Merge branch 'main' into Kavlahkaff-patch-1

poseidon-framework · Nov 22, 2024 · ba67d5c · ba67d5c
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diff --git a/2020_Bongers_SouthPeru/2020_Bongers_SouthPeru.bed b/2020_Bongers_SouthPeru/2020_Bongers_SouthPeru.bed
diff --git a/2020_Bongers_SouthPeru/2020_Bongers_SouthPeru.janno b/2020_Bongers_SouthPeru/2020_Bongers_SouthPeru.janno
@@ -1,7 +1,7 @@
 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
-UC12-12_ss_MNT	F	Peru_Chincha_LH	n/a	n/a	n/a	n/a	n/a	UC12-12	Peru	PE	SouthCoast	n/a	-13.476219	-76.016683	contextual	n/a	n/a	n/a	1400	1450	1500	n/a	A2+(64)+16129	n/a	uc12-12	1	SC79-L1101	Shotgun	half	ss	haploid	https://github.com/nf-core/eager/releases/tag/2.4.6	64.627524	659142	n/a	2.9552786980429076e-2	0.175194	1.002554e-11	ANGSD[v0.935]	Nr Snps (per library): 18180. Estimate and error are weighted means of values per library. Libraries with fewer than 100 SNPs used in contamination estimation were excluded.	PRJEB37726;ERS4421181;ERR4017942	Fehren-Schmitz, Lars	BongersPNAS2020	PASS	n/a	UC12-12_ss	UC12-12	0.0036778307278310003	0.000362870433052	0.9378040341855981	0.006242505794216001
-UC12-20_ss_MNT	M	Peru_Chincha_LH	n/a	n/a	n/a	n/a	n/a	UC12-20	Peru	PE	SouthCoast	n/a	-13.476219	-76.016683	contextual	n/a	n/a	n/a	1400	1450	1500	n/a	C1b +16311	n/a	uc12-20	1	SC79-L1098	Shotgun	half	ss	haploid	https://github.com/nf-core/eager/releases/tag/2.4.6	53.954231	834193	n/a	2.8999766639241295e-2	0.005742	4.6689380000000005e-14	ANGSD[v0.935]	Nr Snps (per library): 12736. Estimate and error are weighted means of values per library. Libraries with fewer than 100 SNPs used in contamination estimation were excluded.	PRJEB37726;ERS4421182;ERR4017943	Fehren-Schmitz, Lars	BongersPNAS2020	PASS	n/a	UC12-20_ss	UC12-20	0.002192551730127	0.0025789810956120002	0.49708731471340706	0.455857143945926
-UC12-24_ss_MNT	M	Peru_Chincha_LH	n/a	n/a	n/a	n/a	n/a	UC12-24	Peru	PE	SouthCoast	n/a	-13.476219	-76.016683	contextual	n/a	n/a	n/a	1400	1450	1500	n/a	C1b	n/a	uc12-24	1	SC79-L1096	Shotgun	half	ss	haploid	https://github.com/nf-core/eager/releases/tag/2.4.6	67.100728	663524	n/a	3.6231935965394695e-2	0.02035	2.147561e-13	ANGSD[v0.935]	Nr Snps (per library): 7055. Estimate and error are weighted means of values per library. Libraries with fewer than 100 SNPs used in contamination estimation were excluded.	PRJEB37726;ERS4421183;ERR4017944	Fehren-Schmitz, Lars	BongersPNAS2020	PASS	n/a	UC12-24_ss	UC12-24	0.0026191747636510002	0.0030634058675530003	0.48878107807005805	0.44319571820121706
-UC12-25_ss_MNT	F	Peru_Chincha_LH	n/a	n/a	n/a	n/a	n/a	UC12-25	Peru	PE	SouthCoast	n/a	-13.477239	-76.025299	contextual	n/a	n/a	n/a	1400	1450	1500	n/a	C1c	n/a	uc12-25	1	SC79-L1097	Shotgun	half	ss	haploid	https://github.com/nf-core/eager/releases/tag/2.4.6	77.587999	864369	n/a	2.9834926876643592e-2	0.18969399999999997	1.554692e-11	ANGSD[v0.935]	Nr Snps (per library): 32440. Estimate and error are weighted means of values per library. Libraries with fewer than 100 SNPs used in contamination estimation were excluded.	PRJEB37726;ERS4421184;ERR4017945	Fehren-Schmitz, Lars	BongersPNAS2020	PASS	n/a	UC12-25_ss	UC12-25	0.002943847456157	0.000312334458473	0.9625981903938851	0.007416751530339
