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Update 2021_PattersonNature.ssf #31

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merged 4 commits into from
Apr 24, 2024
Merged

Update 2021_PattersonNature.ssf #31

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b4332de
Update 2021_PattersonNature.ssf
TCLamnidis Apr 24, 2024
0726dae
Update SSF to new validator format
TCLamnidis Apr 24, 2024
dcd9c7a
[automated] Create package recipe from SSF files
Apr 24, 2024
76b892e
Merge branch 'main' into fix_eof_Patterson
TCLamnidis Apr 24, 2024
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18 changes: 10 additions & 8 deletions packages/2021_PattersonNature/2021_PattersonNature.config
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Original file line number Diff line number Diff line change
@@ -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
Expand All @@ -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)"

/*
Expand All @@ -34,6 +36,6 @@ params {
https://nf-co.re/eager/2.4.6/parameters

You can see the default values for parameters within poseidon-eager at:
https://github.com/poseidon-framework/poseidon-eager/blob/main/conf/Poseidon.config
https://github.com/poseidon-framework/poseidon-eager/blob/main/conf/Minotaur.config
*/
}
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