Add package: 2022_Guellil_Herpes

packages/2022_Guellil_Herpes/2022_Guellil_Herpes.config

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+// 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
+  */
+}

packages/2022_Guellil_Herpes/2022_Guellil_Herpes.janno

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+Poseidon_ID	Genetic_Sex	Group_Name	Individual_ID	Species	Alternative_IDs	Alternative_IDs_Context	Relation_To	Relation_Degree	Relation_Type	Collection_ID	Custodian_Institution	Cultural_Era	Cultural_Era_URL	Archaeological_Culture	Archaeological_Culture_URL	Country	Country_ISO	Location	Site	Latitude	Longitude	Date_Type	Date_C14_Labnr	Date_C14_Uncal_BP	Date_C14_Uncal_BP_Err	Date_BC_AD_Start	Date_BC_AD_Median	Date_BC_AD_Stop	Date_Note	Chromosomal_Anomalies	MT_Haplogroup	Y_Haplogroup	Source_Material	Nr_Libraries	Library_Names	Capture_Type	UDG	Library_Built	Genotype_Ploidy	Data_Preparation_Pipeline_URL	Endogenous	Nr_SNPs	Coverage_on_Target_SNPs	Damage	Contamination	Contamination_Err	Contamination_Meas	Genetic_Source_Accession_IDs	Primary_Contact	Publication	Note	Keywords
+BRO001	M	Russia_Brody_Nevolino_LIA	BRO001	Homo sapiens	n/a	n/a	n/a	n/a	n/a	BRO001	Estonian Biocentre, Institute of Genomics, University of Tartu	Late Iron Age	https://en.wikipedia.org/wiki/Iron_Age_Europe	Nevolino	https://www.academia.edu/8752234/The_Nevolino_culture_in_the_context_of_the_7th_century_East_West_trade_the_finds_from_Bartym	Russia	RU	Brody, Perm Krai	Brodovsky	57.95095	56.45792	C14	Poz-98180	1680	35	253	n/a	530	n/a	n/a	U4a1d	R1b	tooth	n/a	n/a	Shotgun	minus	ds	haploid	n/a	n/a	n/a	n/a	n/a	n/a	n/a	n/a	PRJEB46097	n/a	GuellilScienceAdvances2022	n/a	n/a
+EDI111	F	England_Cambridgeshire_Saxon_EMA	EDI111	Homo sapiens	n/a	n/a	n/a	n/a	n/a	Burial 38, Skeleton 127A	Estonian Biocentre, Institute of Genomics, University of Tartu	Early Medieval	https://en.wikipedia.org/wiki/Early_Middle_Ages	Anglo-Saxon	https://en.wikipedia.org/wiki/Anglo-Saxons	England	GB	Edix Hill, Cambridgeshire	Barrington A	52.13018	0.02987	C14	UBA-44319	1520	27	437	n/a	636	n/a	n/a	H1b	n/a	tooth	n/a	n/a	Shotgun	minus	ds	haploid	n/a	n/a	n/a	n/a	n/a	n/a	n/a	n/a	PRJEB46097	n/a	GuellilScienceAdvances2022	n/a	n/a
+JDS005	M	England_Cambridge_LMA	JDS005	Homo sapiens	n/a	n/a	n/a	n/a	n/a	Burial 2710, Skeleton 1232	Estonian Biocentre, Institute of Genomics, University of Tartu	Late Medieval	https://en.wikipedia.org/wiki/Late_Middle_Ages	n/a	n/a	England	GB	Cambridge	Hospital of St. John	52.20785	0.11859	Contextual	n/a	n/a	n/a	1350	n/a	1450	Archaeological Period	n/a	T1a1	J1a2	tooth	n/a	n/a	Shotgun	minus	ds	haploid	n/a	n/a	n/a	n/a	n/a	n/a	n/a	n/a	PRJEB46097	n/a	GuellilScienceAdvances2022	n/a	n/a
+RIJ001	M	Netherlands_AlphenaandenRijn_EarlyModern	RIJ001	Homo sapiens	n/a	n/a	n/a	n/a	n/a	Burial 11, Skeleton 16	Estonian Biocentre, Institute of Genomics, University of Tartu	Early Modern	https://en.wikipedia.org/wiki/Early_modern_Europe	n/a	n/a	Netherlands	NL	South Holland	Alphen aan den Rijn	52.12947	4.65316	Contextual	n/a	n/a	n/a	1600	n/a	1700	Archaeological Period	n/a	H	I2	tooth	n/a	n/a	Shotgun	minus	ds	haploid	n/a	n/a	n/a	n/a	n/a	n/a	n/a	n/a	PRJEB46097	n/a	GuellilScienceAdvances2022	n/a	n/a