diff --git a/packages/2024_Ellegaard_WellMan/2024_Ellegaard_WellMan.config b/packages/2024_Ellegaard_WellMan/2024_Ellegaard_WellMan.config new file mode 100644 index 0000000..bd778e1 --- /dev/null +++ b/packages/2024_Ellegaard_WellMan/2024_Ellegaard_WellMan.config @@ -0,0 +1,41 @@ +// Keep track of config versions +minotaur_release='1.0.0' // The release tag of the poseidon-eager repository used for processing and config file retrieval +config_template_version='1.0.0' +package_config_version='1.0.0' +minotaur_config_base="https://raw.githubusercontent.com/poseidon-framework/poseidon-eager/${minotaur_release}/conf" + +// This configuration file is designed to be a used with the nf-core/eager pipeline. +// Instead of having to specify all other configurations for the Minotaur pipeline +// on runtime, they are all contained in this file and loaded automatically upon +// specifying this config file during runtime. Additionally, any parameters that +// need to be altered from the defaults can be specified here. +// +// The intention is to make it easy for users to understand and reproduce the output +// from processing with the Minotaur workflow processing from the contents of a +// single file. + +// Load configuration profiles. They are loaded from the minotaur_config_base URL, main branch. +// The loaded config includes code that loads the institutional configs from https://github.com/poseidon-framework/minotaur-institutional-configs. +includeConfig "${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 + */ +} diff --git a/packages/2024_Ellegaard_WellMan/2024_Ellegaard_WellMan.ssf b/packages/2024_Ellegaard_WellMan/2024_Ellegaard_WellMan.ssf new file mode 100644 index 0000000..4e5a233 --- /dev/null +++ b/packages/2024_Ellegaard_WellMan/2024_Ellegaard_WellMan.ssf @@ -0,0 +1,15 @@ +poseidon_IDs udg library_built notes run_accession study_accession sample_accession sample_alias secondary_sample_accession first_public last_updated instrument_model library_layout library_source instrument_platform library_name library_strategy fastq_ftp fastq_aspera fastq_bytes fastq_md5 read_count submitted_ftp submitted_md5 +WM minus ss n/a ERR12268596 PRJEB69227 SAMEA114606680 WM ERS16898600 2024-09-17 2024-09-17 Illumina NovaSeq 6000 PAIRED GENOMIC ILLUMINA WMTN1 WGS ftp.sra.ebi.ac.uk/vol1/fastq/ERR122/096/ERR12268596/ERR12268596_1.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/ERR122/096/ERR12268596/ERR12268596_2.fastq.gz fasp.sra.ebi.ac.uk:/vol1/fastq/ERR122/096/ERR12268596/ERR12268596_1.fastq.gz;fasp.sra.ebi.ac.uk:/vol1/fastq/ERR122/096/ERR12268596/ERR12268596_2.fastq.gz 4603211674;5838732166 fcd11267f15f20d0f323f3818f0474fa;9e79316c6d79c46b7dc8e3a33685abab 288972166 ftp.sra.ebi.ac.uk/vol1/run/ERR122/ERR12268596/WMTN1_FKDL210050469-1a-AK9315-AK3837_HVW7MDSXY_L1_1.fq.gz;ftp.sra.ebi.ac.uk/vol1/run/ERR122/ERR12268596/WMTN1_FKDL210050469-1a-AK9315-AK3837_HVW7MDSXY_L1_2.fq.gz 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ILLUMINA WMTN1 WGS ftp.sra.ebi.ac.uk/vol1/fastq/ERR122/000/ERR12268600/ERR12268600_1.