From 58fb2d4c3e4c8d687d4f198d26dbba854b3fdd92 Mon Sep 17 00:00:00 2001 From: "Thiseas C. Lamnidis" Date: Thu, 1 Aug 2024 14:33:17 +0200 Subject: [PATCH] Update config for renewed processing. --- .../2020_Nagele_Caribbean.config | 16 +++++++++------- 1 file changed, 9 insertions(+), 7 deletions(-) diff --git a/packages/2020_Nagele_Caribbean/2020_Nagele_Caribbean.config b/packages/2020_Nagele_Caribbean/2020_Nagele_Caribbean.config index 1b03016..ca10f8b 100644 --- a/packages/2020_Nagele_Caribbean/2020_Nagele_Caribbean.config +++ b/packages/2020_Nagele_Caribbean/2020_Nagele_Caribbean.config @@ -1,6 +1,8 @@ // Keep track of config versions -config_template_version='0.2.0dev' -package_config_version='0.2.0dev' +minotaur_release='0.3.0dev' // The release tag of the poseidon-eager repository used for processing and config file retrieval +config_template_version='0.3.0dev' +package_config_version='0.3.0dev' +minotaur_config_base="https://raw.githubusercontent.com/poseidon-framework/poseidon-eager/${minotaur_release}/conf" // This configuration file is designed to be a used with the nf-core/eager pipeline. // Instead of having to specify all other configurations for the Minotaur pipeline @@ -12,17 +14,17 @@ package_config_version='0.2.0dev' // from processing with the Minotaur workflow processing from the contents of a // single file. -// Load configuration profiles -includeConfig "../../conf/EVA_cluster.config" // Cluster-specific configurations for nf-core/eager execution at MPI-EVA -includeConfig "../../conf/Minotaur.config" // Default nf-core/eager parameters for Minotaur processing. +// Load configuration profiles. They are loaded from the minotaur_config_base URL, main branch. +includeConfig "${minotaur_config_base}/EVA_cluster.config" // Cluster-specific configurations for nf-core/eager execution at MPI-EVA +includeConfig "${minotaur_config_base}/Minotaur.config" // Default nf-core/eager parameters for Minotaur processing. // The following config file specifies BED files for on-target endogenous DNA calculation and mean coverage as well as pseudohaploid genotyping. // TODO: Select the appropriate config for the CaptureType of the package. -includeConfig '../../conf/CaptureType_profiles/1240K.config' +includeConfig "${minotaur_config_base}/CaptureType_profiles/1240K.config" params { // Keep track of config file versions used when processing - config_profile_description = "${config_profile_description}\nconfig_template_version: ${config_template_version}\npackage_config_version: ${package_config_version}" + config_profile_description = "${config_profile_description}\n - config_template_version: ${config_template_version}\n - package_config_version: ${package_config_version}" config_profile_contact = "Thiseas C. Lamnidis (@TCLamnidis)" /*