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| .DS_Store |
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packages/2023_Ferraz_NatureEcologyEvolution/2023_Ferraz_NatureEcologyEvolution.config
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| // 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 | ||
| */ | ||
| } |
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packages/2023_Ferraz_NatureEcologyEvolution/2023_Ferraz_NatureEcologyEvolution.ssf
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packages/2023_Ferraz_NatureEcologyEvolution/2023_Ferraz_NatureEcologyEvolution.tsv
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,69 @@ | ||
| Sample_Name Library_ID Lane Colour_Chemistry SeqType Organism Strandedness UDG_Treatment R1 R2 BAM R1_target_file R2_target_file | ||
| CBE003_TF CBE003_TF_CBE003.A0101.TF1.1 1 4 SE Homo sapiens (modern human) double half <PATH_TO_DATA>/CBE003_TF_CBE003.A0101.TF1.1_L1_R1.fastq.gz NA NA ERR11769644.fastq.gz NA | ||
| CUB002_TF CUB002_TF_CUB002.A0101.TF1.1 1 4 SE Homo sapiens (modern human) double half <PATH_TO_DATA>/CUB002_TF_CUB002.A0101.TF1.1_L1_R1.fastq.gz NA NA ERR11769646.fastq.gz NA | ||
| GA4002_TF GA4002_TF_GA4002.A0101.TF1.1_2 1 4 SE Homo sapiens (modern human) double half <PATH_TO_DATA>/GA4002_TF_GA4002.A0101.TF1.1_2_L1_R1.fastq.gz NA NA ERR11769654.fastq.gz NA | ||
| JBT009_TF JBT009_TF_JBT009.A0101.TF1.1 1 4 SE Homo sapiens (modern human) double half <PATH_TO_DATA>/JBT009_TF_JBT009.A0101.TF1.1_L1_R1.fastq.gz NA NA ERR11769657.fastq.gz NA | ||
| JBT011_TF JBT011_TF_JBT011.A0101.TF1.1_2 1 4 SE Homo sapiens (modern human) double half <PATH_TO_DATA>/JBT011_TF_JBT011.A0101.TF1.1_2_L1_R1.fastq.gz NA NA ERR11769659.fastq.gz NA | ||
| JBT015_TF JBT015_TF_JBT015.A0101.TF1.1 1 4 SE Homo sapiens (modern human) double half <PATH_TO_DATA>/JBT015_TF_JBT015.A0101.TF1.1_L1_R1.fastq.gz NA NA ERR11769663.fastq.gz NA | ||
| JBT025_TF JBT025_TF_JBT025.A0101.TF1.1 1 4 SE Homo sapiens (modern human) double half <PATH_TO_DATA>/JBT025_TF_JBT025.A0101.TF1.1_L1_R1.fastq.gz NA NA ERR11769670.fastq.gz NA | ||
| JBT026_TF JBT026_TF_JBT026.A0101.TF1.1 1 4 SE Homo sapiens (modern human) double half <PATH_TO_DATA>/JBT026_TF_JBT026.A0101.TF1.1_L1_R1.fastq.gz NA NA ERR11769671.fastq.gz NA | ||
| CBE004_MT CBE004_MT_CBE004.A0101.MT1.1 1 4 SE Homo sapiens (modern human) double half <PATH_TO_DATA>/CBE004_MT_CBE004.A0101.MT1.1_L1_R1.fastq.gz NA NA ERR11770484.fastq.gz NA | ||
| CUB002_MT CUB002_MT_CUB002.A0101.MT1.1 1 4 SE Homo sapiens (modern human) double half <PATH_TO_DATA>/CUB002_MT_CUB002.A0101.MT1.1_L1_R1.fastq.gz NA NA ERR11770485.fastq.gz NA | ||
| CUB008_MT CUB008_MT_CUB008.A0101.MT1.1 1 4 SE Homo sapiens (modern human) double half <PATH_TO_DATA>/CUB008_MT_CUB008.A0101.MT1.1_L1_R1.fastq.gz NA NA ERR11770486.fastq.gz NA | ||
