Merge Jackson2024 #1161

iseultj · 2024-04-04T11:58:17Z

Before merging - should I also add to single genome host assoc.? Raw reads & aligned bams available for T. forsythia and S. mutans (and bams aligned to T. denticola, but this is basically unusable in downstream analysis as is).

Pull Request

This PR is for a

New Publication(s)
Correction

For the following list(s):

ancientmetagenome-environmental (README)
ancientmetagenome-hostassociated (README)
ancientsinglegenome-hostassociated (README)

This is to close #1160

PR Workflow

Open this PR with sample metadata on the samples metadata sheet (:tada: you're already here!)
Wait for checks for sample metdata to pass
(If checks fail) make corrections, and push changes to this branch (no need to open a new PR!)
(Once passed) comment on this PR @spaam-bot please autofill <table_name> <project_id> to get a half-filled template! (may take a minute or so to get the comment with the file)
Fill in the template, and verify autofilled data correct!
Once filled in, append(!) the new rows from the TEMPLATE file to the end of the corresponding library metadata file, and update this PR
Wait for checks for library metadata to pass
Request review!

Pre-review checklist (new publications)

Publication is published
- Preprints currently not accepted?
Checked the publication is not already in the database?
[ x] Checked samples in this publication are not previously published data?
- Newly re-sequenced metagenomes are OK!
Samples are shotgun metagenomes and not amplicon data
- Note: hostassociated-singlegenome may also contain whole-genome enriched data
Checked the list follows conventions as described in the corresponding sample type's README file (e.g. using ERS/SRS accession codes for ENA/SRA)?
Once sample table validation completed Library metadata has been added
- Use @spaam-bot please autofill <table_name> <project_id> to get a half-filled template! May take a minute or so to get the comment with the file
- Fill in template, and verify autofill data correct!
- Once filled in, append(!) the new rows to the end of the corresponding library metadata file
Changelog is updated to include the publication under 'Added'?

…amples.tsv

iseultj · 2024-04-04T14:02:46Z

@spaam-bot please autofill ancientsinglegenome-hostassociated_libraries.tsv Jackson2024

fixed accidentally pasting in header

iseultj · 2024-04-04T14:04:32Z

@spaam-bot please autofill ancientsinglegenome-hostassociated_libraries.tsv Jackson2024

jfy133 · 2024-04-04T14:37:59Z

@iseultj it needs to be the table name without _libraries.tsv suffix, I realise now the terminology is unclear now 😅

iseultj · 2024-04-04T14:40:27Z

@iseultj it needs to be the table name without _libraries.tsv suffix, I realise now the terminology is unclear now 😅

Oh cool! that makes sense 😄 could you merge the other PR I made (#1162) so Streptococcus mutans is an allowed species? Thanks!

jfy133 · 2024-04-04T14:43:06Z

@iseultj it needs to be the table name without _libraries.tsv suffix, I realise now the terminology is unclear now 😅

Oh cool! that makes sense 😄 could you merge the other PR I made (#1162) so Streptococcus mutans is an allowed species? Thanks!

I approved it, do you not have merge permissions?

iseultj · 2024-04-04T14:53:38Z

@iseultj it needs to be the table name without _libraries.tsv suffix, I realise now the terminology is unclear now 😅

Oh cool! that makes sense 😄 could you merge the other PR I made (#1162) so Streptococcus mutans is an allowed species? Thanks!

I approved it, do you not have merge permissions?

No, sorry!

jfy133 · 2024-04-04T15:01:37Z

Oh! Ok! Merged for you!@

iseultj · 2024-04-04T15:02:41Z

@spaam-bot please autofill ancientsinglegenome-hostassociated Jackson2024

iseultj · 2024-04-04T15:18:35Z

All done - I think it might be better to get the ftp link for the submitted file rather than the file generated by the ENA/SRA though (which is what it does currently)- I have put ftp links and md5sums for the submitted files, because with the aligned bam, you get a generated fastq and have to realign anyway (which I assume people would prefer to go to the raw data for anyway). If you prefer the generated file, let me know and I'll modify it again :)

jfy133 · 2024-04-04T19:14:39Z

@spaam-bot please autofill ancientsinglegenome-hostassociated Jackson2024

jfy133 · 2024-04-04T19:14:45Z

@spaam-bot please autofill ancientmetagenome-hostassociated Jackson2024

jfy133

Overall really good :D a couple of structural changes but the accuracy is good!
Regarding the generated/submitted: we prefer to go for the generated one as this is more consistent, I've found occasionally submitted stuff is a bit broken (that has been fixed with the generated one).

