.0.20" : null) if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) { - container "https://depot.galaxyproject.org/singularity/sdrf-pipelines:0.0.18--pyhdfd78af_0" + container "https://depot.galaxyproject.org/singularity/sdrf-pipelines:0.0.20--pyhdfd78af_0" } else { - container "quay.io/biocontainers/sdrf-pipelines:0.0.18--pyhdfd78af_0" + container "quay.io/biocontainers/sdrf-pipelines:0.0.20--pyhdfd78af_0" } input: @@ -36,6 +36,6 @@ process SDRFPARSING { parse_sdrf $options.args -s ${sdrf} > sdrf_parsing.log - echo "0.0.19" > sdrf-pipelines.version.txt + echo "0.0.20" > sdrf-pipelines.version.txt """ } From 7848717513b517eafce1dc63c81d0754e6ff31c2 Mon Sep 17 00:00:00 2001 From: ypriverol Date: Fri, 28 Jan 2022 18:55:16 +0000 Subject: [PATCH 2/2] sdrf -> 0.0.20 idmapper moved to precursor --- conf/modules.config | 1 - 1 file changed, 1 deletion(-) diff --git a/conf/modules.config b/conf/modules.config index 730e92d0..58a6e107 100644 --- a/conf/modules.config +++ b/conf/modules.config @@ -47,7 +47,6 @@ params { } 'isobaricanalyzer' { args = '' - publish_files = ['log': ''] } 'searchenginemsgf' { args = ''