| EPS002_MT EPS002_MT_EPS002.A0101.MT1.1_2 1 4 SE Homo sapiens (modern human) double half <PATH_TO_DATA>/EPS002_MT_EPS002.A0101.MT1.1_2_L1_R1.fastq.gz NA NA ERR11770488.fastq.gz NA | ||
| EPS004_MT EPS004_MT_EPS004.A0101.MT1.1_2 1 4 SE Homo sapiens (modern human) double half <PATH_TO_DATA>/EPS004_MT_EPS004.A0101.MT1.1_2_L1_R1.fastq.gz NA NA ERR11770490.fastq.gz NA | ||
| EPS005_MT EPS005_MT_EPS005.A0101.MT1.1_2 1 4 SE Homo sapiens (modern human) double half <PATH_TO_DATA>/EPS005_MT_EPS005.A0101.MT1.1_2_L1_R1.fastq.gz NA NA ERR11770491.fastq.gz NA | ||
| JBT001_MT JBT001_MT_JBT001.A0101.MT1.1 1 4 SE Homo sapiens (modern human) double half <PATH_TO_DATA>/JBT001_MT_JBT001.A0101.MT1.1_L1_R1.fastq.gz NA NA ERR11770494.fastq.gz NA | ||
| JBT010_MT JBT010_MT_JBT010.A0101.MT1.1 1 4 SE Homo sapiens (modern human) double half <PATH_TO_DATA>/JBT010_MT_JBT010.A0101.MT1.1_L1_R1.fastq.gz NA NA ERR11770497.fastq.gz NA | ||
| JBT012_MT JBT012_MT_JBT012.A0101.MT1.1 1 4 SE Homo sapiens (modern human) double half <PATH_TO_DATA>/JBT012_MT_JBT012.A0101.MT1.1_L1_R1.fastq.gz NA NA ERR11770499.fastq.gz NA | ||
| JBT015_MT JBT015_MT_JBT015.A0101.MT1.1 1 4 SE Homo sapiens (modern human) double half <PATH_TO_DATA>/JBT015_MT_JBT015.A0101.MT1.1_L1_R1.fastq.gz NA NA ERR11770502.fastq.gz NA | ||
| JBT020_MT JBT020_MT_JBT020.A0101.MT1.1_2 1 4 SE Homo sapiens (modern human) double half <PATH_TO_DATA>/JBT020_MT_JBT020.A0101.MT1.1_2_L1_R1.fastq.gz NA NA ERR11770505.fastq.gz NA | ||
| JBT023_MT JBT023_MT_JBT023.A0101.MT1.1 1 4 SE Homo sapiens (modern human) double half <PATH_TO_DATA>/JBT023_MT_JBT023.A0101.MT1.1_L1_R1.fastq.gz NA NA ERR11770508.fastq.gz NA | ||
| JBT025_MT JBT025_MT_JBT025.A0101.MT1.1 1 4 SE Homo sapiens (modern human) double half <PATH_TO_DATA>/JBT025_MT_JBT025.A0101.MT1.1_L1_R1.fastq.gz NA NA ERR11770509.fastq.gz NA | ||
| SAM014_MT SAM014_MT_SAM014.A0101.MT1.1 1 4 SE Homo sapiens (modern human) double half <PATH_TO_DATA>/SAM014_MT_SAM014.A0101.MT1.1_L1_R1.fastq.gz NA NA ERR11770513.fastq.gz NA | ||
| TDA002_MT TDA002_MT_TDA002.A0101.MT1.1 1 4 SE Homo sapiens (modern human) double none <PATH_TO_DATA>/TDA002_MT_TDA002.A0101.MT1.1_L1_R1.fastq.gz NA NA ERR11770514.fastq.gz NA | ||
| CAP007_TF CAP007_TF_CAP007.A0101.TF1.1_2 1 4 SE Homo sapiens (modern human) double half <PATH_TO_DATA>/CAP007_TF_CAP007.A0101.TF1.1_2_L1_R1.fastq.gz NA NA ERR11769643.fastq.gz NA | ||
| EPS001_TF EPS001_TF_EPS001.A0102.TF1.1 1 4 SE Homo sapiens (modern human) double half <PATH_TO_DATA>/EPS001_TF_EPS001.A0102.TF1.1_L1_R1.fastq.gz NA NA ERR11769648.fastq.gz NA | ||
| EPS005_TF EPS005_TF_EPS005.A0101.TF1.1 1 4 SE Homo sapiens (modern human) double half <PATH_TO_DATA>/EPS005_TF_EPS005.A0101.TF1.1_L1_R1.fastq.gz NA NA ERR11769652.fastq.gz NA | ||
