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[automated] Create package recipe from SSF files
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‎packages/2022_Tiesler_colonialCampeche/2022_Tiesler_colonialCampeche.config‎

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// Keep track of config versions
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minotaur_release='1.0.0' // The release tag of the poseidon-eager repository used for processing and config file retrieval
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config_template_version='1.0.0'
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package_config_version='1.0.0'
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minotaur_config_base="https://raw.githubusercontent.com/poseidon-framework/poseidon-eager/${minotaur_release}/conf"
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// This configuration file is designed to be a used with the nf-core/eager pipeline.
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// Instead of having to specify all other configurations for the Minotaur pipeline
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// on runtime, they are all contained in this file and loaded automatically upon
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// specifying this config file during runtime. Additionally, any parameters that
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// need to be altered from the defaults can be specified here.
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//
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// The intention is to make it easy for users to understand and reproduce the output
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// from processing with the Minotaur workflow processing from the contents of a
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// single file.
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// Load configuration profiles. They are loaded from the minotaur_config_base URL, main branch.
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// The loaded config includes code that loads the institutional configs from https://github.com/poseidon-framework/minotaur-institutional-configs.
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includeConfig "${minotaur_config_base}/Minotaur.config" // Default nf-core/eager parameters for Minotaur processing.
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// The following config file specifies BED files for on-target endogenous DNA calculation and mean coverage as well as pseudohaploid genotyping.
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// TODO: Select the appropriate config for the CaptureType of the package.
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includeConfig "${minotaur_config_base}/CaptureType_profiles/1240K.config"
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params {
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// Keep track of config file versions used when processing
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config_profile_description = "${config_profile_description}\n - config_template_version: ${config_template_version}\n - package_config_version: ${package_config_version}"
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config_profile_contact = "Thiseas C. Lamnidis (@TCLamnidis)"
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/*
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TODO: If you need to change any of the default processing parameters for this package
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you can specify these parameters below.
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Any parameters not specified in any of the config files default to their nf-core/eager default values.
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For information on all available parameters and their default values see:
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https://nf-co.re/eager/2.5.1/parameters
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You can see the latest default values for parameters within poseidon-eager at:
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https://github.com/poseidon-framework/poseidon-eager/blob/main/conf/Minotaur.config
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*/
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}

‎packages/2022_Tiesler_colonialCampeche/2022_Tiesler_colonialCampeche.tsv‎

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Sample_Name Library_ID Lane Colour_Chemistry SeqType Organism Strandedness UDG_Treatment R1 R2 BAM R1_target_file R2_target_file BAM_target
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I10859 I10859_ERS12558320 1 4 SE Homo sapiens (modern human) double half <PATH_TO_DATA>/I10859_ERS12558320_L1_R1.fastq.gz NA NA ERR10024820.fastq.gz NA NA
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I10860 I10860_ERS12558322 1 4 SE Homo sapiens (modern human) double half <PATH_TO_DATA>/I10860_ERS12558322_L1_R1.fastq.gz NA NA ERR10024822.fastq.gz NA NA
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I10860 I10860_ERS12558323 1 4 SE Homo sapiens (modern human) double half <PATH_TO_DATA>/I10860_ERS12558323_L1_R1.fastq.gz NA NA ERR10024823.fastq.gz NA NA
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I10861 I10861_ERS12558324 1 4 SE Homo sapiens (modern human) double half <PATH_TO_DATA>/I10861_ERS12558324_L1_R1.fastq.gz NA NA ERR10024824.fastq.gz NA NA
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I10861 I10861_ERS12558325 1 4 SE Homo sapiens (modern human) double half <PATH_TO_DATA>/I10861_ERS12558325_L1_R1.fastq.gz NA NA ERR10024825.fastq.gz NA NA
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I10862 I10862_ERS12558326 1 4 SE Homo sapiens (modern human) double half <PATH_TO_DATA>/I10862_ERS12558326_L1_R1.fastq.gz NA NA ERR10024826.fastq.gz NA NA
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I10863 I10863_ERS12558328 1 4 SE Homo sapiens (modern human) double half <PATH_TO_DATA>/I10863_ERS12558328_L1_R1.fastq.gz NA NA ERR10024828.fastq.gz NA NA
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I8558 I8558_ERS12558336 1 4 SE Homo sapiens (modern human) double half NA NA <PATH_TO_DATA>/I8558_ERS12558336_L1.bam NA NA I8558_auto.bam
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I8558 I8558_ERS12558337 1 4 SE Homo sapiens (modern human) double half <PATH_TO_DATA>/I8558_ERS12558337_L1_R1.fastq.gz NA NA ERR10024837.fastq.gz NA NA
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I8559 I8559_ERS12558339 1 4 SE Homo sapiens (modern human) double half <PATH_TO_DATA>/I8559_ERS12558339_L1_R1.fastq.gz NA NA ERR10024839.fastq.gz NA NA
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I10859 I10859_ERS12558321 1 4 SE Homo sapiens (modern human) double half <PATH_TO_DATA>/I10859_ERS12558321_L1_R1.fastq.gz NA NA ERR10024821.fastq.gz NA NA
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I10862 I10862_ERS12558327 1 4 SE Homo sapiens (modern human) double half <PATH_TO_DATA>/I10862_ERS12558327_L1_R1.fastq.gz NA NA ERR10024827.fastq.gz NA NA
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I10863 I10863_ERS12558329 1 4 SE Homo sapiens (modern human) double half <PATH_TO_DATA>/I10863_ERS12558329_L1_R1.fastq.gz NA NA ERR10024829.fastq.gz NA NA
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I8555 I8555_ERS12558330 1 4 SE Homo sapiens (modern human) double half NA NA <PATH_TO_DATA>/I8555_ERS12558330_L1.bam NA NA I8555_auto.bam
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I8556 I8556_ERS12558332 1 4 SE Homo sapiens (modern human) double half <PATH_TO_DATA>/I8556_ERS12558332_L1_R1.fastq.gz NA NA ERR10024832.fastq.gz NA NA
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I8555 I8555_ERS12558331 1 4 SE Homo sapiens (modern human) double half <PATH_TO_DATA>/I8555_ERS12558331_L1_R1.fastq.gz NA NA ERR10024831.fastq.gz NA NA
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I8556 I8556_ERS12558333 1 4 SE Homo sapiens (modern human) double half <PATH_TO_DATA>/I8556_ERS12558333_L1_R1.fastq.gz NA NA ERR10024833.fastq.gz NA NA
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I8557 I8557_ERS12558334 1 4 SE Homo sapiens (modern human) double half NA NA <PATH_TO_DATA>/I8557_ERS12558334_L1.bam NA NA I8557_auto.bam
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I8557 I8557_ERS12558335 1 4 SE Homo sapiens (modern human) double half <PATH_TO_DATA>/I8557_ERS12558335_L1_R1.fastq.gz NA NA ERR10024835.fastq.gz NA NA
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I8559 I8559_ERS12558338 1 4 SE Homo sapiens (modern human) double half NA NA <PATH_TO_DATA>/I8559_ERS12558338_L1.bam NA NA I8559_auto.bam