Thank you @iseultj !

ancientmetagenome-hostassociated/samples/ancientmetagenome-hostassociated_samples.tsv

jfy133 · 2024-04-04T19:24:13Z

ancientsinglegenome-hostassociated/samples/ancientsinglegenome-hostassociated_samples.tsv

+Jackson2024	2024	10.1093/molbev/msae017	Killuragh	52.6	-8.33	Ireland	KGH2-F	Homo sapiens	3775	10.1093/molbev/msae017	bacteria	Tannerella forsythia	tooth	chromosome	ENA	"raw,reference_aligned"	PRJEB64128	ERS15977755
+Jackson2024	2024	10.1093/molbev/msae017	Killuragh	52.6	-8.33	Ireland	KGH2-B	Homo sapiens	3775	10.1093/molbev/msae017	bacteria	Streptococcus mutans	tooth	chromosome	ENA	"raw,reference_aligned"	PRJEB64128	ERS15977754
+Jackson2024	2024	10.1093/molbev/msae017	Killuragh	52.6	-8.33	Ireland	KGH1-E	Homo sapiens	3775	10.1093/molbev/msae017	bacteria	Tannerella forsythia	tooth	chromosome	ENA	"raw,reference_aligned"	PRJEB64128	ERS15977753


See comment above about having sample IDs per tooth, however in this case you would just have two KGH2 lines, each for the two species.

You can remove the quotes around the raw,reference_aligned bit

jfy133 · 2024-04-04T19:43:37Z

ancientsinglegenome-hostassociated/libraries/ancientsinglegenome-hostassociated_libraries.tsv

+Jackson2024	2024	10.1093/molbev/msae017	KGH2-B	ENA	PRJEB64128	ERS15977754	KGH2-B-EX3-UDG1-Hi4.mutans	double	AccuPrime Pfx DNA	full-udg	Illumina HiSeq 2500	SINGLE	WGS	3493602	ERR11658334	bam_mapped	ftp.sra.ebi.ac.uk/vol1/run/ERR116/ERR11658334/KGH2-B-EX3-UDG1-Hi4.trimmed25bp25q.mutans.sorted.grouped.bam;ftp.sra.ebi.ac.uk/vol1/run/ERR116/ERR11658334/KGH2-B-EX3-UDG1-Hi4.trimmed25bp25q.mutans.sorted.grouped.bam.bai	4990a7e776b5881a681f3c2d31a82a1c;bcb496be7425fd6b653f0c96a3826c48	171788860;6736
+Jackson2024	2024	10.1093/molbev/msae017	KGH2-F	ENA	PRJEB64128	ERS15977755	KGH2-F-EX3-UDG1.forsythia	double	AccuPrime Pfx DNA	full-udg	Illumina HiSeq 2500	SINGLE	WGS	221487	ERR11658336	bam_mapped	ftp.sra.ebi.ac.uk/vol1/run/ERR116/ERR11658336/KGH2-F-EX3-UDG1.trimmed25bp25q.forsythia.sorted.grouped.fish.bam;ftp.sra.ebi.ac.uk/vol1/run/ERR116/ERR11658336/KGH2-F-EX3-UDG1.trimmed25bp25q.forsythia.sorted.grouped.fish.bam.bai	8358ef4f9945c68d64cb650ea2ca44e6;36939624efba902cdd817ce0485b8c06	11720746;8664
+Jackson2024	2024	10.1093/molbev/msae017	KGH1-E	ENA	PRJEB64128	ERS15977753	KGH1-E-WEX1-UDG1.forsythia	double	AccuPrime Pfx DNA	full-udg	Illumina NovaSeq 6000	PAIRED	WGS	841339	ERR11658335	bam_mapped	ftp.sra.ebi.ac.uk/vol1/run/ERR116/ERR11658335/KGH1-E-WEX1-UDG1.trimmed25bp25q.forsythia.sorted.grouped.fish.bam;ftp.sra.ebi.ac.uk/vol1/run/ERR116/ERR11658335/KGH1-E-WEX1-UDG1.trimmed25bp25q.forsythia.sorted.grouped.fish.bam.bai	8e5939d645c3c5e5935b2e2dc8468e89;efc79ec9b721cfd9a0b482f71f4a3483	33654513;9720


Also for the BAMs should be fastq_mapped and use the generated file, as ENA doesn't offer a regenerated BAM file.