-UC8-8168_ss_MNT	F	Peru_Chincha_LH	n/a	n/a	n/a	n/a	n/a	UC8-8168	Peru	PE	SouthCoast	n/a	-13.476219	-76.016683	contextual	n/a	n/a	n/a	1400	1450	1500	n/a	B2b	n/a	uc8-8168	1	SC79-L1099	Shotgun	half	ss	haploid	https://github.com/nf-core/eager/releases/tag/2.4.6	41.473265	503053	n/a	4.800801542978008e-2	0.174397	1.745724e-12	ANGSD[v0.935]	Nr Snps (per library): 9599. Estimate and error are weighted means of values per library. Libraries with fewer than 100 SNPs used in contamination estimation were excluded.	PRJEB37726;ERS4421185;ERR4017946	Fehren-Schmitz, Lars	BongersPNAS2020	PASS	n/a	UC8-8168_ss	UC8-8168	0.004553026203634	0.00044834816249900004	0.929809197736119	0.006163228942574
-UC8-8173_ss_MNT	M	Peru_Chincha_LH	n/a	n/a	n/a	n/a	n/a	UC8-8173	Peru	PE	SouthCoast	n/a	-13.477239	-76.025299	contextual	n/a	n/a	n/a	1400	1450	1500	n/a	B2b	Q1a2a1a	uc8-8173	1	SC79-L1095	Shotgun	half	ss	haploid	https://github.com/nf-core/eager/releases/tag/2.4.6	63.387807	717533	n/a	4.0810946463713735e-2	0.00394	8.432734e-14	ANGSD[v0.935]	Nr Snps (per library): 8928. Estimate and error are weighted means of values per library. Libraries with fewer than 100 SNPs used in contamination estimation were excluded.	PRJEB37726;ERS4421186;ERR4017947	Fehren-Schmitz, Lars	BongersPNAS2020	PASS	n/a	UC8-8173_ss	UC8-8173	0.0025831521904110004	0.0030217875354850003	0.5173068863522	0.469441459565386
+UC12-12_ss_MNT	F	Peru_Chincha_LH	n/a	n/a	n/a	n/a	n/a	UC12-12	Peru	PE	SouthCoast	n/a	-13.476219	-76.016683	contextual	n/a	n/a	n/a	1400	1450	1500	n/a	A2+(64)+16129	n/a	uc12-12	1	SC79-L1101	Shotgun	half	ss	haploid	https://github.com/nf-core/eager/releases/tag/2.5.1	64.623018	659147	n/a	2.97539993963175e-2	0.175198	4.333311e-12	ANGSD[v0.935]	Nr Snps (per library): 18178. Estimate and error are weighted means of values per library. Libraries with fewer than 100 SNPs used in contamination estimation were excluded.	PRJEB37726;ERS4421181;ERR4017942	Fehren-Schmitz, Lars	n/a	PASS	n/a	UC12-12_ss	UC12-12	0.0036779032724780004	0.000362252944412	0.9378493736652561	0.0062213491921190005
+UC12-20_ss_MNT	M	Peru_Chincha_LH	n/a	n/a	n/a	n/a	n/a	UC12-20	Peru	PE	SouthCoast	n/a	-13.476219	-76.016683	contextual	n/a	n/a	n/a	1400	1450	1500	n/a	C1b +16311	n/a	uc12-20	1	SC79-L1098	Shotgun	half	ss	haploid	https://github.com/nf-core/eager/releases/tag/2.5.1	53.951534	834181	n/a	2.8177322422549e-2	0.005742	1.014989e-13	ANGSD[v0.935]	Nr Snps (per library): 12735. Estimate and error are weighted means of values per library. Libraries with fewer than 100 SNPs used in contamination estimation were excluded.	PRJEB37726;ERS4421182;ERR4017943	Fehren-Schmitz, Lars	n/a	PASS	n/a	UC12-20_ss	UC12-20	0.002192540378467	0.0025789927718020004	0.497080083309806	0.45585919471114805
+UC12-24_ss_MNT	M	Peru_Chincha_LH	n/a	n/a	n/a	n/a	n/a	UC12-24	Peru	PE	SouthCoast	n/a	-13.476219	-76.016683	contextual	n/a	n/a	n/a	1400	1450	1500	n/a	C1b	n/a	uc12-24	1	SC79-L1096	Shotgun	half	ss	haploid	https://github.com/nf-core/eager/releases/tag/2.5.1	67.098032	663531	n/a	3.60829908790217e-2	0.020349	5.973964e-14	ANGSD[v0.935]	Nr Snps (per library): 7056. Estimate and error are weighted means of values per library. Libraries with fewer than 100 SNPs used in contamination estimation were excluded.	PRJEB37726;ERS4421183;ERR4017944	Fehren-Schmitz, Lars	n/a	PASS	n/a	UC12-24_ss	UC12-24	0.002619112155784	0.0030637863334150002	0.488755909875806	0.443302380718023
+UC12-25_ss_MNT	F	Peru_Chincha_LH	n/a	n/a	n/a	n/a	n/a	UC12-25	Peru	PE	SouthCoast	n/a	-13.477239	-76.025299	contextual	n/a	n/a	n/a	1400	1450	1500	n/a	C1c	n/a	uc12-25	1	SC79-L1097	Shotgun	half	ss	haploid	https://github.com/nf-core/eager/releases/tag/2.5.1	77.580438	864367	n/a	2.98567366717787e-2	0.189742	7.393421e-12	ANGSD[v0.935]	Nr Snps (per library): 32439. Estimate and error are weighted means of values per library. Libraries with fewer than 100 SNPs used in contamination estimation were excluded.	PRJEB37726;ERS4421184;ERR4017945	Fehren-Schmitz, Lars	n/a	PASS	n/a	UC12-25_ss	UC12-25	0.00294390467649	0.000312888103372	0.9626334834610931	0.007443057625777001