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/ERR122/000/ERR12268600/ERR12268600_2.fastq.gz fasp.sra.ebi.ac.uk:/vol1/fastq/ERR122/000/ERR12268600/ERR12268600_1.fastq.gz;fasp.sra.ebi.ac.uk:/vol1/fastq/ERR122/000/ERR12268600/ERR12268600_2.fastq.gz 13648262149;13959146528 95282b8d36348c46bb4594fdc2d9dfbf;3ce33e0b2b8281a0740534fe979c24a4 772351510 ftp.sra.ebi.ac.uk/vol1/run/ERR122/ERR12268600/WMTN1_EKDL210002175-1a_H5T3NDSX2_L4_1.fq.gz;ftp.sra.ebi.ac.uk/vol1/run/ERR122/ERR12268600/WMTN1_EKDL210002175-1a_H5T3NDSX2_L4_2.fq.gz cb3f4b1de7460ce0167d80c9b4cb2dbc;49b865ab700f7c7d608aa940fe997df4 +WM minus ss n/a ERR12268597 PRJEB69227 SAMEA114606680 WM ERS16898600 2024-09-17 2024-09-17 Illumina NovaSeq 6000 PAIRED GENOMIC ILLUMINA WMTN1 WGS ftp.sra.ebi.ac.uk/vol1/fastq/ERR122/097/ERR12268597/ERR12268597_1.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/ERR122/097/ERR12268597/ERR12268597_2.fastq.gz 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ftp.sra.ebi.ac.uk/vol1/run/ERR122/ERR12268601/WMTN2_FKDL210050469-1a-AK36040-AK7764_HVW7MDSXY_L1_1.fq.gz;ftp.sra.ebi.ac.uk/vol1/run/ERR122/ERR12268601/WMTN2_FKDL210050469-1a-AK36040-AK7764_HVW7MDSXY_L1_2.fq.gz dd4318776b9011e8bf0aebd9e904fc14;00512a2c59c0ef50b1b8942580b1fcf3 +WM minus ss n/a ERR12268602 PRJEB69227 SAMEA114606680 WM ERS16898600 2024-09-17 2024-09-17 Illumina NovaSeq 6000 PAIRED GENOMIC ILLUMINA WMTN3 WGS ftp.sra.ebi.ac.uk/vol1/fastq/ERR122/002/ERR12268602/ERR12268602_1.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/ERR122/002/ERR12268602/ERR12268602_2.fastq.gz fasp.sra.ebi.ac.uk:/vol1/fastq/ERR122/002/ERR12268602/ERR12268602_1.fastq.gz;fasp.sra.ebi.ac.uk:/vol1/fastq/ERR122/002/ERR12268602/ERR12268602_2.fastq.gz 2582549581;3621271887 e10217a927a3c5b8557daab692f4c5af;b6e47295b34b49178b3ae156ea7bed69 161777748 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PAIRED GENOMIC ILLUMINA WMTU1 WGS ftp.sra.ebi.ac.uk/vol1/fastq/ERR122/003/ERR12268603/ERR12268603_1.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/ERR122/003/ERR12268603/ERR12268603_2.fastq.gz fasp.sra.ebi.ac.uk:/vol1/fastq/ERR122/003/ERR12268603/ERR12268603_1.fastq.gz;fasp.sra.ebi.ac.uk:/vol1/fastq/ERR122/003/ERR12268603/ERR12268603_2.fastq.gz 5942208653;7150046877 ee9343774c025724f84b29b2ba5d5f2e;43fa6aba09a089c71db58d33f2764189 333411234 ftp.sra.ebi.ac.uk/vol1/run/ERR122/ERR12268603/WMTU1_FKDL210050469-1a-AK3384-AK17268_HVW7MDSXY_L1_1.fq.gz;ftp.sra.ebi.ac.uk/vol1/run/ERR122/ERR12268603/WMTU1_FKDL210050469-1a-AK3384-AK17268_HVW7MDSXY_L1_2.fq.gz 14b2b9e7e92e1856709d3d9fd0584010;5c9d7b2f4e580380a20f8db55b3b7963 +WM half ss USER-treated ERR12268605 PRJEB69227 SAMEA114606680 WM ERS16898600 2024-09-17 2024-09-17 Illumina NovaSeq 6000 PAIRED GENOMIC ILLUMINA WMTU1 WGS ftp.sra.ebi.ac.uk/vol1/fastq/ERR122/005/ERR12268605/ERR12268605_1.