Merge pull request #14 from poseidon-framework/2022_Fischer_Gauls

2022_Fischer_Gauls

2022_Fischer_Gauls/2022_Fischer_Gauls.bib

@@ -0,0 +1,31 @@
+@ARTICLE{FischerIScience2022,
+  title     = "{Origin and mobility of Iron Age Gaulish groups in present-day
+               France revealed through archaeogenomics}",
+  author    = "Fischer, Claire-Elise and Pemonge, Marie-Hélène and Ducoussau,
+               Isaure and Arzelier, Ana and Rivollat, Maïté and Santos, Frederic
+               and Barrand Emam, Hélène and Bertaud, Alexandre and Beylier,
+               Alexandre and Ciesielski, Elsa and Dedet, Bernard and Desenne,
+               Sophie and Duday, Henri and Chenal, Fanny and Gailledrat, Eric
+               and Goepfert, Sébastien and Gorgé, Olivier and Gorgues, Alexis
+               and Kuhnle, Gertrud and Lambach, François and Lefort, Anthony and
+               Mauduit, Amandine and Maziere, Florent and Oudry, Sophie and
+               Paresys, Cécile and Pinard, Estelle and Plouin, Suzanne and
+               Richard, Isabelle and Roth-Zehner, Muriel and Roure, Réjane and
+               Thevenet, Corinne and Thomas, Yohann and Rottier, Stéphane and
+               Deguilloux, Marie-France and Pruvost, Mélanie",
+  journal   = "iScience",
+  publisher = "Elsevier BV",
+  volume    =  25,
+  number    =  4,
+  pages     =  104094,
+  month     =  apr,
+  year      =  2022,
+  url       = "http://dx.doi.org/10.1016/j.isci.2022.104094",
+  keywords  = "Biological sciences; Evolutionary biology; Genetics; Genomics;
+               Paleobiology; Paleogenetics",
+  doi       = "10.1016/j.isci.2022.104094",
+  pmc       = "PMC8983337",
+  pmid      =  35402880,
+  issn      = "2589-0042",
+  language  = "en"
+}

2022_Fischer_Gauls/2022_Fischer_Gauls.fam

@@ -0,0 +1,49 @@
+French_IA_North	BLH447_MNT	0	0	2	0
+French_IA_Paris_Basin	GLN29-A_MNT	0	0	2	0
+French_IA_Paris_Basin	GLN32_MNT	0	0	1	0
+French_EIA_Alsace	CROI1-4_MNT	0	0	1	0
+French_IA_Paris_Basin	GLN126A_MNT	0	0	1	0
+French_LIA_Alsace	SCPG2_MNT	0	0	2	0
+French_IA_Champagne	BUCH48-1_MNT	0	0	1	0
+French_IA_North	Att52-2_MNT	0	0	2	0
+French_IA_North	VAS79-2_MNT	0	0	1	0
+French_IA_South	BES1154_MNT	0	0	2	0
+French_IA_South	Pech9_MNT	0	0	2	0
+French_IA_South	PEY73_MNT	0	0	2	0
+French_IA_South	Pech3_MNT	0	0	1	0
+French_IA_South	CLR23_MNT	0	0	1	0
+French_LIA_Alsace	WET429_MNT	0	0	1	0
+French_IA_Champagne	BUCH82_MNT	0	0	2	0
+French_IA_Paris_Basin	GDF1341_MNT	0	0	2	0
+French_IA_South	CLR24_MNT	0	0	1	0
+French_IA_South	CLR31_MNT	0	0	1	0
+French_LIA_Alsace_o	Col239_MNT	0	0	1	0
+French_IA_Champagne	BUCH48-2_MNT	0	0	1	0
+French_LIA_Alsace	ERS83-2_MNT	0	0	1	0
+French_IA_Champagne	CHF106_MNT	0	0	1	0
+French_BA_Paris_Basin	BPV1445_MNT	0	0	2	0
+French_EIA_Alsace	CROI11_MNT	0	0	2	0
+French_IA_North	Att27_MNT	0	0	2	0
+French_EIA_Alsace	CROI12-2_MNT	0	0	2	0
+French_IA_Paris_Basin	GLN141_MNT	0	0	1	0
+French_IA_Normandy	UN19_MNT	0	0	1	0
+French_IA_Paris_Basin	GLN126B_MNT	0	0	1	0
+French_IA_South	CLR44_MNT	0	0	1	0
+French_IA_South	BES1096B_MNT	0	0	1	0
+French_IA_North	Att3_MNT	0	0	1	0
+French_IA_South	bES1249_MNT	0	0	1	0
+French_EIA_Alsace	Gox287_MNT	0	0	1	0
+French_IA_Normandy	UN129_MNT	0	0	1	0
+French_BA_Paris_Basin	BPV1455_MNT	0	0	1	0
+French_IA_North	BFT228_MNT	0	0	1	0
+French_IA_North	PAL170_MNT	0	0	2	0
+French_LIA_Alsace	Col330_MNT	0	0	1	0
+French_IA_North	VAS75_MNT	0	0	2	0
+French_IA_South	PT7_MNT	0	0	2	0
+French_IA_Normandy	UN85_MNT	0	0	1	0
+French_IA_Champagne	ISL6950_MNT	0	0	1	0
+French_IA_South	CLR35_MNT	0	0	1	0
+French_IA_Paris_Basin	GDF1348_MNT	0	0	1	0
+French_IA_Paris_Basin	GDF1264_MNT	0	0	1	0
+French_IA_Paris_Basin	GDF1231_MNT	0	0	2	0
+French_IA_Paris_Basin	GDF1349B_MNT	0	0	2	0