| EPS011_TF EPS011_TF_EPS011.A0101.TF1.1_2 1 4 SE Homo sapiens (modern human) double half <PATH_TO_DATA>/EPS011_TF_EPS011.A0101.TF1.1_2_L1_R1.fastq.gz NA NA ERR11769653.fastq.gz NA | ||
| JBT001_TF JBT001_TF_JBT001.A0101.TF1.1 1 4 SE Homo sapiens (modern human) double half <PATH_TO_DATA>/JBT001_TF_JBT001.A0101.TF1.1_L1_R1.fastq.gz NA NA ERR11769655.fastq.gz NA | ||
| JBT002_TF JBT002_TF_JBT002.A0101.TF1.1 1 4 SE Homo sapiens (modern human) double half <PATH_TO_DATA>/JBT002_TF_JBT002.A0101.TF1.1_L1_R1.fastq.gz NA NA ERR11769656.fastq.gz NA | ||
| JBT010_TF JBT010_TF_JBT010.A0101.TF1.1 1 4 SE Homo sapiens (modern human) double half <PATH_TO_DATA>/JBT010_TF_JBT010.A0101.TF1.1_L1_R1.fastq.gz NA NA ERR11769658.fastq.gz NA | ||
| JBT013_TF JBT013_TF_JBT013.A0101.TF1.1 1 4 SE Homo sapiens (modern human) double half <PATH_TO_DATA>/JBT013_TF_JBT013.A0101.TF1.1_L1_R1.fastq.gz NA NA ERR11769661.fastq.gz NA | ||
| JBT014_TF JBT014_TF_JBT014.A0101.TF1.1 1 4 SE Homo sapiens (modern human) double half <PATH_TO_DATA>/JBT014_TF_JBT014.A0101.TF1.1_L1_R1.fastq.gz NA NA ERR11769662.fastq.gz NA | ||
| JBT019_TF JBT019_TF_JBT019.A0101.TF1.1 1 4 SE Homo sapiens (modern human) double half <PATH_TO_DATA>/JBT019_TF_JBT019.A0101.TF1.1_L1_R1.fastq.gz NA NA ERR11769665.fastq.gz NA | ||
| JBT021_TF JBT021_TF_JBT021.A0101.TF1.1 1 4 SE Homo sapiens (modern human) double half <PATH_TO_DATA>/JBT021_TF_JBT021.A0101.TF1.1_L1_R1.fastq.gz NA NA ERR11769667.fastq.gz NA | ||
| JBT023_TF JBT023_TF_JBT023.A0101.TF1.1 1 4 SE Homo sapiens (modern human) double half <PATH_TO_DATA>/JBT023_TF_JBT023.A0101.TF1.1_L1_R1.fastq.gz NA NA ERR11769669.fastq.gz NA | ||
| PAI001_TF PAI001_TF_PAI001.A0101.TF1.1_2 1 4 SE Homo sapiens (modern human) double half <PATH_TO_DATA>/PAI001_TF_PAI001.A0101.TF1.1_2_L1_R1.fastq.gz NA NA ERR11769672.fastq.gz NA | ||
| PLM001_TF PLM001_TF_PLM001.A0101.TF1.1 1 4 SE Homo sapiens (modern human) double half <PATH_TO_DATA>/PLM001_TF_PLM001.A0101.TF1.1_L1_R1.fastq.gz NA NA ERR11769673.fastq.gz NA | ||
| CBE003_MT CBE003_MT_CBE003.A0101.MT1.1 1 4 SE Homo sapiens (modern human) double half <PATH_TO_DATA>/CBE003_MT_CBE003.A0101.MT1.1_L1_R1.fastq.gz NA NA ERR11770483.fastq.gz NA | ||
| EPS001_MT EPS001_MT_EPS001.A0101.MT1.1 1 4 SE Homo sapiens (modern human) double none <PATH_TO_DATA>/EPS001_MT_EPS001.A0101.MT1.1_L1_R1.fastq.gz NA NA ERR11770487.fastq.gz NA | ||
| JBT009_MT JBT009_MT_JBT009.A0101.MT1.1 1 4 SE Homo sapiens (modern human) double half <PATH_TO_DATA>/JBT009_MT_JBT009.A0101.MT1.1_L1_R1.fastq.gz NA NA ERR11770496.fastq.gz NA | ||
| JBT018_MT JBT018_MT_JBT018.A0101.MT1.1 1 4 SE Homo sapiens (modern human) double half <PATH_TO_DATA>/JBT018_MT_JBT018.A0101.MT1.1_L1_R1.fastq.gz NA NA ERR11770503.fastq.gz NA | ||
