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Merge pull request #8 from poseidon-framework/update_Carlhoff2021
Update: 2021_CarlhoffNature
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| // Config template version: 0.1.0dev | ||
| // Keep track of config versions | ||
| minotaur_release='0.2.1' // 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/${minotaur_release}/conf" | ||
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| // Load in main poseidon configuration file with default params and which loads other poseidon-specific profiles | ||
| includeConfig '../../conf/Poseidon.config' | ||
| // This configuration file is designed to be a used with the nf-core/eager pipeline. | ||
| // Instead of having to specify all other configurations for the Minotaur pipeline | ||
| // on runtime, they are all contained in this file and loaded automatically upon | ||
| // specifying this config file during runtime. Additionally, any parameters that | ||
| // need to be altered from the defaults can be specified here. | ||
| // | ||
| // The intention is to make it easy for users to understand and reproduce the output | ||
| // from processing with the Minotaur workflow processing from the contents of a | ||
| // single file. | ||
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| // Load configuration profiles. They are loaded from the minotaur_config_base URL, main branch. | ||
| includeConfig "${minotaur_config_base}/EVA_cluster.config" // Cluster-specific configurations for nf-core/eager execution at MPI-EVA | ||
| includeConfig "${minotaur_config_base}/Minotaur.config" // Default nf-core/eager parameters for Minotaur processing. | ||
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| // The following config file specifies BED files for on-target endogenous DNA calculation and mean coverage as well as pseudohaploid genotyping. | ||
| // TODO: Select the appropriate config for the CaptureType of the package. | ||
| includeConfig "${minotaur_config_base}/CaptureType_profiles/1240K.config" | ||
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| 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)" | ||
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| /* | ||
| 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. | ||
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| For information on all available parameters and their default values see: | ||
| https://nf-co.re/eager/2.4.6/parameters | ||
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| You can see the default values for parameters within poseidon-eager at: | ||
| https://github.com/poseidon-framework/poseidon-eager/blob/main/conf/Minotaur.config | ||
| */ | ||
| } |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1,17 +1,11 @@ | ||
| Sample_Name Library_ID Lane Colour_Chemistry SeqType Organism Strandedness UDG_Treatment R1 R2 BAM | ||
| GUP001 GUP001_GUP001.A0101 1 4 SE Homo sapiens (modern human) double half <PATH_TO_DATA>/GUP001_GUP001.A0101_L1_R1.fastq.gz NA NA | ||
| GUP001 GUP001_GUP001.A0101 2 4 SE Homo sapiens (modern human) double half <PATH_TO_DATA>/GUP001_GUP001.A0101_L2_R1.fastq.gz NA NA | ||
| GUP001 GUP001_GUP001.A0101 3 4 SE Homo sapiens (modern human) double half <PATH_TO_DATA>/GUP001_GUP001.A0101_L3_R1.fastq.gz NA NA | ||
| GUP001 GUP001_GUP001.A0101 4 4 SE Homo sapiens (modern human) double half <PATH_TO_DATA>/GUP001_GUP001.A0101_L4_R1.fastq.gz NA NA | ||
| GUP001_SG GUP001_SG_GUP001.A0101 1 4 SE Homo sapiens (modern human) double half <PATH_TO_DATA>/GUP001_SG_GUP001.A0101_L1_R1.fastq.gz NA NA | ||