2022_Fischer_Gauls/CHANGELOG.md

@@ -0,0 +1,7 @@
+- V 0.1.7: Update bibFile: pretty print
+- V 0.1.6: Add contributor
+- V 0.1.5: Remove empty columns from janno
+- V 0.1.4: Update bibFile
+- V 0.1.3: Add janno info collected by @Kavlahkaff. Mirror info to fam file.
+- V 0.1.2: Add BibTex info. Add contributor. Add description.
+- V 0.1.1: Automatic update of janno file from Minotaur processing.

2022_Fischer_Gauls/POSEIDON.yml

@@ -0,0 +1,29 @@
+poseidonVersion: 2.7.1
+title: 2022_Fischer_Gauls
+description: Origin and mobility of Iron Age Gaulish groups in present-day France
+  revealed through archaeogenomics
+contributor:
+- name: Thiseas C. Lamnidis
+  email: [email protected]
+  orcid: 0000-0003-4485-8570
+- name: Luca Berndt Thale-Bombien
+  email: [email protected]
+packageVersion: 0.1.7
+lastModified: 2024-12-06
+genotypeData:
+  format: PLINK
+  genoFile: 2022_Fischer_Gauls.bed
+  genoFileChkSum: 8a5db45e612a6b9ab4b576199e613428
+  snpFile: 2022_Fischer_Gauls.bim
+  snpFileChkSum: 433fa85a23f3123bade02348e4628b75
+  indFile: 2022_Fischer_Gauls.fam
+  indFileChkSum: b4826484b98a96e154356d1f90be3cbb
+  snpSet: 1240K
+jannoFile: 2022_Fischer_Gauls.janno
+jannoFileChkSum: 6759105e1d193ea065c4fed9e35d4de5
+sequencingSourceFile: 2022_Fischer_Gauls.ssf
+sequencingSourceFileChkSum: 0d5c665a18728ad8757126dfeb76df64
+bibFile: 2022_Fischer_Gauls.bib
+bibFileChkSum: 0aabf7650b1d841e5b32af8584c1cb9e
+readmeFile: README.md
+changelogFile: CHANGELOG.md

2022_Fischer_Gauls/README.md

@@ -0,0 +1,34 @@
+# 2022_Fischer_Gauls
+This package was created on 2024-05-29 and was processed using the following versions:
+ - nf-core/eager version:  2.4.6
+ - Minotaur config version: 0.2.1dev
+ - CaptureType profile: 1240K
+ - CaptureType config version: 0.2.2dev
+ - Config template version: 0.3.0dev
+ - Package config version: 0.3.0dev
+ - Minotaur-packager version: 0.3.0dev
+ - populate_janno.py version: 0.3.2dev
+
+## Mirror Group_Name and Genetic_Sex from janno to fam
+```bash
+paste -d "\t" 2022_Fischer_Gauls/2022_Fischer_Gauls.fam <(cut -f 1-3 2022_Fischer_Gauls/2022_Fischer_Gauls.janno |tail -n +2) | \
+  awk '
+  BEGIN{
+    OFS=IFS="\t"
+  }
+  {
+    $1=$9
+    if ($8 == "M") {
+      $5=1
+    } else if ($8 == "F") {
+      $5=2
+    }
+    print $1,$2,$3,$4,$5,$6
+  }
+  ' > tmp.fam
+## Cannot overwrite in the same command that reads in the file, so an extra mv is needed.
+mv tmp.fam 2022_Fischer_Gauls/2022_Fischer_Gauls.fam
+
+## trident version: 1.5.4.0
+trident rectify --packageVersion Patch --logText "Add janno info collected by @Kavlahkaff. Mirror info to fam file."  --checksumAll -d 2022_Fischer_Gauls
+```