+UC8-8168_ss_MNT	F	Peru_Chincha_LH	n/a	n/a	n/a	n/a	n/a	UC8-8168	Peru	PE	SouthCoast	n/a	-13.476219	-76.016683	contextual	n/a	n/a	n/a	1400	1450	1500	n/a	B2b	n/a	uc8-8168	1	SC79-L1099	Shotgun	half	ss	haploid	https://github.com/nf-core/eager/releases/tag/2.5.1	41.471467	503049	n/a	4.76525779484052e-2	0.174391	9.354036e-13	ANGSD[v0.935]	Nr Snps (per library): 9599. Estimate and error are weighted means of values per library. Libraries with fewer than 100 SNPs used in contamination estimation were excluded.	PRJEB37726;ERS4421185;ERR4017946	Fehren-Schmitz, Lars	n/a	PASS	n/a	UC8-8168_ss	UC8-8168	0.004552921489778	0.000447160690243	0.929767190487595	0.006130624941876
+UC8-8173_ss_MNT	M	Peru_Chincha_LH	n/a	n/a	n/a	n/a	n/a	UC8-8173	Peru	PE	SouthCoast	n/a	-13.477239	-76.025299	contextual	n/a	n/a	n/a	1400	1450	1500	n/a	B2b	Q1a2a1a	uc8-8173	1	SC79-L1095	Shotgun	half	ss	haploid	https://github.com/nf-core/eager/releases/tag/2.5.1	63.3829	717519	n/a	4.1235022171903e-2	0.00394	2.7943649999999998e-14	ANGSD[v0.935]	Nr Snps (per library): 8927. Estimate and error are weighted means of values per library. Libraries with fewer than 100 SNPs used in contamination estimation were excluded.	PRJEB37726;ERS4421186;ERR4017947	Fehren-Schmitz, Lars	n/a	PASS	n/a	UC8-8173_ss	UC8-8173	0.0025831450742550004	0.003021716653648	0.517305476663749	0.46942098501586604
diff --git a/2020_Bongers_SouthPeru/CHANGELOG.md b/2020_Bongers_SouthPeru/CHANGELOG.md
@@ -1,3 +1,4 @@
+- V 2.0.0: Updated package contents due to reprocessing of sequence data
 - V 1.0.0: Bump version for release
 - V 0.2.0: Arranged Poseidon_IDs alphabetically
 - V 0.1.5: Fill Lon/Lat, mtDNA/Y haplos, Country_ISO, Publication columns

diff --git a/2020_Bongers_SouthPeru/POSEIDON.yml b/2020_Bongers_SouthPeru/POSEIDON.yml
@@ -6,19 +6,19 @@ contributor:
 - name: Thiseas C. Lamnidis
   email: [email protected]
   orcid: 0000-0003-4485-8570
-packageVersion: 1.0.0
-lastModified: 2024-07-17
+packageVersion: 2.0.0
+lastModified: 2024-11-08
 genotypeData:
   format: PLINK
   genoFile: 2020_Bongers_SouthPeru.bed
-  genoFileChkSum: f80d808156b11be3ff454a2cce6ee2ad
+  genoFileChkSum: 47583daa76e973022c7632899c039a4f
   snpFile: 2020_Bongers_SouthPeru.bim
   snpFileChkSum: 433fa85a23f3123bade02348e4628b75
   indFile: 2020_Bongers_SouthPeru.fam
   indFileChkSum: c92b6bd217075f64d0e1bcde9c499080
   snpSet: 1240K
 jannoFile: 2020_Bongers_SouthPeru.janno
-jannoFileChkSum: 6c1ed98562021eeb751fbc647824b513
+jannoFileChkSum: cc6235e9868ee944cf9d4263c8bd9d1a
 sequencingSourceFile: 2020_Bongers_SouthPeru.ssf
 sequencingSourceFileChkSum: a6b5fd5157b862791c5247ec47975d77
 bibFile: 2020_Bongers_SouthPeru.bib

diff --git a/2020_Bongers_SouthPeru/README.md b/2020_Bongers_SouthPeru/README.md
@@ -1,4 +1,79 @@
-# 2020_Bongers_SouthPeru
+# 2020_Bongers_SouthPeru-2.0.0
+This package was updated on 2024-11-05 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: 0.4.2dev
+ - populate_janno.py version: 0.4.1dev
+
+## CHANGELOG:
+ - Fixed a problem with the processing of PE sequenced data from ssDNA libraries [minotaur-recipes #53](https://github.com/poseidon-framework/minotaur-recipes/issues/53)
+   - New genotypes were generated.
