Merge branch '2023_Peltola_VolgaOka' of github.com:poseidon-framework…

…/minotaur-archive into 2023_Peltola_VolgaOka
poseidon-framework · Jul 17, 2024 · 9ecd8f6 · 9ecd8f6
2 parents 38e2149 + 5f107b9
commit 9ecd8f6
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diff --git a/.github/workflows/validation.yml b/.github/workflows/validation.yml
@@ -11,12 +11,12 @@ jobs:
     name: validate packages
     runs-on: ubuntu-latest
     steps:
-        
+
     - name: Install trident
       run: |
         wget https://github.com/poseidon-framework/poseidon-hs/releases/latest/download/trident-Linux
         chmod +x trident-Linux
-        
+
     - name: Clone data repo
       uses: actions/checkout@v3
       with:
@@ -36,3 +36,7 @@ jobs:
     - name: Check if all files have UTF-8 encoding and Unix line endings
       run: ./checkFileEncoding.sh
       working-directory: ./data
+
+    - name: Check if any .janno and .ssf files start with a single or double-quote character
+      run: ./checkQuotes.sh
+      working-directory: ./data
diff --git a/2021_CarlhoffNature/2021_CarlhoffNature.janno b/2021_CarlhoffNature/2021_CarlhoffNature.janno
@@ -1,3 +1,3 @@
-Poseidon_ID	Genetic_Sex	Group_Name	Alternative_IDs	Relation_To	Relation_Degree	Relation_Type	Relation_Note	Collection_ID	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	MT_Haplogroup	Y_Haplogroup	Source_Tissue	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	Contamination_Note	Genetic_Source_Accession_IDs	Primary_Contact	Publication	Note	Keywords	Eager_ID	Individual_ID	RateErrX	RateErrY	RateX	RateY
+Poseidon_ID	Genetic_Sex	Group_Name	Alternative_IDs	Relation_To	Relation_Degree	Relation_Type	Relation_Note	Collection_ID	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	MT_Haplogroup	Y_Haplogroup	Source_Tissue	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	Contamination_Note	Genetic_Source_Accession_IDs	Primary_Contact	Publication	Note	Keywords	Eager_ID	Main_ID	RateErrX	RateErrY	RateX	RateY
 GUP001_MNT	F	Leang_Panninge	n/a	GUP001_ss_MNT	identical	same_as	n/a	30 B. PANNINGE Skull block region 9 petrous	Indonesia	ID	Southern Sulawesi	Leang Panninge	-4.7741	119.9396	C14	Wk-48639	6317	19	-5314	-5265	-5215	n/a	M	n/a	bone_petrous	1	GUP001.A0101	1240K;Shotgun	half	ds	haploid	https://github.com/nf-core/eager/releases/tag/2.4.6	6.762222	272731	n/a	0.4636218846261551	0.11128	3.536035e-14	ANGSD[v0.935]	Nr Snps (per library): 691. Estimate and error are weighted means of values per library. Libraries with fewer than 100 SNPs used in contamination estimation were excluded.	PRJEB43715;ERS5956814;ERR5490520;ERR5490521;ERR5490522;ERR5490523;ERR5490524;ERR5490525;ERR5490526	Selina Carlhoff	CarlhoffNature2021	C14 dates from charcoal and seeds associated with burial; damage for ds SG; mtcontam for ss with AuthentiCT	n/a	GUP001	GUP001	0.007582631999185001	0.001447150678242	0.8115348979428191	0.020098725775262002
 GUP001_ss_MNT	F	Leang_Panninge	n/a	GUP001_MNT	identical	same_as	n/a	30 B. PANNINGE Skull block region 9 petrous	Indonesia	ID	Southern Sulawesi	Leang Panninge	-4.7741	119.9396	C14	Wk-48639	6317	19	-5314	-5265	-5215	n/a	M	n/a	bone_petrous	1	GUP001.A0102	1240K;Shotgun	minus	ss	haploid	https://github.com/nf-core/eager/releases/tag/2.4.6	13.339985	134067	n/a	0.5877457008717157	0.097276	3.860919e-15	ANGSD[v0.935]	Nr Snps (per library): 345. Estimate and error are weighted means of values per library. Libraries with fewer than 100 SNPs used in contamination estimation were excluded.	PRJEB43715;ERS5956814;ERR5490527;ERR5490528;ERR5490529	Selina Carlhoff	CarlhoffNature2021	C14 dates from charcoal and seeds associated with burial; damage for ds SG; mtcontam for ss with AuthentiCT	n/a	GUP001_ss	GUP001	0.008514648295196001	0.0016382538785210002	0.7711635308594431	0.019378750752398
diff --git a/2021_CarlhoffNature/CHANGELOG.md b/2021_CarlhoffNature/CHANGELOG.md
@@ -1,3 +1,4 @@
+- V 1.0.1: rename Individual_ID to Main_ID for consistency
 - V 1.0.0: Bump version for release
 - V 0.1.7: Update .bib
 - V 0.1.6: Add contributor and description

