Merge pull request #1120 from SPAAM-community/clavel2023-fixes

Fix Clavel2023
SPAAM-community · Sep 30, 2023 · b3f25bb · b3f25bb
2 parents 6d6c230 + 2bf654e
commit b3f25bb
Show file tree

Hide file tree

Showing 3 changed files with 3 additions and 2 deletions.
diff --git a/...entsinglegenome-hostassociated/libraries/ancientsinglegenome-hostassociated_libraries.tsv b/...entsinglegenome-hostassociated/libraries/ancientsinglegenome-hostassociated_libraries.tsv
@@ -2526,7 +2526,7 @@ Clavel2023	2023	10.1016/j.isci.2023.106787	MAJ46	ENA	PRJEB59233	ERS14555596	MAJ4
 Clavel2023	2023	10.1016/j.isci.2023.106787	MAJ46	ENA	PRJEB59233	ERS14555596	MAJ46t11_Ages_2_9349_lr28_i56_T2.5min	double	AccuPrime Pfx DNA	half-udg	Illumina MiniSeq	SINGLE	Targeted-Capture	14264	ERR10822153	fastq_all	ftp.sra.ebi.ac.uk/vol1/fastq/ERR108/053/ERR10822153/ERR10822153.fastq.gz	c56d2a92b0c401fe9c00c556c6ca8506	562321
 Clavel2023	2023	10.1016/j.isci.2023.106787	MAJ46	ENA	PRJEB59233	ERS14555596	MAJ46t11_Ages_2_9349_lr29_i57_T5min	double	AccuPrime Pfx DNA	half-udg	Illumina MiniSeq	SINGLE	Targeted-Capture	19919	ERR10822154	fastq_all	ftp.sra.ebi.ac.uk/vol1/fastq/ERR108/054/ERR10822154/ERR10822154.fastq.gz	f6881046c5082f70699ae33fd2c17b15	769422
 Clavel2023	2023	10.1016/j.isci.2023.106787	MAJ46	ENA	PRJEB59233	ERS14555596	MAJ46t11_Ages_2_9349_lr31_i59_T10min	double	AccuPrime Pfx DNA	half-udg	Illumina MiniSeq	SINGLE	Targeted-Capture	78331	ERR10822156	fastq_all	ftp.sra.ebi.ac.uk/vol1/fastq/ERR108/056/ERR10822156/ERR10822156.fastq.gz	8534b3ef0f6985186f81ccee4e6bfc63	2790324
-Clavel2023	2023	10.1016/j.isci.2023.106787	ERS14555628	ENA	PRJEB59234	ERS14555592	MAJ38t6_Ages_2_8153_lr03_i03_SN1	double	AccuPrime Pfx DNA	half-udg	Illumina MiniSeq	SINGLE	Targeted-Capture	61848	ERR10822090	fastq_all	ftp.sra.ebi.ac.uk/vol1/fastq/ERR108/090/ERR10822090/ERR10822090.fastq.gz	1d821e71a831c88178975b35559c7cef	2712563
+Clavel2023	2023	10.1016/j.isci.2023.106787	MAJ38	ENA	PRJEB59234	ERS14555592	MAJ38t6_Ages_2_8153_lr03_i03_SN1	double	AccuPrime Pfx DNA	half-udg	Illumina MiniSeq	SINGLE	Targeted-Capture	61848	ERR10822090	fastq_all	ftp.sra.ebi.ac.uk/vol1/fastq/ERR108/090/ERR10822090/ERR10822090.fastq.gz	1d821e71a831c88178975b35559c7cef	2712563
 Clavel2023	2023	10.1016/j.isci.2023.106787	MAJ38	ENA	PRJEB59234	ERS14555592	MAJ38t6_Ages_2_8153_lr16_i26_SN2	double	AccuPrime Pfx DNA	half-udg	Illumina MiniSeq	SINGLE	Targeted-Capture	95389	ERR10822091	fastq_all	ftp.sra.ebi.ac.uk/vol1/fastq/ERR108/091/ERR10822091/ERR10822091.fastq.gz	4d93d79f34612c23da1d931fc31871ca	4278163
 Clavel2023	2023	10.1016/j.isci.2023.106787	MAJ38	ENA	PRJEB59234	ERS14555592	MAJ38t6_Ages_2_8153_lr03_i03_SN1	double	AccuPrime Pfx DNA	half-udg	Illumina MiniSeq	PAIRED	Targeted-Capture	18911	ERR10822438	fastq_all	ftp.sra.ebi.ac.uk/vol1/fastq/ERR108/038/ERR10822438/ERR10822438_1.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/ERR108/038/ERR10822438/ERR10822438_2.fastq.gz	755eb7c0958a7286895a07358211d721;94b8a89f869e88c85e290addaa99ccef	906081;944788
 Clavel2023	2023	10.1016/j.isci.2023.106787	MAJ38	ENA	PRJEB59234	ERS14555592	MAJ38t6_Ages_2_8153_lr16_i26_SN2	double	AccuPrime Pfx DNA	half-udg	Illumina MiniSeq	PAIRED	Targeted-Capture	69510	ERR10822439	fastq_all	ftp.sra.ebi.ac.uk/vol1/run/ERR108/ERR10822439/MAJ38_E6_L18_R1_M.fastq.gz;ftp.sra.ebi.ac.uk/vol1/run/ERR108/ERR10822439/MAJ38_E6_L18_R2_M.fastq.gz	5b21c69e610f47178058addd5c49674b;a559f05ff8beb017a8efaf7a1a3d7203	2939990;2939990

