[automated] Create package recipe from SSF files

packages/2024_Sasso_PNAS/2024_Sasso_PNAS.config

@@ -0,0 +1,41 @@
+// 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
+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/2.4.6/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/2024_Sasso_PNAS/2024_Sasso_PNAS.tsv

@@ -0,0 +1,49 @@
+Sample_Name	Library_ID	Lane	Colour_Chemistry	SeqType	Organism	Strandedness	UDG_Treatment	R1	R2	BAM	R1_target_file	R2_target_file
+n/a	n/a_utigKOS007	1	4	SE	Homo sapiens (modern human)			<PATH_TO_DATA>/n/a_utigKOS007_L1_R1.fastq.gz	NA	NA	ERR13189827.fastq.gz	NA
+n/a	n/a_utigKOS010	1	4	SE	Homo sapiens (modern human)			<PATH_TO_DATA>/n/a_utigKOS010_L1_R1.fastq.gz	NA	NA	ERR13189830.fastq.gz	NA
+n/a	n/a_utigKOS013	1	4	SE	Homo sapiens (modern human)			<PATH_TO_DATA>/n/a_utigKOS013_L1_R1.fastq.gz	NA	NA	ERR13189833.fastq.gz	NA
+n/a	n/a_utigKOS022	1	4	SE	Homo sapiens (modern human)			<PATH_TO_DATA>/n/a_utigKOS022_L1_R1.fastq.gz	NA	NA	ERR13189839.fastq.gz	NA
+n/a	n/a_utigKOS024	1	4	SE	Homo sapiens (modern human)			<PATH_TO_DATA>/n/a_utigKOS024_L1_R1.fastq.gz	NA	NA	ERR13189840.fastq.gz	NA
+n/a	n/a_utigKOS033	1	4	SE	Homo sapiens (modern human)			<PATH_TO_DATA>/n/a_utigKOS033_L1_R1.fastq.gz	NA	NA	ERR13189845.fastq.gz	NA
+n/a	n/a_utigKOS036	1	4	SE	Homo sapiens (modern human)			<PATH_TO_DATA>/n/a_utigKOS036_L1_R1.fastq.gz	NA	NA	ERR13189848.fastq.gz	NA
+n/a	n/a_utigWPK006	1	4	SE	Homo sapiens (modern human)			<PATH_TO_DATA>/n/a_utigWPK006_L1_R1.fastq.gz	NA	NA	ERR13189856.fastq.gz	NA
+n/a	n/a_utigOLV050	1	4	SE	Homo sapiens (modern human)			<PATH_TO_DATA>/n/a_utigOLV050_L1_R1.fastq.gz	NA	NA	ERR13189859.fastq.gz	NA
+n/a	n/a_utigOLV056	1	4	SE	Homo sapiens (modern human)			<PATH_TO_DATA>/n/a_utigOLV056_L1_R1.fastq.gz	NA	NA	ERR13189863.fastq.gz	NA
+n/a	n/a_utigKOS002	1	4	SE	Homo sapiens (modern human)			<PATH_TO_DATA>/n/a_utigKOS002_L1_R1.fastq.gz	NA	NA	ERR13189822.fastq.gz	NA
+n/a	n/a_utigKOS004A	1	4	SE	Homo sapiens (modern human)			<PATH_TO_DATA>/n/a_utigKOS004A_L1_R1.fastq.gz	NA	NA	ERR13189824.fastq.gz	NA
+n/a	n/a_utigKOS005	1	4	SE	Homo sapiens (modern human)			<PATH_TO_DATA>/n/a_utigKOS005_L1_R1.fastq.gz	NA	NA	ERR13189825.fastq.gz	NA
+n/a	n/a_utigKOS008C	1	4	SE	Homo sapiens (modern human)			<PATH_TO_DATA>/n/a_utigKOS008C_L1_R1.fastq.gz	NA	NA	ERR13189828.fastq.gz	NA
+n/a	n/a_utigKOS009	1	4	SE	Homo sapiens (modern human)			<PATH_TO_DATA>/n/a_utigKOS009_L1_R1.fastq.gz	NA	NA	ERR13189829.fastq.gz	NA