diff --git a/2021_CarlhoffNature/POSEIDON.yml b/2021_CarlhoffNature/POSEIDON.yml
@@ -5,8 +5,8 @@ contributor:
 - name: Thiseas C. Lamnidis
   email: [email protected]
   orcid: 0000-0003-4485-8570
-packageVersion: 1.0.0
-lastModified: 2024-04-08
+packageVersion: 1.0.1
+lastModified: 2024-05-29
 genotypeData:
   format: PLINK
   genoFile: 2021_CarlhoffNature.bed
@@ -17,7 +17,7 @@ genotypeData:
   indFileChkSum: d5982f4cd410501dd26c0b2f2b95a83b
   snpSet: 1240K
 jannoFile: 2021_CarlhoffNature.janno
-jannoFileChkSum: 9b1fc8f11211767fbb5868128327a6cd
+jannoFileChkSum: 38b75f7f7bee6820b4f0a4b56cea064e
 sequencingSourceFile: 2021_CarlhoffNature.ssf
 sequencingSourceFileChkSum: ac4cec11100b5ab343548313c86c68b2
 bibFile: 2021_CarlhoffNature.bib

diff --git a/2021_Saag_EastEuropean/2021_Saag_EastEuropean.janno b/2021_Saag_EastEuropean/2021_Saag_EastEuropean.janno
@@ -1,4 +1,4 @@
-Poseidon_ID	Genetic_Sex	Group_Name	Alternative_IDs	Relation_To	Relation_Degree	Relation_Type	Relation_Note	Collection_ID	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	MT_Haplogroup	Y_Haplogroup	Source_Tissue	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	Contamination_Note	Genetic_Source_Accession_IDs	Primary_Contact	Publication	Note	Keywords	Eager_ID	Individual_ID	RateErrX	RateErrY	RateX	RateY
+Poseidon_ID	Genetic_Sex	Group_Name	Alternative_IDs	Relation_To	Relation_Degree	Relation_Type	Relation_Note	Collection_ID	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	MT_Haplogroup	Y_Haplogroup	Source_Tissue	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	Contamination_Note	Genetic_Source_Accession_IDs	Primary_Contact	Publication	Note	Keywords	Eager_ID	Main_ID	RateErrX	RateErrY	RateX	RateY
 HAN003_MNT	U	Fatyanovo	n/a	n/a	n/a	n/a	n/a	n/a	Russian Federation	RU	Moscow	Khanevo	55.63639	35.89972	n/a	n/a	n/a	n/a	n/a	n/a	n/a	n/a	n/a	n/a	tooth	1	unspecified	Shotgun	minus	ds	haploid	https://github.com/nf-core/eager/releases/tag/2.4.6	99.10002	896	n/a	0.17801590044936053	n/a	n/a	n/a	Nr Snps (per library): 0. Estimate and error are weighted means of values per library. Libraries with fewer than 100 SNPs used in contamination estimation were excluded.	PRJEB40698;ERS5500809;ERR5032514	n/a	SaagScienceAdvances2021	n/a	n/a	HAN003	HAN003	0.11039409610091401	0.13464525869124802	0.45079846344425406	0.44378068581963204
 TIM001_MNT	M	Fatyanovo	n/a	n/a	n/a	n/a	n/a	n/a	Russian Federation	RU	Ivanovo	Timofeyevka	57.13447	39.97571	n/a	n/a	n/a	n/a	n/a	n/a	n/a	n/a	K1b1a1+199	R1a	tooth	1	unspecified	Shotgun	minus	ds	haploid	https://github.com/nf-core/eager/releases/tag/2.4.6	99.571303	16564	n/a	9.598967562986363e-2	n/a	n/a	n/a	Nr Snps (per library): 0. Estimate and error are weighted means of values per library. Libraries with fewer than 100 SNPs used in contamination estimation were excluded.	PRJEB40698;ERS5500830;ERR5032535	n/a	SaagScienceAdvances2021	n/a	n/a	TIM001	TIM001	0.025895105282729	0.028701492605426003	0.46082793745530903	0.375512663170518
 TIM011_MNT	F	Fatyanovo	n/a	n/a	n/a	n/a	n/a	n/a	Russian Federation	RU	Ivanovo	Timofeyevka	57.13447	39.97571	n/a	n/a	n/a	n/a	n/a	n/a	n/a	n/a	U5b2a1a+16311	n/a	tooth	1	unspecified	Shotgun	minus	ds	haploid	https://github.com/nf-core/eager/releases/tag/2.4.6	99.647917	5462	n/a	0.10822709163346614	n/a	n/a	n/a	Nr Snps (per library): 1. Estimate and error are weighted means of values per library. Libraries with fewer than 100 SNPs used in contamination estimation were excluded.	PRJEB40698;ERS5500838;ERR5032543	n/a	SaagScienceAdvances2021	n/a	n/a	TIM011	TIM011	0.061573573867055004	0.009419188399547	0.836002448923796	0.013318226120096002

