Merge branch 'main' into main

.gitignore

@@ -0,0 +1 @@
+.DS_Store

assets/template.config

@@ -1,5 +1,5 @@
 // Keep track of config versions
-minotaur_release='0.3.0dev' // The release tag of the poseidon-eager repository used for processing and config file retrieval
+minotaur_release='0.4.0dev' // 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"
@@ -33,9 +33,9 @@ params {
   Any parameters not specified in any of the config files default to their nf-core/eager default values.
 
   For information on all available parameters and their default values see: 
-    https://nf-co.re/eager/2.4.6/parameters
+    https://nf-co.re/eager/2.5.1/parameters
 
-  You can see the default values for parameters within poseidon-eager at: 
+  You can see the latest default values for parameters within poseidon-eager at:
     https://github.com/poseidon-framework/poseidon-eager/blob/main/conf/Minotaur.config
   */
 }

packages/2020_Bongers_SouthPeru/2020_Bongers_SouthPeru.config

@@ -1,5 +1,5 @@
 // Keep track of config versions
-minotaur_release='0.2.1' // The release tag of the poseidon-eager repository used for processing and config file retrieval
+minotaur_release='0.4.0dev' // 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"
@@ -33,9 +33,9 @@ params {
   Any parameters not specified in any of the config files default to their nf-core/eager default values.
 
   For information on all available parameters and their default values see: 
-    https://nf-co.re/eager/2.4.6/parameters
+    https://nf-co.re/eager/2.5.1/parameters
 
-  You can see the default values for parameters within poseidon-eager at: 
+  You can see the latest default values for parameters within poseidon-eager at:
     https://github.com/poseidon-framework/poseidon-eager/blob/main/conf/Minotaur.config
   */
 }

packages/2020_Bongers_SouthPeru/script_versions.txt

@@ -1,7 +1,7 @@
 create_eager_input.sh:	0.2.1dev
-source_me.sh for initial TSV:	0.2.1dev
-download_ena_data.py:	0.3.0dev
-validate_downloaded_data.sh:	0.2.2dev
-source_me.sh for data validation:	0.2.1dev
+source_me.sh for initial TSV:	0.2.3dev
+download_ena_data.py:	0.4.0dev
+validate_downloaded_data.sh:	0.4.0dev
+source_me.sh for data validation:	0.2.3dev
 2020_Bongers_SouthPeru.tsv_patch.sh:	0.2.1dev
-source_me.sh for final TSV:	0.2.1dev
+source_me.sh for final TSV:	0.2.3dev

packages/2021_Yaka_Anatolia/2021_Yaka_Anatolia.config

@@ -1,6 +1,8 @@
 // Keep track of config versions
-config_template_version='0.2.0dev'
-package_config_version='0.2.0dev'
+minotaur_release='0.4.0dev' // 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)"
 
   /* 
@@ -31,9 +33,10 @@ params {
   Any parameters not specified in any of the config files default to their nf-core/eager default values.
 
   For information on all available parameters and their default values see: 
-    https://nf-co.re/eager/2.4.6/parameters
+    https://nf-co.re/eager/2.5.1/parameters
 
-  You can see the default values for parameters within poseidon-eager at: 
+  You can see the latest default values for parameters within poseidon-eager at:
     https://github.com/poseidon-framework/poseidon-eager/blob/main/conf/Minotaur.config
   */
+  qualitymax = 60 // The uploaded data is already collapsed, so the quality scored for PE data exceed the default max quality score of 41. (ASCII 93)
 }

packages/2021_Yaka_Anatolia/2021_Yaka_Anatolia.tsv_patch.sh

@@ -2,21 +2,21 @@
 set -uo pipefail ## Pipefail, complain on new unassigned variables.
 
 ## Track the version of the TSV_patch template used
-VERSION='0.2.0dev'
+VERSION='0.2.1dev'
 
 ## This script is applied to the eager input TSV file locally to edit the dummy
 ##    path to the fastQ files added by `create_eager_input.sh` to a real local
 ##    path provided as a positional argument. Any further local tweaks to the
 ##    TSV before running eager should be added below that in the form of bash
 ##    commands to aid in reproducibility.
 
-## usage tsv_patch.sh <local_data_dir> <input_tsv>
+## usage tsv_patch.sh <local_data_dir> <input_tsv> <path/to/source_me.sh>
 
 local_data_dir="$(readlink -f ${1})"
 input_tsv="$(readlink -f ${2})"
 output_tsv="$(dirname ${local_data_dir})/$(basename -s ".tsv" ${input_tsv}).finalised.tsv"
 columns_to_keep=("Sample_Name" "Library_ID" "Lane" "Colour_Chemistry" "SeqType" "Organism" "Strandedness" "UDG_Treatment" "R1" "R2" "BAM")
-source $(dirname ${2})/../../scripts/source_me.sh ## Load helper functions
+source $(readlink -f ${3}) ## Path to helper function script should be provided as 3rd argument. https://github.com/poseidon-framework/poseidon-eager/blob/main/scripts/source_me.sh
 
 ## Index non-proliferated columns and exclude them from the finalised TSV
 cut_selector=''

packages/2022_Kennett_Belize/2022_Kennett_Belize.config

@@ -0,0 +1,41 @@
+// Keep track of config versions
+minotaur_release='0.4.0dev' // 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/${minotaur_release}/conf"
+
+// This configuration file is designed to be a used with the nf-core/eager pipeline.
+//   Instead of having to specify all other configurations for the Minotaur pipeline
+//   on runtime, they are all contained in this file and loaded automatically upon
+//   specifying this config file during runtime. Additionally, any parameters that
+//   need to be altered from the defaults can be specified here.
+//
+// The intention is to make it easy for users to understand and reproduce the output
+//  from processing with the Minotaur workflow processing from the contents of a
+//  single file.
+
+// Load configuration profiles. They are loaded from the minotaur_config_base URL, main branch.
+includeConfig "${minotaur_config_base}/EVA_cluster.config" // Cluster-specific configurations for nf-core/eager execution at MPI-EVA
+includeConfig "${minotaur_config_base}/Minotaur.config"    // Default nf-core/eager parameters for Minotaur processing.
+
+// The following config file specifies BED files for on-target endogenous DNA calculation and mean coverage as well as pseudohaploid genotyping.
+// TODO: Select the appropriate config for the CaptureType of the package.
+includeConfig "${minotaur_config_base}/CaptureType_profiles/1240K.config"
+
+params {
+  // Keep track of config file versions used when processing
+  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)"
+
+  /* 
+  TODO: If you need to change any of the default processing parameters for this package
+  you can specify these parameters below.
+  Any parameters not specified in any of the config files default to their nf-core/eager default values.
+
+  For information on all available parameters and their default values see: 
+    https://nf-co.re/eager/2.5.1/parameters
+
+  You can see the latest default values for parameters within poseidon-eager at:
+    https://github.com/poseidon-framework/poseidon-eager/blob/main/conf/Minotaur.config
+  */
+}