+n/a	n/a_utigKOS016	1	4	SE	Homo sapiens (modern human)			<PATH_TO_DATA>/n/a_utigKOS016_L1_R1.fastq.gz	NA	NA	ERR13189836.fastq.gz	NA
+n/a	n/a_utigKOS026	1	4	SE	Homo sapiens (modern human)			<PATH_TO_DATA>/n/a_utigKOS026_L1_R1.fastq.gz	NA	NA	ERR13189841.fastq.gz	NA
+n/a	n/a_utigKOS028	1	4	SE	Homo sapiens (modern human)			<PATH_TO_DATA>/n/a_utigKOS028_L1_R1.fastq.gz	NA	NA	ERR13189843.fastq.gz	NA
+n/a	n/a_utigKOS034	1	4	SE	Homo sapiens (modern human)			<PATH_TO_DATA>/n/a_utigKOS034_L1_R1.fastq.gz	NA	NA	ERR13189846.fastq.gz	NA
+n/a	n/a_utigKOS038	1	4	SE	Homo sapiens (modern human)			<PATH_TO_DATA>/n/a_utigKOS038_L1_R1.fastq.gz	NA	NA	ERR13189849.fastq.gz	NA
+n/a	n/a_utigWPK004	1	4	SE	Homo sapiens (modern human)			<PATH_TO_DATA>/n/a_utigWPK004_L1_R1.fastq.gz	NA	NA	ERR13189854.fastq.gz	NA
+n/a	n/a_utigOLV021	1	4	SE	Homo sapiens (modern human)			<PATH_TO_DATA>/n/a_utigOLV021_L1_R1.fastq.gz	NA	NA	ERR13189857.fastq.gz	NA
+n/a	n/a_utigOLV054	1	4	SE	Homo sapiens (modern human)			<PATH_TO_DATA>/n/a_utigOLV054_L1_R1.fastq.gz	NA	NA	ERR13189861.fastq.gz	NA
+n/a	n/a_utigOLV055	1	4	SE	Homo sapiens (modern human)			<PATH_TO_DATA>/n/a_utigOLV055_L1_R1.fastq.gz	NA	NA	ERR13189862.fastq.gz	NA
+n/a	n/a_utigOLV058	1	4	SE	Homo sapiens (modern human)			<PATH_TO_DATA>/n/a_utigOLV058_L1_R1.fastq.gz	NA	NA	ERR13189864.fastq.gz	NA
+n/a	n/a_utigOLV065	1	4	SE	Homo sapiens (modern human)			<PATH_TO_DATA>/n/a_utigOLV065_L1_R1.fastq.gz	NA	NA	ERR13189865.fastq.gz	NA
+n/a	n/a_utigOLV067	1	4	SE	Homo sapiens (modern human)			<PATH_TO_DATA>/n/a_utigOLV067_L1_R1.fastq.gz	NA	NA	ERR13189866.fastq.gz	NA
+n/a	n/a_utigOLV071	1	4	SE	Homo sapiens (modern human)			<PATH_TO_DATA>/n/a_utigOLV071_L1_R1.fastq.gz	NA	NA	ERR13189867.fastq.gz	NA
+n/a	n/a_utigKOS001	1	4	SE	Homo sapiens (modern human)			<PATH_TO_DATA>/n/a_utigKOS001_L1_R1.fastq.gz	NA	NA	ERR13189821.fastq.gz	NA
+n/a	n/a_utigKOS003	1	4	SE	Homo sapiens (modern human)			<PATH_TO_DATA>/n/a_utigKOS003_L1_R1.fastq.gz	NA	NA	ERR13189823.fastq.gz	NA
+n/a	n/a_utigKOS006	1	4	SE	Homo sapiens (modern human)			<PATH_TO_DATA>/n/a_utigKOS006_L1_R1.fastq.gz	NA	NA	ERR13189826.fastq.gz	NA
+n/a	n/a_utigKOS011	1	4	SE	Homo sapiens (modern human)			<PATH_TO_DATA>/n/a_utigKOS011_L1_R1.fastq.gz	NA	NA	ERR13189831.fastq.gz	NA
+n/a	n/a_utigKOS012	1	4	SE	Homo sapiens (modern human)			<PATH_TO_DATA>/n/a_utigKOS012_L1_R1.fastq.gz	NA	NA	ERR13189832.fastq.gz	NA
+n/a	n/a_utigKOS014	1	4	SE	Homo sapiens (modern human)			<PATH_TO_DATA>/n/a_utigKOS014_L1_R1.fastq.gz	NA	NA	ERR13189834.fastq.gz	NA
