Add 2023_Salazar_MachuPicchu

2023_Salazar_MachuPicchu/2023_Salazar_MachuPicchu.bib

@@ -0,0 +1,17 @@
+@ARTICLE{SalazarScienceAdvances2023,
+  title = "{Insights into the genetic histories and lifeways of Machu Picchu's occupants}",
+  author = "Salazar, Lucy and Burger, Richard and Forst, Janine and Barquera, Rodrigo and Nesbitt, Jason and Calero, Jorge and Washburn, Eden and Verano, John and Zhu, Kimberly and Sop, Korey and Kassadjikova, Kalina and Ibarra Asencios, Bebel and Davidson, Roberta and Bradley, Brenda and Krause, Johannes and Fehren-Schmitz, Lars",
+  journal = "Science advances",
+  publisher = "American Association for the Advancement of Science",
+  volume =  9,
+  number =  30,
+  pages = "eadg3377",
+  month =  jul,
+  year =  2023,
+  url = "https://www.science.org/doi/10.1126/sciadv.adg3377",
+  doi = "10.1126/sciadv.adg3377",
+  pmc = "PMC11318671",
+  pmid =  37494435,
+  issn = "2375-2548",
+  language = "en"
+}

2023_Salazar_MachuPicchu/2023_Salazar_MachuPicchu.fam

@@ -0,0 +1,56 @@
+Urubamba_Valley	CCA-7-2_MNT	0	0	2	0
+Cusco_City	KCA-1108_MNT	0	0	2	0
+Cusco_City	KCA-1298_MNT	0	0	2	0
+Cusco_City	KCA-1364_MNT	0	0	2	0
+Cusco_City	KCA-3089_MNT	0	0	2	0
+Espinar_Province	KMA-15A-1_MNT	0	0	2	0
+Espinar_Province	KMA-19-1_MNT	0	0	2	0
+Espinar_Province	KMA-2-2_MNT	0	0	2	0
+Espinar_Province	KMA-28-1_MNT	0	0	2	0
+Urubamba_Valley	MP107B_MNT	0	0	2	0
+Urubamba_Valley	MP13_MNT	0	0	2	0
+Urubamba_Valley	MP23_MNT	0	0	2	0
+Urubamba_Valley	MP27_MNT	0	0	1	0
+Urubamba_Valley	MP31A_MNT	0	0	0	0
+Urubamba_Valley	MP32_MNT	0	0	0	0
+Urubamba_Valley	MP33_MNT	0	0	1	0
+Urubamba_Valley	MP3a_MNT	0	0	0	0
+Urubamba_Valley	MP42A_MNT	0	0	2	0
+Urubamba_Valley	MP42B_MNT	0	0	0	0
+Urubamba_Valley	MP42C_MNT	0	0	2	0
+Urubamba_Valley	MP45A_MNT	0	0	1	0
+Urubamba_Valley	MP48B_MNT	0	0	1	0
+Urubamba_Valley	MP4B_MNT	0	0	2	0
+Urubamba_Valley	MP4D_MNT	0	0	2	0
+Urubamba_Valley	MP4E_MNT	0	0	0	0
+Urubamba_Valley	MP4f_MNT	0	0	2	0
+Urubamba_Valley	MP4i_MNT	0	0	1	0
+Urubamba_Valley	MP50A_MNT	0	0	0	0
+Urubamba_Valley	MP51_MNT	0	0	2	0
+Urubamba_Valley	MP53A_MNT	0	0	2	0
+Urubamba_Valley	MP55_MNT	0	0	2	0
+Urubamba_Valley	MP5A_MNT	0	0	2	0
+Urubamba_Valley	MP61_MNT	0	0	2	0
+Urubamba_Valley	MP63_MNT	0	0	1	0
+Urubamba_Valley	MP65B_MNT	0	0	2	0
+Urubamba_Valley	MP71_MNT	0	0	2	0
+Urubamba_Valley	MP77A_MNT	0	0	2	0
+Urubamba_Valley	MP78A_MNT	0	0	0	0
+Urubamba_Valley	MP80_MNT	0	0	2	0
+Urubamba_Valley	MP82_MNT	0	0	0	0
+Urubamba_Valley	MP84A_MNT	0	0	2	0
+Urubamba_Valley	MP84C_MNT	0	0	1	0
+Urubamba_Valley	OTT-1144_MNT	0	0	1	0
+Urubamba_Valley	OTT-1160_MNT	0	0	1	0
+Urubamba_Valley	OTT-1165_MNT	0	0	2	0
+Urubamba_Valley	OTT-1174_MNT	0	0	2	0
+Urubamba_Valley	OTT-1187_MNT	0	0	1	0
+Cusco_City	QKI-21-1_MNT	0	0	1	0
+Cusco_City	QKI-4_MNT	0	0	2	0
+Cusco_City	QKI-809_MNT	0	0	1	0
+Cusco_City	QKI-9-3_MNT	0	0	2	0
+Cusco_City	SHN-212_MNT	0	0	1	0
+Cusco_City	SHN-355_MNT	0	0	1	0
+Cusco_City	SHN-492_MNT	0	0	2	0
+Cusco_City	SHN-575_MNT	0	0	1	0
+Cusco_City	SHN-902_MNT	0	0	2	0