+   - Data processing statistics were updated in the janno file to match latest processing.
+
+## Fill metadata from the minotaur archive package (2020_Bongers_SouthPeru-1.0.0).
+
+```bash
+package_name="2020_Bongers_SouthPeru"
+fill_from_archive="minotaur-archive"
+fill_from_package="2020_Bongers_SouthPeru-1.0.0"
+## trident v1.5.4.0
+## First fill-in missing metadata from relevant columns (no processing-based info).
+trident jannocoalesce \
+  -s ../../archives/${fill_from_archive}/${fill_from_package}/2020_Bongers_SouthPeru.janno \
+  -t 2020_Bongers_SouthPeru/2020_Bongers_SouthPeru.janno \
+  --stripIdRegex "(_ss_MNT$)|(_MNT$)" \
+  --includeColumns 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,Primary_Contact,Note,Keywords
+
+## Then fill in Group_Name and Genetic_Sex
+trident jannocoalesce \
+  -s ../../archives/${fill_from_archive}/${fill_from_package}/2020_Bongers_SouthPeru.janno \
+  -t 2020_Bongers_SouthPeru/2020_Bongers_SouthPeru.janno \
+  --stripIdRegex "(_ss_MNT$)|(_MNT$)" \
+  --includeColumns Genetic_Sex,Group_Name \
+  --force
+
+## Mirror Sex and Group name info to the fam file.
+paste -d "\t" 2020_Bongers_SouthPeru/2020_Bongers_SouthPeru.fam <(cut -f 1-3 2020_Bongers_SouthPeru/2020_Bongers_SouthPeru.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 2020_Bongers_SouthPeru/2020_Bongers_SouthPeru.fam
+
+## trident v1.5.4.0
+trident rectify --checksumAll -d 2020_Bongers_SouthPeru/
+
+## Arrange Poseidon_IDs alphabetically
+## First, move the old directory out of the way (avoids all files being renamed by trident forge)
+cd ../ ## Start from the parent directory, since we need to rename the directory we were in.
+mv ${package_name} ${package_name}_old
+
+##   qjanno v1.0.0.1
+qjanno "SELECT '<'||Poseidon_ID||'>' FROM d(${package_name}_old) ORDER BY Poseidon_ID" --raw --noOutHeader > desiredOrder.txt
+
+## Rearrange package contents to the desired order.
+## trident v1.5.4.0
+trident forge -d ${package_name}_old --forgeFile desiredOrder.txt -o ${package_name} --ordered --preservePyml
+trident rectify -d ${package_name} --packageVersion Major --logText "Updated package contents due to reprocessing of sequence data" --checksumAll
+## Once the new package has been verified, the '_old' directory can be removed.
+```
+
+# 2020_Bongers_SouthPeru-1.0.0
 This package was created on 2024-05-06 and was processed using the following versions:
  - nf-core/eager version:  2.4.6
  - Minotaur config version: 0.2.1dev

diff --git a/archive.chron b/archive.chron
@@ -1,11 +1,15 @@
 title: Poseidon minotaur-archive chronicle
-chronicleVersion: 1.6.0
-lastModified: 2024-07-17
+chronicleVersion: 1.7.0
+lastModified: 2024-11-08
 packages:
 - title: 2020_Bongers_SouthPeru
   version: 1.0.0
   commit: a3a4f0ee2699238d9abb4bfbda721bddca07303b
   path: 2020_Bongers_SouthPeru
+- title: 2020_Bongers_SouthPeru
+  version: 2.0.0
+  commit: bbdb17e36bdecdf25120c4870aa26d606f6284b2
+  path: 2020_Bongers_SouthPeru
 - title: 2020_Margaryan_Viking
   version: 1.0.0
   commit: 9118d90debbf4ec47ac90de01dfb5c0f31e0b53d