[IGBF-3392] Make sample sheet for 2022 Palanivelu - JIRA UNCC

Details

Type: Task
Status: Closed (View Workflow)
Priority: Major
Resolution: Done
Affects Version/s: None
Fix Version/s: None
Labels:
None

Story Points:
2
Epic Link:
Process and deploy Palanivelu Lab data
Sprint:
Summer 6 2023 July 24, Summer 7 2023 Aug 7, Summer 8 2023 Aug 21

Description

Original Directory: /projects/tomato_genome/rnaseq/ravi-2022-fullrun/30-681594536/00_fastq
Nf-core run: /nobackup/tomato_genome/Ravi_2022

Make a new sample sheet for this 2022 experiment/data

Notes:
Study_name column: /projects/tomato_genome/rnaseq/ravi-2022-fullrun/30-681594536/00_fastq could be: "Hz Mal Nag Tam heat-treated unpollinated pistils RP Lab"

Attachments

Issue Links

relates to

IGBF-3390 Run Nextflow with 2022 Palanivelu Lab-generated samples

Closed

IGBF-3391 Create scaled and junction files for 2022 Palanivelu Lab-generated samples

Closed

Activity

Ascending order - Click to sort in descending order

Molly Davis created issue - 19/Jul/23 4:20 PM

Molly Davis made changes - 19/Jul/23 4:20 PM

Field	Original Value	New Value
Epic Link		IGBF-3251 [ 22132 ]

Molly Davis made changes - 19/Jul/23 4:20 PM

Link

This issue relates to IGBF-3367 [ IGBF-3367 ]

Molly Davis made changes - 19/Jul/23 4:20 PM

Link

This issue relates to ~~IGBF-3390~~ [ ~~IGBF-3390~~ ]

Molly Davis made changes - 19/Jul/23 4:20 PM

Link

This issue relates to ~~IGBF-3391~~ [ ~~IGBF-3391~~ ]

Molly Davis made changes - 20/Jul/23 10:23 AM

Summary

Add 2022 Palanavelu to sample sheet and run XML script

Make sample sheet 2022 Palanivelu to sample sheet and run XML script

Molly Davis made changes - 20/Jul/23 10:23 AM

Summary

Make sample sheet 2022 Palanivelu to sample sheet and run XML script

Make sample sheet for 2022 Palanivelu and run XML script

Molly Davis made changes - 21/Jul/23 3:16 PM

Sprint

Summer 5 2023 July 10 [ 174 ]

Summer 6 2023 July 24 [ 175 ]

Molly Davis made changes - 26/Jul/23 3:16 PM

Status

To-Do [ 10305 ]

In Progress [ 3 ]

Molly Davis made changes - 26/Jul/23 3:16 PM

Status

In Progress [ 3 ]

To-Do [ 10305 ]

Molly Davis made changes - 26/Jul/23 3:37 PM

Status

To-Do [ 10305 ]

In Progress [ 3 ]

Molly Davis made changes - 27/Jul/23 3:52 PM

Summary

Make sample sheet for 2022 Palanivelu and run XML script

Make sample sheet for 2022 Palanivelu

Molly Davis made changes - 27/Jul/23 4:06 PM

Status

In Progress [ 3 ]

To-Do [ 10305 ]

Molly Davis made changes - 27/Jul/23 4:17 PM

Status

To-Do [ 10305 ]

In Progress [ 3 ]

Molly Davis made changes - 27/Jul/23 4:20 PM

Description

Directory: /projects/tomato_genome/rnaseq/ravi-2022-fullrun/30-681594536/00_fastq
Nf-core run: /nobackup/tomato_genome/ravi-55/sl5-nfcore/results # but there are no scaled or junction files.

* Add files to KP_sample_sheet.xlsx
* Run "makeAnnotsXml.py" after merge

Notes:
Study_name column: /projects/tomato_genome/rnaseq/ravi-2022-fullrun/30-681594536/00_fastq could be: "Hz Mal Nag Tam heat-treated unpollinated pistils RP Lab"

Directory: /projects/tomato_genome/rnaseq/ravi-2022-fullrun/30-681594536/00_fastq
Nf-core run: /nobackup/tomato_genome/ravi-55/sl5-nfcore/results # but there are no scaled or junction files.

* Make a new sample sheet for this 2022 experiment/data

Notes:
Study_name column: /projects/tomato_genome/rnaseq/ravi-2022-fullrun/30-681594536/00_fastq could be: "Hz Mal Nag Tam heat-treated unpollinated pistils RP Lab"

Molly Davis made changes - 27/Jul/23 4:20 PM

Description

Directory: /projects/tomato_genome/rnaseq/ravi-2022-fullrun/30-681594536/00_fastq
Nf-core run: /nobackup/tomato_genome/ravi-55/sl5-nfcore/results # but there are no scaled or junction files.

* Make a new sample sheet for this 2022 experiment/data

Notes:
Study_name column: /projects/tomato_genome/rnaseq/ravi-2022-fullrun/30-681594536/00_fastq could be: "Hz Mal Nag Tam heat-treated unpollinated pistils RP Lab"

Directory: /projects/tomato_genome/rnaseq/ravi-2022-fullrun/30-681594536/00_fastq

* Make a new sample sheet for this 2022 experiment/data

Notes:
Study_name column: /projects/tomato_genome/rnaseq/ravi-2022-fullrun/30-681594536/00_fastq could be: "Hz Mal Nag Tam heat-treated unpollinated pistils RP Lab"

Molly Davis made changes - 27/Jul/23 4:21 PM

Description

Original Directory: /projects/tomato_genome/rnaseq/ravi-2022-fullrun/30-681594536/00_fastq
Nf-core run: /nobackup/tomato_genome/Ravi_2022