2023_Salazar_MachuPicchu/CHANGELOG.md

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+- V 0.2.2: Add BibFile and publication info
+- V 0.2.1: Add janno info collected by @Kavlahkaff. Mirror info to fam file.
+- V 0.2.0: Rearrange Poseidon_IDs alphabetically.
+- V 0.1.2: Automatic update of janno file from Minotaur processing.
+- V 0.1.1: Added self as contributor to package.

2023_Salazar_MachuPicchu/POSEIDON.yml

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+poseidonVersion: 2.7.1
+title: 2023_Salazar_MachuPicchu
+description: Empty package template. Please add a description
+contributor:
+- name: Thiseas C. Lamnidis
+  email: [email protected]
+packageVersion: 0.2.2
+lastModified: 2024-11-28
+genotypeData:
+  format: PLINK
+  genoFile: 2023_Salazar_MachuPicchu.bed
+  genoFileChkSum: 97f258ab42087b1906d212517b0cca89
+  snpFile: 2023_Salazar_MachuPicchu.bim
+  snpFileChkSum: 433fa85a23f3123bade02348e4628b75
+  indFile: 2023_Salazar_MachuPicchu.fam
+  indFileChkSum: 4f17963dddce26ffe81f56a01563decf
+  snpSet: 1240K
+jannoFile: 2023_Salazar_MachuPicchu.janno
+jannoFileChkSum: 65ef1882cd8884f3031bd610d4eb2863
+sequencingSourceFile: 2023_Salazar_MachuPicchu.ssf
+sequencingSourceFileChkSum: 07d1d6ce1b8e976615cf530e543075bb
+bibFile: 2023_Salazar_MachuPicchu.bib
+bibFileChkSum: efbcf469f724eba20acfa0d4c8425b26
+readmeFile: README.md
+changelogFile: CHANGELOG.md

2023_Salazar_MachuPicchu/README.md

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+# 2023_Salazar_MachuPicchu
+This package was created on 2024-09-06 and was processed using the following versions:
+ - nf-core/eager version:  2.5.1
+ - Minotaur config version: 0.2.1dev
+ - CaptureType profile: 1240K
+ - CaptureType config version: 0.2.2dev
+ - Config template version: 0.3.0dev
+ - Package config version: 0.3.1
+ - Minotaur-packager version: 0.4.2dev
+ - populate_janno.py version: 0.3.3dev
+
+## Mirror Group_Name and Genetic_Sex from janno to fam
+```bash
+paste -d "\t" 2023_Salazar_MachuPicchu/2023_Salazar_MachuPicchu.fam <(cut -f 1-3 2023_Salazar_MachuPicchu/2023_Salazar_MachuPicchu.janno |tail -n +2) | \
+  awk '
+  BEGIN{
+    OFS=IFS="\t"
+  }
+  {
+    split($9,groups,";");
+    $1=groups[1]
+    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 2023_Salazar_MachuPicchu/2023_Salazar_MachuPicchu.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 2023_Salazar_MachuPicchu
+```