+n/a	n/a_utigKOS015	1	4	SE	Homo sapiens (modern human)			<PATH_TO_DATA>/n/a_utigKOS015_L1_R1.fastq.gz	NA	NA	ERR13189835.fastq.gz	NA
+n/a	n/a_utigKOS017	1	4	SE	Homo sapiens (modern human)			<PATH_TO_DATA>/n/a_utigKOS017_L1_R1.fastq.gz	NA	NA	ERR13189837.fastq.gz	NA
+n/a	n/a_utigKOS018	1	4	SE	Homo sapiens (modern human)			<PATH_TO_DATA>/n/a_utigKOS018_L1_R1.fastq.gz	NA	NA	ERR13189838.fastq.gz	NA
+n/a	n/a_utigKOS027	1	4	SE	Homo sapiens (modern human)			<PATH_TO_DATA>/n/a_utigKOS027_L1_R1.fastq.gz	NA	NA	ERR13189842.fastq.gz	NA
+n/a	n/a_utigKOS032	1	4	SE	Homo sapiens (modern human)			<PATH_TO_DATA>/n/a_utigKOS032_L1_R1.fastq.gz	NA	NA	ERR13189844.fastq.gz	NA
+n/a	n/a_utigKOS035A	1	4	SE	Homo sapiens (modern human)			<PATH_TO_DATA>/n/a_utigKOS035A_L1_R1.fastq.gz	NA	NA	ERR13189847.fastq.gz	NA
+n/a	n/a_utigKOS039	1	4	SE	Homo sapiens (modern human)			<PATH_TO_DATA>/n/a_utigKOS039_L1_R1.fastq.gz	NA	NA	ERR13189850.fastq.gz	NA
+n/a	n/a_utigWPK001A	1	4	SE	Homo sapiens (modern human)			<PATH_TO_DATA>/n/a_utigWPK001A_L1_R1.fastq.gz	NA	NA	ERR13189851.fastq.gz	NA
+n/a	n/a_utigWPK002	1	4	SE	Homo sapiens (modern human)			<PATH_TO_DATA>/n/a_utigWPK002_L1_R1.fastq.gz	NA	NA	ERR13189852.fastq.gz	NA
+n/a	n/a_utigWPK003	1	4	SE	Homo sapiens (modern human)			<PATH_TO_DATA>/n/a_utigWPK003_L1_R1.fastq.gz	NA	NA	ERR13189853.fastq.gz	NA
+n/a	n/a_utigWPK005	1	4	SE	Homo sapiens (modern human)			<PATH_TO_DATA>/n/a_utigWPK005_L1_R1.fastq.gz	NA	NA	ERR13189855.fastq.gz	NA
+n/a	n/a_utigOLV038	1	4	SE	Homo sapiens (modern human)			<PATH_TO_DATA>/n/a_utigOLV038_L1_R1.fastq.gz	NA	NA	ERR13189858.fastq.gz	NA
+n/a	n/a_utigOLV051	1	4	SE	Homo sapiens (modern human)			<PATH_TO_DATA>/n/a_utigOLV051_L1_R1.fastq.gz	NA	NA	ERR13189860.fastq.gz	NA
+n/a	n/a_utigOLV072	1	4	SE	Homo sapiens (modern human)			<PATH_TO_DATA>/n/a_utigOLV072_L1_R1.fastq.gz	NA	NA	ERR13189868.fastq.gz	NA

packages/2024_Sasso_PNAS/2024_Sasso_PNAS.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='0.2.1dev'
+
+## 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> <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 $(readlink -f ${3}) ## Path to helper function script should be provided as 3rd argument. https://github.com/poseidon-framework/poseidon-eager/blob/main/scripts/source_me.sh
+
+## Index non-proliferated columns and exclude them from the finalised TSV
+cut_selector=''
+tsv_header=($(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/2024_Sasso_PNAS/script_versions.txt

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