diff --git a/ancientsinglegenome-hostassociated/samples/ancientsinglegenome-hostassociated_samples.tsv b/ancientsinglegenome-hostassociated/samples/ancientsinglegenome-hostassociated_samples.tsv
@@ -587,7 +587,7 @@ Swali2023	2023	10.1038/s41467-023-38393-w	Charterhouse Warren, Mendip Hills, Som
 Swali2023	2023	10.1038/s41467-023-38393-w	Levens Deer Park ring cairn, Leven, Cumbria	54.268	-2.761	United Kingdom	C10928	Homo sapiens	3900	10.1038/s41467-023-38393-w	bacteria	Yersinia pestis	tooth	chromosome	ENA	raw	PRJEB61230	ERS14909714,ERS14891343
 Clavel2023	2023	10.1016/j.isci.2023.106787	La Major Cathedral, Marseille, Bouches-du-Rhône	43.3	5.365	France	MAJ75	Homo sapiens	300	10.1016/j.isci.2023.106787	bacteria	Yersinia pestis	tooth	chromosome	ENA	raw	PRJEB59233	ERS14555610,ERS14555611,ERS14555612,ERS14555613,ERS14555614,ERS14555615,ERS14555616,ERS14555617
 Clavel2023	2023	10.1016/j.isci.2023.106787	La Major Cathedral, Marseille, Bouches-du-Rhône	43.3	5.365	France	MAJ46	Homo sapiens	300	10.1016/j.isci.2023.106787	bacteria	Yersinia pestis	tooth	chromosome	ENA	raw	PRJEB59233	ERS14555595,ERS14555596,ERS14555597,ERS14555598,ERS14555599,ERS14555600,ERS14555601,ERS14555602,ERS14555603,ERS14555604
-Clavel2023	2023	10.1016/j.isci.2023.106787	La Major Cathedral, Marseille, Bouches-du-Rhône	43.3	5.365	France	MAJ38	Homo sapiens	300	10.1016/j.isci.2023.106787	bacteria	Yersinia pestis	tooth	chromosome	ENA	raw	PRJEB59233	ERS14555592,ERS14555591,ERS14555590,ERS14555589,ERS14555588,ERS14555587
+Clavel2023	2023	10.1016/j.isci.2023.106787	La Major Cathedral, Marseille, Bouches-du-Rhône	43.3	5.365	France	MAJ38	Homo sapiens	300	10.1016/j.isci.2023.106787	bacteria	Yersinia pestis	tooth	chromosome	ENA	raw	PRJEB59233,PRJEB59234	ERS14555592,ERS14555591,ERS14555590,ERS14555589,ERS14555588,ERS14555587
 Clavel2023	2023	10.1016/j.isci.2023.106787	Hôtel-Dieu Saint-Jean-Baptiste, Amiens	49.898	2.299	France	AMIENS268	Homo sapiens	400	10.1016/j.isci.2023.106787	bacteria	Yersinia pestis	tooth	chromosome	ENA	raw	PRJEB59233	ERS14555669,ERS14555670,ERS14555671
 Clavel2023	2023	10.1016/j.isci.2023.106787	Les Rayettes, Martigues	43.415	5.039	France	RAY1015	Homo sapiens	300	10.1016/j.isci.2023.106787	bacteria	Yersinia pestis	tooth	chromosome	ENA	raw	PRJEB59233	ERS14555624,ERS14555625,ERS14555626
 Clavel2023	2023	10.1016/j.isci.2023.106787	Les Rayettes, Martigues	43.415	5.039	France	RAY1028	Homo sapiens	300	10.1016/j.isci.2023.106787	bacteria	Yersinia pestis	tooth	chromosome	ENA	raw	PRJEB59233	ERS14555627,ERS14555628

diff --git a/assets/analysis/prerelease-validation-crosstable.R b/assets/analysis/prerelease-validation-crosstable.R
@@ -33,4 +33,5 @@ cat("\n")
 cat("POSSIBLE PROBLEMS FOR:", paste0(unique(publication_doi_na$project_name), sep = ","), "\n")
 cat("EXCEPTIONS ALLOWED:\n")
 cat("-(ancientmetagenome-hostassociated): Klapper2023 [reseq. of FellowsYates2023 - no new samples]\n")
+cat("-(ancientsinglegenome-hostassociated): Clavel2023 [Reseq of previous human study not in AMDir, different PRJ code]")
 cat("\n")