| JBT019_MT JBT019_MT_JBT019.A0101.MT1.1 1 4 SE Homo sapiens (modern human) double half <PATH_TO_DATA>/JBT019_MT_JBT019.A0101.MT1.1_L1_R1.fastq.gz NA NA ERR11770504.fastq.gz NA | ||
| JBT022_MT JBT022_MT_JBT022.A0101.MT1.1 1 4 SE Homo sapiens (modern human) double half <PATH_TO_DATA>/JBT022_MT_JBT022.A0101.MT1.1_L1_R1.fastq.gz NA NA ERR11770507.fastq.gz NA | ||
| PAI001_MT PAI001_MT_PAI001.A0101.MT1.1 1 4 SE Homo sapiens (modern human) double half <PATH_TO_DATA>/PAI001_MT_PAI001.A0101.MT1.1_L1_R1.fastq.gz NA NA ERR11770511.fastq.gz NA | ||
| PLM001_MT PLM001_MT_PLM001.A0101.MT1.1 1 4 SE Homo sapiens (modern human) double half <PATH_TO_DATA>/PLM001_MT_PLM001.A0101.MT1.1_L1_R1.fastq.gz NA NA ERR11770512.fastq.gz NA | ||
| CBE004_TF CBE004_TF_CBE004.A0101.TF1.1 1 4 SE Homo sapiens (modern human) double half <PATH_TO_DATA>/CBE004_TF_CBE004.A0101.TF1.1_L1_R1.fastq.gz NA NA ERR11769645.fastq.gz NA | ||
| CUB008_TF CUB008_TF_CUB008.A0101.TF1.1_2 1 4 SE Homo sapiens (modern human) double half <PATH_TO_DATA>/CUB008_TF_CUB008.A0101.TF1.1_2_L1_R1.fastq.gz NA NA ERR11769647.fastq.gz NA | ||
| EPS002_TF EPS002_TF_EPS002.A0101.TF1.1_2 1 4 SE Homo sapiens (modern human) double half <PATH_TO_DATA>/EPS002_TF_EPS002.A0101.TF1.1_2_L1_R1.fastq.gz NA NA ERR11769649.fastq.gz NA | ||
| EPS003_TF EPS003_TF_EPS003.A0101.TF1.1 1 4 SE Homo sapiens (modern human) double half <PATH_TO_DATA>/EPS003_TF_EPS003.A0101.TF1.1_L1_R1.fastq.gz NA NA ERR11769650.fastq.gz NA | ||
| EPS004_TF EPS004_TF_EPS004.A0101.TF1.1_2 1 4 SE Homo sapiens (modern human) double half <PATH_TO_DATA>/EPS004_TF_EPS004.A0101.TF1.1_2_L1_R1.fastq.gz NA NA ERR11769651.fastq.gz NA | ||
| JBT012_TF JBT012_TF_JBT012.A0101.TF1.1 1 4 SE Homo sapiens (modern human) double half <PATH_TO_DATA>/JBT012_TF_JBT012.A0101.TF1.1_L1_R1.fastq.gz NA NA ERR11769660.fastq.gz NA | ||
| JBT018_TF JBT018_TF_JBT018.A0101.TF1.1 1 4 SE Homo sapiens (modern human) double half <PATH_TO_DATA>/JBT018_TF_JBT018.A0101.TF1.1_L1_R1.fastq.gz NA NA ERR11769664.fastq.gz NA | ||
| JBT020_TF JBT020_TF_JBT020.A0101.TF1.1_2 1 4 SE Homo sapiens (modern human) double half <PATH_TO_DATA>/JBT020_TF_JBT020.A0101.TF1.1_2_L1_R1.fastq.gz NA NA ERR11769666.fastq.gz NA | ||
| JBT022_TF JBT022_TF_JBT022.A0101.TF1.1 1 4 SE Homo sapiens (modern human) double half <PATH_TO_DATA>/JBT022_TF_JBT022.A0101.TF1.1_L1_R1.fastq.gz NA NA ERR11769668.fastq.gz NA | ||
| SAM014_TF SAM014_TF_SAM014.A0101.TF1.1 1 4 SE Homo sapiens (modern human) double half <PATH_TO_DATA>/SAM014_TF_SAM014.A0101.TF1.1_L1_R1.fastq.gz NA NA ERR11769674.fastq.gz NA | ||
| TDA002_TF TDA002_TF_TDA002.A0102.TF1.1_2_3 1 4 SE Homo sapiens (modern human) double none <PATH_TO_DATA>/TDA002_TF_TDA002.A0102.TF1.1_2_3_L1_R1.fastq.gz NA NA ERR11769675.fastq.gz NA | ||
