Merge branch 'main' into dev

packages/2020_Nagele_Caribbean/2020_Nagele_Caribbean.config

@@ -0,0 +1,39 @@
+// Keep track of config versions
+config_template_version='0.2.0dev'
+package_config_version='0.2.0dev'
+
+// 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
+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.
+
+// 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'
+
+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_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/2.4.6/parameters
+
+  You can see the default values for parameters within poseidon-eager at: 
+    https://github.com/poseidon-framework/poseidon-eager/blob/main/conf/Minotaur.config
+  */
+}

packages/2020_Nagele_Caribbean/2020_Nagele_Caribbean.tsv_patch.sh

@@ -0,0 +1,45 @@
+#!/usr/bin/env bash
+set -uo pipefail ## Pipefail, complain on new unassigned variables.
+
+## Track the version of the TSV_patch template used
+VERSION='0.2.0dev'
+
+## 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>
+
+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 ${2})/../../scripts/source_me.sh ## Load helper functions
+
+## Index non-proliferated columns and exclude them from the finalised TSV
+cut_selector=''
+tsv_header=($(head -n1 ${input_tsv}))
+for col_name in ${columns_to_keep[@]}; do
+  let idx=$(get_index_of ${col_name} "${columns_to_keep[@]}")+1 ## awk uses 1-based indexing
+  if [[ ! ${idx} -eq -1 ]]; then
+    cut_selector+="${idx},"
+  fi
+done
+
+## Remove added columns, and put columns in right order
+cut -f ${cut_selector%,} ${input_tsv} > ${output_tsv}
+sed -i -e "s|<PATH_TO_DATA>|${local_data_dir}|g" ${output_tsv}
+
+## Any further commands to edit the file before finalisation should be added below as shown
+# sed -ie 's/replace_this/with_this/g' ${output_tsv}
+
+## Keep track of versions
+version_file="$(dirname ${input_tsv})/script_versions.txt"
+##    Remove versions from older run if there
+grep -v -F -e "$(basename ${0})" -e "source_me.sh for final TSV" ${version_file} >${version_file}.new
+##    Then add new versions
+echo -e "$(basename ${0}):\t${VERSION}" >> ${version_file}.new
+echo -e "source_me.sh for final TSV:\t${HELPER_FUNCTION_VERSION}" >>${version_file}.new
+mv ${version_file}.new ${version_file}

packages/2020_Nagele_Caribbean/script_versions.txt

@@ -0,0 +1,2 @@
+create_eager_input.sh:	0.2.1dev
+source_me.sh for initial TSV:	0.2.1dev

packages/2021_Saag_EastEuropean/2021_Saag_EastEuropean.config

@@ -0,0 +1,39 @@
+// Keep track of config versions
+config_template_version='0.2.0dev'
+package_config_version='0.2.0dev'
+
+// 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
+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.
+
+// 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'
+
+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_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/2.4.6/parameters
+
+  You can see the default values for parameters within poseidon-eager at: 
+    https://github.com/poseidon-framework/poseidon-eager/blob/main/conf/Minotaur.config
+  */
+}