‎packages/2022_Tiesler_colonialCampeche/2022_Tiesler_colonialCampeche.tsv_patch.sh‎

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#!/usr/bin/env bash
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set -uo pipefail ## Pipefail, complain on new unassigned variables.
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## Track the version of the TSV_patch template used
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VERSION='0.2.1dev'
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## This script is applied to the eager input TSV file locally to edit the dummy
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## path to the fastQ files added by `create_eager_input.sh` to a real local
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## path provided as a positional argument. Any further local tweaks to the
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## TSV before running eager should be added below that in the form of bash
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## commands to aid in reproducibility.
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## usage tsv_patch.sh <local_data_dir> <input_tsv> <path/to/source_me.sh>
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local_data_dir="$(readlink -f ${1})"
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input_tsv="$(readlink -f ${2})"
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output_tsv="$(dirname ${local_data_dir})/$(basename -s ".tsv" ${input_tsv}).finalised.tsv"
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columns_to_keep=("Sample_Name" "Library_ID" "Lane" "Colour_Chemistry" "SeqType" "Organism" "Strandedness" "UDG_Treatment" "R1" "R2" "BAM")
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source $(readlink -f ${3}) ## Path to helper function script should be provided as 3rd argument. https://github.com/poseidon-framework/poseidon-eager/blob/main/scripts/source_me.sh
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## Index non-proliferated columns and exclude them from the finalised TSV
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cut_selector=''
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tsv_header=($(head -n1 ${input_tsv}))
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for col_name in ${columns_to_keep[@]}; do
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let idx=$(get_index_of ${col_name} "${columns_to_keep[@]}")+1 ## awk uses 1-based indexing
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if [[ ! ${idx} -eq -1 ]]; then
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cut_selector+="${idx},"
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fi
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done
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## Remove added columns, and put columns in right order
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cut -f ${cut_selector%,} ${input_tsv} > ${output_tsv}
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sed -i -e "s|<PATH_TO_DATA>|${local_data_dir}|g" ${output_tsv}
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## Any further commands to edit the file before finalisation should be added below as shown
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# sed -ie 's/replace_this/with_this/g' ${output_tsv}
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## Keep track of versions
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version_file="$(dirname ${input_tsv})/script_versions.txt"
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## Remove versions from older run if there
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grep -v -F -e "$(basename ${0})" -e "source_me.sh for final TSV" ${version_file} >${version_file}.new
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## Then add new versions
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echo -e "$(basename ${0}):\t${VERSION}" >> ${version_file}.new
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echo -e "source_me.sh for final TSV:\t${HELPER_FUNCTION_VERSION}" >>${version_file}.new
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mv ${version_file}.new ${version_file}

‎packages/2022_Tiesler_colonialCampeche/script_versions.txt‎

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create_eager_input.sh: 0.5.1
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source_me.sh for initial TSV: 0.5.2

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