| VSM001_TF VSM001_TF_VSM001.A0101.TF1.1_2 1 4 SE Homo sapiens (modern human) double half <PATH_TO_DATA>/VSM001_TF_VSM001.A0101.TF1.1_2_L1_R1.fastq.gz NA NA ERR11769676.fastq.gz NA | ||
| CAP007_MT CAP007_MT_CAP007.A0101.MT1.1 1 4 SE Homo sapiens (modern human) double half <PATH_TO_DATA>/CAP007_MT_CAP007.A0101.MT1.1_L1_R1.fastq.gz NA NA ERR11770482.fastq.gz NA | ||
| EPS003_MT EPS003_MT_EPS003.A0101.MT1.1_2 1 4 SE Homo sapiens (modern human) double half <PATH_TO_DATA>/EPS003_MT_EPS003.A0101.MT1.1_2_L1_R1.fastq.gz NA NA ERR11770489.fastq.gz NA | ||
| EPS011_MT EPS011_MT_EPS011.A0101.MT1.1_2 1 4 SE Homo sapiens (modern human) double half <PATH_TO_DATA>/EPS011_MT_EPS011.A0101.MT1.1_2_L1_R1.fastq.gz NA NA ERR11770492.fastq.gz NA | ||
| GA4002_MT GA4002_MT_GA4002.A0101.MT1.1_2 1 4 SE Homo sapiens (modern human) double half <PATH_TO_DATA>/GA4002_MT_GA4002.A0101.MT1.1_2_L1_R1.fastq.gz NA NA ERR11770493.fastq.gz NA | ||
| JBT002_MT JBT002_MT_JBT002.A0101.MT1.1_2 1 4 SE Homo sapiens (modern human) double half <PATH_TO_DATA>/JBT002_MT_JBT002.A0101.MT1.1_2_L1_R1.fastq.gz NA NA ERR11770495.fastq.gz NA | ||
| JBT011_MT JBT011_MT_JBT011.A0101.MT1.1_2 1 4 SE Homo sapiens (modern human) double half <PATH_TO_DATA>/JBT011_MT_JBT011.A0101.MT1.1_2_L1_R1.fastq.gz NA NA ERR11770498.fastq.gz NA | ||
| JBT013_MT JBT013_MT_JBT013.A0101.MT1.1 1 4 SE Homo sapiens (modern human) double half <PATH_TO_DATA>/JBT013_MT_JBT013.A0101.MT1.1_L1_R1.fastq.gz NA NA ERR11770500.fastq.gz NA | ||
| JBT014_MT JBT014_MT_JBT014.A0101.MT1.1 1 4 SE Homo sapiens (modern human) double half <PATH_TO_DATA>/JBT014_MT_JBT014.A0101.MT1.1_L1_R1.fastq.gz NA NA ERR11770501.fastq.gz NA | ||
| JBT021_MT JBT021_MT_JBT021.A0101.MT1.1 1 4 SE Homo sapiens (modern human) double half <PATH_TO_DATA>/JBT021_MT_JBT021.A0101.MT1.1_L1_R1.fastq.gz NA NA ERR11770506.fastq.gz NA | ||
| JBT026_MT JBT026_MT_JBT026.A0101.MT1.1 1 4 SE Homo sapiens (modern human) double half <PATH_TO_DATA>/JBT026_MT_JBT026.A0101.MT1.1_L1_R1.fastq.gz NA NA ERR11770510.fastq.gz NA | ||
| VSM001_MT VSM001_MT_VSM001.A0101.MT1.1 1 4 SE Homo sapiens (modern human) double half <PATH_TO_DATA>/VSM001_MT_VSM001.A0101.MT1.1_L1_R1.fastq.gz NA NA ERR11770515.fastq.gz NA |
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packages/2023_Ferraz_NatureEcologyEvolution/2023_Ferraz_NatureEcologyEvolution.tsv_patch.sh
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -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} |
2 changes: 2 additions & 0 deletions
2
packages/2023_Ferraz_NatureEcologyEvolution/script_versions.txt
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,2 @@ | ||
| create_eager_input.sh: 0.2.1dev | ||
| source_me.sh for initial TSV: 0.2.3dev |
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