Add 2023_Ferraz_NatureEcologyEvolution

2023_Ferraz_NatureEcologyEvolution/2023_Ferraz_NatureEcologyEvolution.bib

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+@ARTICLE{2023FerrazNatureEcologyEvolution,
+  title     = "{Genomic history of coastal societies from eastern South America}",
+  author    = "Ferraz, Tiago and Suarez Villagran, Ximena and Nägele, Kathrin
+               and Radzevičiūtė, Rita and Barbosa Lemes, Renan and
+               Salazar-García, Domingo C and Wesolowski, Verônica and Lopes
+               Alves, Marcony and Bastos, Murilo and Rapp Py-Daniel, Anne and
+               Pinto Lima, Helena and Mendes Cardoso, Jéssica and Estevam,
+               Renata and Liryo, Andersen and Guimarães, Geovan M and Figuti,
+               Levy and Eggers, Sabine and Plens, Cláudia R and Azevedo Erler,
+               Dionne Miranda and Valadares Costa, Henrique Antônio and da Silva
+               Erler, Igor and Koole, Edward and Henriques, Gilmar and Solari,
+               Ana and Martin, Gabriela and Serafim Monteiro da Silva, Sérgio
+               Francisco and Kipnis, Renato and Müller, Letícia Morgana and
+               Ferreira, Mariane and Carvalho Resende, Janine and Chim, Eliane
+               and da Silva, Carlos Augusto and Borella, Ana Claudia and Tomé,
+               Tiago and Müller Plumm Gomes, Lisiane and Barros Fonseca, Diego
+               and Santos da Rosa, Cassia and de Moura Saldanha, João Darcy and
+               Costa Leite, Lúcio and Cunha, Claudia M S and Viana, Sibeli
+               Aparecida and Ozorio Almeida, Fernando and Klokler, Daniela and
+               Fernandes, Henry Luydy Abraham and Talamo, Sahra and DeBlasis,
+               Paulo and Mendonça de Souza, Sheila and de Paula Moraes, Claide
+               and Elias Oliveira, Rodrigo and Hünemeier, Tábita and Strauss,
+               André and Posth, Cosimo",
+  journal   = "Nature ecology \& evolution",
+  publisher = "Nature Publishing Group",
+  volume    =  7,
+  number    =  8,
+  pages     = "1315--1330",
+  month     =  aug,
+  year      =  2023,
+  url       = "https://www.nature.com/articles/s41559-023-02114-9",
+  doi       = "10.1038/s41559-023-02114-9",
+  pmc       = "PMC10406606",
+  pmid      =  37524799,
+  issn      = "2397-334X,2397-334X",
+  language  = "en"
+}

2023_Ferraz_NatureEcologyEvolution/2023_Ferraz_NatureEcologyEvolution.fam

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+Capelinha	CAP007_MNT	0	0	1	0
+Cabeçuda	CBE003_MNT	0	0	1	0
+Cabeçuda	CBE004_MNT	0	0	1	0
+CubatãoI	CUB002_MNT	0	0	2	0
+CubatãoI	CUB008_MNT	0	0	2	0
+Limão	EPS001_MNT	0	0	2	0
+Limão	EPS002_MNT	0	0	1	0
+Limão	EPS003_MNT	0	0	2	0
+Limão	EPS004_MNT	0	0	1	0
+Limão	EPS005_MNT	0	0	2	0
+Limão	EPS011_MNT	0	0	2	0
+GalhetaIV	GA4002_MNT	0	0	2	0
+JabuticabeiraII	JBT001_MNT	0	0	2	0
+JabuticabeiraII	JBT002_MNT	0	0	1	0
+JabuticabeiraII	JBT009_MNT	0	0	1	0
+JabuticabeiraII	JBT010_MNT	0	0	2	0
+JabuticabeiraII	JBT011_MNT	0	0	1	0
+JabuticabeiraII	JBT012_MNT	0	0	1	0
+JabuticabeiraII	JBT013_MNT	0	0	1	0
+JabuticabeiraII	JBT014_MNT	0	0	2	0
+JabuticabeiraII	JBT015_MNT	0	0	2	0
+JabuticabeiraII	JBT018_MNT	0	0	2	0
+JabuticabeiraII	JBT019_MNT	0	0	2	0
+JabuticabeiraII	JBT020_MNT	0	0	1	0
+JabuticabeiraII	JBT021_MNT	0	0	1	0
+JabuticabeiraII	JBT022_MNT	0	0	2	0
+JabuticabeiraII	JBT023_MNT	0	0	2	0
+JabuticabeiraII	JBT025_MNT	0	0	1	0
+JabuticabeiraII	JBT026_MNT	0	0	1	0
+LocaDoSuin	PAI001_MNT	0	0	1	0
+Palmeiras_Xingu	PLM001_MNT	0	0	1	0
+Kaingang	SAM014_MNT	0	0	1	0
+PedraDoAlexandre_2	TDA002_MNT	0	0	1	0
+Vau_Una	VSM001_MNT	0	0	1	0