diff --git a/2021_Saag_EastEuropean/CHANGELOG.md b/2021_Saag_EastEuropean/CHANGELOG.md
@@ -1,3 +1,4 @@
+- V 1.0.1: rename Individual_ID to Main_ID for consistency
 - V 1.0.0: Bump version for release
 - V 0.1.4: Add Country_ISO information
 - V 0.1.3: Fill-in metadata from community-archive: 2021_Saag_EastEuropean-3.2.0

diff --git a/2021_Saag_EastEuropean/POSEIDON.yml b/2021_Saag_EastEuropean/POSEIDON.yml
@@ -6,8 +6,8 @@ contributor:
 - name: Thiseas C. Lamnidis
   email: [email protected]
   orcid: 0000-0003-4485-8570
-packageVersion: 1.0.0
-lastModified: 2024-04-08
+packageVersion: 1.0.1
+lastModified: 2024-05-29
 genotypeData:
   format: PLINK
   genoFile: 2021_Saag_EastEuropean.bed
@@ -18,7 +18,7 @@ genotypeData:
   indFileChkSum: 319d167cf360277e6a0d0c2ebdfa4ccc
   snpSet: 1240K
 jannoFile: 2021_Saag_EastEuropean.janno
-jannoFileChkSum: b2903911f5ad62108d738d84e006b256
+jannoFileChkSum: 28056a3463bb1d7899b1afa88929ca14
 sequencingSourceFile: 2021_Saag_EastEuropean.ssf
 sequencingSourceFileChkSum: ede192f2a129e62c78ea8f48c17b50c8
 bibFile: 2021_Saag_EastEuropean.bib

diff --git a/archive.chron b/archive.chron
@@ -1,6 +1,6 @@
 title: Poseidon minotaur-archive chronicle
-chronicleVersion: 1.3.0
-lastModified: 2024-04-30
+chronicleVersion: 1.4.0
+lastModified: 2024-05-29
 packages:
 - title: 2020_Margaryan_Viking
   version: 1.0.0
@@ -10,10 +10,18 @@ packages:
   version: 1.0.0
   commit: fa09bafe346791c1cba137b8afc905f9fdbb6a17
   path: 2021_CarlhoffNature
+- title: 2021_CarlhoffNature
+  version: 1.0.1
+  commit: 7b598465b8637841f554b84cd1fc43af84a329b1
+  path: 2021_CarlhoffNature
 - title: 2021_Saag_EastEuropean
   version: 1.0.0
   commit: fa09bafe346791c1cba137b8afc905f9fdbb6a17
   path: 2021_Saag_EastEuropean
+- title: 2021_Saag_EastEuropean
+  version: 1.0.1
+  commit: 7b598465b8637841f554b84cd1fc43af84a329b1
+  path: 2021_Saag_EastEuropean
 - title: 2023_OlaldeCarrion_Roman
   version: 1.0.0
   commit: 3a8c6d97bf581e45b183671ac0171b37045ed805

diff --git a/checkQuotes.sh b/checkQuotes.sh
@@ -0,0 +1,28 @@
+#!/bin/bash
+
+# function to check if a file starts with a double-quote
+starts_with_quote() {
+  if grep -q ^[\"\'] "${1}"; then
+    return 0
+  else
+    return 1
+  fi
+}
+
+# file extensions to search for
+extensions=("janno" "ssf")
+
+# initialize exit code
+exit_code=0
+
+# recursive search for files and check them
+for ext in "${extensions[@]}"; do
+  while IFS= read -r -d '' file; do
+    if starts_with_quote "${file}"; then
+      echo "FAIL: ${file}"
+      exit_code=1
+    fi
+  done < <(find . -type f -name "*.${ext}" -not -path "./.git*" -print0)
+done
+
+exit ${exit_code}