…tassociated_samples.tsv rounded to nearest century Co-authored-by: James A. Fellows Yates <[email protected]>

Fixed date to nearest century and removed quotation marks around data type

updated FTP to ENA-generated

iseultj · 2024-04-05T07:40:56Z

@spaam-bot please autofill ancientmetagenome-hostassociated Jackson2024

Changed ftp to ena-generated

iseultj · 2024-04-05T07:52:18Z

@jfy133 I've made most of those changes - I don't think it really makes sense to treat them as one sample, given that when analysed there are 2 different genomes from each tooth, and if people want to include them in metagenomic analysis, each subsample of the tooth is pretty different. If you're ok with that, I think this is ready to merge - I have updated the dates and ftp links, and the automatically generated table is working well :)

jfy133

Fair enough if you consider the subsamples as distinct samples! Will retain structure as is :)

OK looks good, I see you removed the BAM files but I guess that's OK still has you have the raw reads anyway, so no need to duplicate :) I will fix the conflict and merge in - thanks for the rapid turn around @iseultj !

…Dir into jackson2024

github-actions · 2024-04-05T11:14:16Z

AMDirT, version 1.5.0

Samples

Ancient Metagenome Host Associated

ancientmetagenome-hostassociated_samples.tsv is valid

Ancient Single Genome Host Associated

ancientsinglegenome-hostassociated_samples.tsv is valid

Ancient Metagenome Environmental

ancientmetagenome-environmental_samples.tsv is valid

Libraries

Ancient Metagenome Host Associated

ancientmetagenome-hostassociated_libraries.tsv is valid

Ancient Single Genome Host Associated

ancientsinglegenome-hostassociated_libraries.tsv is valid

Ancient Metagenome Environmental

ancientmetagenome-environmental_libraries.tsv is valid

iseultj added 4 commits April 4, 2024 13:52

added jackson2024 to ancientmetagenome-hostassociated_samples.tsv

cd2eb1a

added jackson2024 ancientmetagenome-hostassociated_libraries.tsv

c15146e

fixed dois ancientmetagenome-hostassociated_libraries.tsv

39a531f

fixed dois ancientmetagenome-hostassociated_samples.tsv

29fae64

iseultj requested a review from jfy133 April 4, 2024 12:35

added jackson2024 samples Update ancientsinglegenome-hostassociated_s…

dfa5df1

…amples.tsv

Update ancientsinglegenome-hostassociated_samples.tsv

74de608

fixed accidentally pasting in header

Update ancientsinglegenome-hostassociated_libraries.tsv

93081e9

jfy133 requested changes Apr 4, 2024

View reviewed changes

iseultj and others added 3 commits April 5, 2024 09:17

Update ancientmetagenome-hostassociated/samples/ancientmetagenome-hos…

4ec55be

…tassociated_samples.tsv rounded to nearest century Co-authored-by: James A. Fellows Yates <[email protected]>

Update ancientsinglegenome-hostassociated_samples.tsv

b3e8835

Fixed date to nearest century and removed quotation marks around data type

Update ancientsinglegenome-hostassociated_libraries.tsv

3294b63

updated FTP to ENA-generated

Update ancientmetagenome-hostassociated_libraries.tsv

9c2e15b

Changed ftp to ena-generated

Update CHANGELOG.md

e7cd3e5

jfy133 self-requested a review April 5, 2024 11:11

jfy133 approved these changes Apr 5, 2024

View reviewed changes

Merge branch 'master' of github.com:SPAAM-community/AncientMetagenome…

174f61d

…Dir into jackson2024

jfy133 approved these changes Apr 5, 2024

View reviewed changes

jfy133 merged commit d7e1cb2 into master Apr 5, 2024
1 check passed

jfy133 deleted the jackson2024 branch April 5, 2024 11:15

jfy133 mentioned this pull request Apr 5, 2024

Rozwalak2024 #1138

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Merge Jackson2024 #1161

Merge Jackson2024 #1161

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Merge Jackson2024 #1161

Merge Jackson2024 #1161

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iseultj commented Apr 4, 2024

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Samples

Ancient Metagenome Host Associated

Ancient Single Genome Host Associated

Ancient Metagenome Environmental

Libraries

Ancient Metagenome Host Associated

Ancient Single Genome Host Associated

Ancient Metagenome Environmental