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/ERR122/005/ERR12268605/ERR12268605_2.fastq.gz fasp.sra.ebi.ac.uk:/vol1/fastq/ERR122/005/ERR12268605/ERR12268605_1.fastq.gz;fasp.sra.ebi.ac.uk:/vol1/fastq/ERR122/005/ERR12268605/ERR12268605_2.fastq.gz 20386620160;19258562017 6b14403d7dbac24458c8eb4e94db330b;9134168063dfd64ef14addd28969b2b5 1034445802 ftp.sra.ebi.ac.uk/vol1/run/ERR122/ERR12268605/WMTU1_EKDL210002174-1a_H7KWWDSX2_L2_1.fq.gz;ftp.sra.ebi.ac.uk/vol1/run/ERR122/ERR12268605/WMTU1_EKDL210002174-1a_H7KWWDSX2_L2_2.fq.gz fba6c258357d304132f3ec547d644ea7;2ba33c9590d9a40cb16671e0c0befc9d +WM half ss USER-treated ERR12268608 PRJEB69227 SAMEA114606680 WM ERS16898600 2024-09-17 2024-09-17 Illumina NovaSeq 6000 PAIRED GENOMIC ILLUMINA WMTU2 WGS ftp.sra.ebi.ac.uk/vol1/fastq/ERR122/008/ERR12268608/ERR12268608_1.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/ERR122/008/ERR12268608/ERR12268608_2.fastq.gz fasp.sra.ebi.ac.uk:/vol1/fastq/ERR122/008/ERR12268608/ERR12268608_1.fastq.gz;fasp.sra.ebi.ac.uk:/vol1/fastq/ERR122/008/ERR12268608/ERR12268608_2.fastq.gz 4791897606;3812260643 29f2aa9820c2d6386326b8557bc71da2;7492c37e64c82e7a518b841b3a55b7ce 224513544 ftp.sra.ebi.ac.uk/vol1/run/ERR122/ERR12268608/WMTU2_FKDL210050469-1a-AK3825-AK17270_HVW7MDSXY_L1_1.fq.gz;ftp.sra.ebi.ac.uk/vol1/run/ERR122/ERR12268608/WMTU2_FKDL210050469-1a-AK3825-AK17270_HVW7MDSXY_L1_2.fq.gz 48c076a78401b738550ecd7e7c3ab944;641b1a8373da861490b2048c45a575e4 +WM half ss USER-treated ERR12268609 PRJEB69227 SAMEA114606680 WM ERS16898600 2024-09-17 2024-09-17 Illumina NovaSeq 6000 PAIRED GENOMIC ILLUMINA WMTU3 WGS ftp.sra.ebi.ac.uk/vol1/fastq/ERR122/009/ERR12268609/ERR12268609_1.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/ERR122/009/ERR12268609/ERR12268609_2.fastq.gz fasp.sra.ebi.ac.uk:/vol1/fastq/ERR122/009/ERR12268609/ERR12268609_1.fastq.gz;fasp.sra.ebi.ac.uk:/vol1/fastq/ERR122/009/ERR12268609/ERR12268609_2.fastq.gz 9021696524;9617280497 e2a8f741b6e693c05ec039c4e43b78a3;c82b4c45831fee7cc1a23639a3c44e5c 394387606 ftp.sra.ebi.ac.uk/vol1/run/ERR122/ERR12268609/WMTU3_FKDL210050469-1a-AK2790-AK6045_HVW7MDSXY_L1_1.fq.gz;ftp.sra.ebi.ac.uk/vol1/run/ERR122/ERR12268609/WMTU3_FKDL210050469-1a-AK2790-AK6045_HVW7MDSXY_L1_2.fq.gz 53fe5b76c5689f00ca66e88c3d857440;fe86b548d1ad5fc46910a7fd05ca0732 diff --git a/packages/2024_Ellegaard_WellMan/2024_Ellegaard_WellMan.tsv b/packages/2024_Ellegaard_WellMan/2024_Ellegaard_WellMan.tsv new file mode 100644 index 0000000..23ae225 --- /dev/null +++ b/packages/2024_Ellegaard_WellMan/2024_Ellegaard_WellMan.tsv @@ -0,0 +1,15 @@ +Sample_Name Library_ID Lane Colour_Chemistry SeqType Organism Strandedness UDG_Treatment R1 R2 BAM R1_target_file R2_target_file BAM_target +WM_ss WM_ss_WMTN1_ss 1 4 PE Homo sapiens (modern human) single none /WM_ss_WMTN1_ss_L1_R1.fastq.gz /WM_ss_WMTN1_ss_L1_R2.fastq.gz NA ERR12268596_1.fastq.gz ERR12268596_2.fastq.gz NA +WM_ss WM_ss_WMTN1_ss 2 4 PE Homo sapiens (modern human) single none /WM_ss_WMTN1_ss_L2_R1.fastq.gz /WM_ss_WMTN1_ss_L2_R2.fastq.gz NA ERR12268599_1.fastq.gz ERR12268599_2.fastq.gz NA +WM_ss WM_ss_WMTN1_ss 3 4 PE Homo sapiens (modern human) single none /WM_ss_WMTN1_ss_L3_R1.fastq.gz /WM_ss_WMTN1_ss_L3_R2.fastq.gz NA ERR12268600_1.fastq.gz ERR12268600_2.fastq.gz NA +WM_ss WM_ss_WMTN1_ss 4 4 PE Homo sapiens (modern human) single none /WM_ss_WMTN1_ss_L4_R1.fastq.gz /WM_ss_WMTN1_ss_L4_R2.fastq.gz NA ERR12268597_1.fastq.gz ERR12268597_2.fastq.gz NA +WM_ss WM_ss_WMTN1_ss 5 4 PE Homo sapiens (modern human) single none /WM_ss_WMTN1_ss_L5_R1.fastq.gz /WM_ss_WMTN1_ss_L5_R2.fastq.gz NA ERR12268598_1.fastq.gz ERR12268598_2.fastq.gz NA +WM_ss WM_ss_WMTN2_ss 1 4 PE Homo sapiens (modern human) single none /WM_ss_WMTN2_ss_L1_R1.fastq.gz /WM_ss_WMTN2_ss_L1_R2.fastq.gz NA ERR12268601_1.fastq.gz ERR12268601_2.fastq.gz NA +WM_ss WM_ss_WMTN3_ss 1 4 PE Homo sapiens (modern human) single none /WM_ss_WMTN3_ss_L1_R1.fastq.gz /WM_ss_WMTN3_ss_L1_R2.fastq.gz NA ERR12268602_1.fastq.gz ERR12268602_2.fastq.gz NA +WM_ss WM_ss_WMTU1_ss 1 4 PE Homo sapiens (modern human) single half /WM_ss_WMTU1_ss_L1_R1.fastq.gz /WM_ss_WMTU1_ss_L1_R2.fastq.gz NA ERR12268604_1.fastq.gz ERR12268604_2.fastq.gz NA +WM_ss WM_ss_WMTU1_ss 2 4 PE Homo sapiens (modern human) single half /WM_ss_WMTU1_ss_L2_R1.fastq.gz /WM_ss_WMTU1_ss_L2_R2.fastq.gz NA ERR12268606_1.fastq.gz ERR12268606_2.fastq.gz NA +WM_ss WM_ss_WMTU1_ss 3 4 PE Homo sapiens (modern human) single half /WM_ss_WMTU1_ss_L3_R1.fastq.gz /WM_ss_WMTU1_ss_L3_R2.fastq.gz NA ERR12268607_1.fastq.gz ERR12268607_2.fastq.gz NA +WM_ss WM_ss_WMTU1_ss 4 4 PE Homo sapiens (modern human) single half /WM_ss_WMTU1_ss_L4_R1.fastq.gz /WM_ss_WMTU1_ss_L4_R2.fastq.gz NA ERR12268603_1.fastq.gz ERR12268603_2.fastq.gz NA +WM_ss WM_ss_WMTU1_ss 5 4 PE Homo sapiens (modern human) single half /WM_ss_WMTU1_ss_L5_R1.fastq.gz /WM_ss_WMTU1_ss_L5_R2.fastq.gz NA ERR12268605_1.fastq.gz ERR12268605_2.fastq.gz NA +WM_ss WM_ss_WMTU2_ss 1 4 PE Homo sapiens (modern human) single half /WM_ss_WMTU2_ss_L1_R1.fastq.gz /WM_ss_WMTU2_ss_L1_R2.fastq.gz NA ERR12268608_1.fastq.gz ERR12268608_2.fastq.gz NA +WM_ss WM_ss_WMTU3_ss 1 4 PE Homo sapiens (modern human) single half /WM_ss_WMTU3_ss_L1_R1.fastq.gz /WM_ss_WMTU3_ss_L1_R2.fastq.gz NA ERR12268609_1.fastq.gz ERR12268609_2.fastq.gz NA diff --git a/packages/2024_Ellegaard_WellMan/2024_Ellegaard_WellMan.tsv_patch.sh b/packages/2024_Ellegaard_WellMan/2024_Ellegaard_WellMan.tsv_patch.sh new file mode 100755 index 0000000..a73f9af --- /dev/null +++ b/packages/2024_Ellegaard_WellMan/2024_Ellegaard_WellMan.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="$(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} > ${output_tsv} +sed -i -e "s||${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} diff --git a/packages/2024_Ellegaard_WellMan/script_versions.txt b/packages/2024_Ellegaard_WellMan/script_versions.txt new file mode 100644 index 0000000..13ace45 --- /dev/null +++ b/packages/2024_Ellegaard_WellMan/script_versions.txt @@ -0,0 +1,2 @@ +create_eager_input.sh: 0.5.1 +source_me.sh for initial TSV: 0.5.2