| GUP001 GUP001_GUP001.A0101 5 4 SE Homo sapiens (modern human) double half <PATH_TO_DATA>/GUP001_GUP001.A0101_L5_R1.fastq.gz NA NA | ||
| GUP001_TF GUP001_TF_GUP001.A0101 1 4 SE Homo sapiens (modern human) double half <PATH_TO_DATA>/GUP001_TF_GUP001.A0101_L1_R1.fastq.gz NA NA | ||
| GUP001 GUP001_GUP001.A0101 6 4 SE Homo sapiens (modern human) double half <PATH_TO_DATA>/GUP001_GUP001.A0101_L6_R1.fastq.gz NA NA | ||
| GUP001_TF GUP001_TF_GUP001.A0101 2 4 SE Homo sapiens (modern human) double half <PATH_TO_DATA>/GUP001_TF_GUP001.A0101_L2_R1.fastq.gz NA NA | ||
| GUP001 GUP001_GUP001.A0101 7 4 SE Homo sapiens (modern human) double half <PATH_TO_DATA>/GUP001_GUP001.A0101_L7_R1.fastq.gz NA NA | ||
| GUP001_TF GUP001_TF_GUP001.A0101 3 4 SE Homo sapiens (modern human) double half <PATH_TO_DATA>/GUP001_TF_GUP001.A0101_L3_R1.fastq.gz NA NA | ||
| GUP001_ss GUP001_ss_GUP001.A0102_ss 1 4 SE Homo sapiens (modern human) single none <PATH_TO_DATA>/GUP001_ss_GUP001.A0102_ss_L1_R1.fastq.gz NA NA | ||
| GUP001_ss GUP001_ss_GUP001.A0102_ss 2 4 SE Homo sapiens (modern human) single none <PATH_TO_DATA>/GUP001_ss_GUP001.A0102_ss_L2_R1.fastq.gz NA NA | ||
| GUP001_SG_ss GUP001_SG_ss_GUP001.A0102_ss 1 4 SE Homo sapiens (modern human) single none <PATH_TO_DATA>/GUP001_SG_ss_GUP001.A0102_ss_L1_R1.fastq.gz NA NA | ||
| GUP001_ss GUP001_ss_GUP001.A0102_ss 3 4 SE Homo sapiens (modern human) single none <PATH_TO_DATA>/GUP001_ss_GUP001.A0102_ss_L3_R1.fastq.gz NA NA | ||
| GUP001_TF_ss GUP001_TF_ss_GUP001.A0102_ss 1 4 SE Homo sapiens (modern human) single none <PATH_TO_DATA>/GUP001_TF_ss_GUP001.A0102_ss_L1_R1.fastq.gz NA NA | ||
| Sample_Name Library_ID Lane Colour_Chemistry SeqType Organism Strandedness UDG_Treatment R1 R2 BAM R1_target_file R2_target_file | ||
| GUP001 GUP001_GUP001.A0101 1 4 SE Homo sapiens (modern human) double half <PATH_TO_DATA>/GUP001_GUP001.A0101_L1_R1.fastq.gz NA NA ERR5490520.fastq.gz NA | ||
| GUP001 GUP001_GUP001.A0101 2 4 SE Homo sapiens (modern human) double half <PATH_TO_DATA>/GUP001_GUP001.A0101_L2_R1.fastq.gz NA NA ERR5490521.fastq.gz NA | ||
| GUP001 GUP001_GUP001.A0101 3 4 SE Homo sapiens (modern human) double half <PATH_TO_DATA>/GUP001_GUP001.A0101_L3_R1.fastq.gz NA NA ERR5490522.fastq.gz NA | ||
| GUP001 GUP001_GUP001.A0101 4 4 SE Homo sapiens (modern human) double half <PATH_TO_DATA>/GUP001_GUP001.A0101_L4_R1.fastq.gz NA NA ERR5490523.fastq.gz NA | ||
| GUP001 GUP001_GUP001.A0101 5 4 SE Homo sapiens (modern human) double half <PATH_TO_DATA>/GUP001_GUP001.A0101_L5_R1.fastq.gz NA NA ERR5490524.fastq.gz NA | ||
| GUP001 GUP001_GUP001.A0101 6 4 SE Homo sapiens (modern human) double half <PATH_TO_DATA>/GUP001_GUP001.A0101_L6_R1.fastq.gz NA NA ERR5490525.fastq.gz NA | ||
| GUP001 GUP001_GUP001.A0101 7 4 SE Homo sapiens (modern human) double half <PATH_TO_DATA>/GUP001_GUP001.A0101_L7_R1.fastq.gz NA NA ERR5490526.fastq.gz NA | ||
| GUP001_ss GUP001_ss_GUP001.A0102_ss 1 4 SE Homo sapiens (modern human) single none <PATH_TO_DATA>/GUP001_ss_GUP001.A0102_ss_L1_R1.fastq.gz NA NA ERR5490527.fastq.gz NA | ||
| GUP001_ss GUP001_ss_GUP001.A0102_ss 2 4 SE Homo sapiens (modern human) single none <PATH_TO_DATA>/GUP001_ss_GUP001.A0102_ss_L2_R1.fastq.gz NA NA ERR5490528.fastq.gz NA | ||
| GUP001_ss GUP001_ss_GUP001.A0102_ss 3 4 SE Homo sapiens (modern human) single none <PATH_TO_DATA>/GUP001_ss_GUP001.A0102_ss_L3_R1.fastq.gz NA NA ERR5490529.fastq.gz NA |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1 +1,2 @@ | ||
| create_eager_input.sh: 0.1.0dev | ||
| create_eager_input.sh: 0.2.1dev | ||
| source_me.sh for initial TSV: 0.2.1dev |