2023_Ferraz_NatureEcologyEvolution/CHANGELOG.md

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+- V 0.3.1: Add bibFile and Publication info.
+- V 0.3.0: Add janno info collected by @Kavlahkaff. Mirror info to fam file.Add @Kavlahkaff as Contributor. Update checksums.
+- 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_Ferraz_NatureEcologyEvolution/POSEIDON.yml

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+poseidonVersion: 2.7.1
+title: 2023_Ferraz_NatureEcologyEvolution
+description: Empty package template. Please add a description
+contributor:
+- name: Thiseas C. Lamnidis
+  email: [email protected]
+- name: Luca Thale-Bombien
+  email: [email protected]
+packageVersion: 0.3.1
+lastModified: 2024-12-13
+genotypeData:
+  format: PLINK
+  genoFile: 2023_Ferraz_NatureEcologyEvolution.bed
+  genoFileChkSum: 41f64d7dca8f3dbcbccaf99b2d456aa2
+  snpFile: 2023_Ferraz_NatureEcologyEvolution.bim
+  snpFileChkSum: 433fa85a23f3123bade02348e4628b75
+  indFile: 2023_Ferraz_NatureEcologyEvolution.fam
+  indFileChkSum: b59de35142b2831413188ed8f22f1d4a
+  snpSet: 1240K
+jannoFile: 2023_Ferraz_NatureEcologyEvolution.janno
+jannoFileChkSum: 792f8711600cc551a2696492a01207a8
+sequencingSourceFile: 2023_Ferraz_NatureEcologyEvolution.ssf
+sequencingSourceFileChkSum: a00efeb96763bbfa1356954c00ba3174
+bibFile: 2023_Ferraz_NatureEcologyEvolution.bib
+bibFileChkSum: 5f1d10005b0df45de56ea0750264cd34
+readmeFile: README.md
+changelogFile: CHANGELOG.md

2023_Ferraz_NatureEcologyEvolution/README.md

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+# 2023_Ferraz_NatureEcologyEvolution
+This package was created on 2024-12-13 and was processed using the following versions:
+ - nf-core/eager version:  2.5.1
+ - Minotaur config version: 0.4.0dev
+ - CaptureType profile: 1240K
+ - CaptureType config version: 0.2.2dev
+ - Config template version: 0.3.0dev
+ - Package config version: 0.3.0dev
+ - Minotaur-packager version: 0.4.3dev
+ - populate_janno.py version: 0.5.0dev
+
+## Mirror Group_Name and Genetic_Sex from janno to fam
+```bash
+package_name="2023_Ferraz_NatureEcologyEvolution"
+paste -d "\t" ${package_name}/${package_name}.fam <(cut -f 1-3 ${package_name}/${package_name}.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 ${package_name}/${package_name}.fam
+
+## trident version: 1.5.4.0
+trident rectify --packageVersion Patch --logText "Add janno info collected by @Kavlahkaff. Mirror info to fam file.Add @Kavlahkaff as Contributor."  --checksumAll -d ${package_name}
+```