* Make a new sample sheet for this 2022 experiment/data

Notes:
Study_name column: /projects/tomato_genome/rnaseq/ravi-2022-fullrun/30-681594536/00_fastq could be: "Hz Mal Nag Tam heat-treated unpollinated pistils RP Lab"

Molly Davis made changes - 27/Jul/23 4:21 PM

Description

*Original Directory*: /projects/tomato_genome/rnaseq/ravi-2022-fullrun/30-681594536/00_fastq
*Nf-core run*: /nobackup/tomato_genome/Ravi_2022

* Make a new sample sheet for this 2022 experiment/data

Notes:
Study_name column: /projects/tomato_genome/rnaseq/ravi-2022-fullrun/30-681594536/00_fastq could be: "Hz Mal Nag Tam heat-treated unpollinated pistils RP Lab"

Molly Davis made changes - 28/Jul/23 1:38 PM

Status

In Progress [ 3 ]

To-Do [ 10305 ]

Ann Loraine made changes - 07/Aug/23 10:16 AM

Sprint

Summer 6 2023 July 24 [ 175 ]

Summer 6 2023 July 24, Summer 7 2023 Aug 7 [ 175, 176 ]

Ann Loraine made changes - 07/Aug/23 10:16 AM

Rank

Ranked higher

Molly Davis made changes - 07/Aug/23 1:52 PM

Status

To-Do [ 10305 ]

In Progress [ 3 ]

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Molly Davis added a comment - 09/Aug/23 3:52 PM

I have finished creating the sample sheet. Next step is to commit the file after 2022 nextflow multiqc reports and csv file are merged.

Show

Molly Davis added a comment - 09/Aug/23 3:52 PM I have finished creating the sample sheet. Next step is to commit the file after 2022 nextflow multiqc reports and csv file are merged.

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Molly Davis added a comment - 10/Aug/23 1:58 PM

Branch: https://bitbucket.org/mdavis4290/molly-pistil-rna-seq/branch/IGBF-3392

Show

Molly Davis added a comment - 10/Aug/23 1:58 PM Branch : https://bitbucket.org/mdavis4290/molly-pistil-rna-seq/branch/IGBF-3392

Molly Davis made changes - 10/Aug/23 1:58 PM

Assignee

Molly Davis [ molly ]

Molly Davis made changes - 10/Aug/23 1:58 PM

Status

In Progress [ 3 ]

Needs 1st Level Review [ 10005 ]

Molly Davis made changes - 10/Aug/23 2:01 PM

Assignee

Ann Loraine [ aloraine ]

Ann Loraine made changes - 11/Aug/23 9:22 AM

Status

Needs 1st Level Review [ 10005 ]

First Level Review in Progress [ 10301 ]

Ann Loraine made changes - 11/Aug/23 9:22 AM

Status

First Level Review in Progress [ 10301 ]

Ready for Pull Request [ 10304 ]

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Ann Loraine added a comment - 11/Aug/23 9:22 AM

Looks great. Thanks [~molly]!

Show

Ann Loraine added a comment - 11/Aug/23 9:22 AM Looks great. Thanks [~molly] !

Ann Loraine made changes - 11/Aug/23 9:23 AM

Assignee

Ann Loraine [ aloraine ]

Molly Davis [ molly ]

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Molly Davis added a comment - 11/Aug/23 1:11 PM - edited

Pull request: https://bitbucket.org/hotpollen/pistil-rna-seq/pull-requests/8

Of course! Thank you!

Show

Molly Davis added a comment - 11/Aug/23 1:11 PM - edited Pull request : https://bitbucket.org/hotpollen/pistil-rna-seq/pull-requests/8 Of course! Thank you!

Molly Davis made changes - 11/Aug/23 1:12 PM

Status

Ready for Pull Request [ 10304 ]

Pull Request Submitted [ 10101 ]

Molly Davis made changes - 11/Aug/23 1:12 PM

Assignee

Molly Davis [ molly ]

Ann Loraine [ aloraine ]

Ann Loraine made changes - 11/Aug/23 1:21 PM

Status

Pull Request Submitted [ 10101 ]

Reviewing Pull Request [ 10303 ]

Ann Loraine made changes - 11/Aug/23 1:21 PM

Status

Reviewing Pull Request [ 10303 ]

Merged Needs Testing [ 10002 ]

Ann Loraine made changes - 11/Aug/23 1:21 PM

Assignee

Ann Loraine [ aloraine ]

Ann Loraine made changes - 15/Aug/23 10:07 AM

Assignee

Ann Loraine [ aloraine ]

Ann Loraine made changes - 18/Aug/23 1:52 PM

Status

Merged Needs Testing [ 10002 ]

Post-merge Testing In Progress [ 10003 ]

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Ann Loraine added a comment - 20/Aug/23 2:36 PM

Made multiple edits to the 2022 sample sheet, including:

Added azenta identifier
Changed "deploy dir" to azenta identifier
Changed study name

Began deploying data to IGB Quickload host. Copied data with:

root@cci-vm12:/mnt/igbdata/hotpollen/S_lycopersicum_Jun_2022# rsync -avzhP aloraine@10.16.115.244:/projects/tomato_genome/fnb/dataprocessing/Ravi_2022/for_quickload/S_lycopersicum_Jun_2022/30-681594536/ 30-681594536
Connected.

Show

Ann Loraine added a comment - 20/Aug/23 2:36 PM Made multiple edits to the 2022 sample sheet, including: Added azenta identifier Changed "deploy dir" to azenta identifier Changed study name Began deploying data to IGB Quickload host. Copied data with: root@cci-vm12:/mnt/igbdata/hotpollen/S_lycopersicum_Jun_2022# rsync -avzhP aloraine@10.16.115.244:/projects/tomato_genome/fnb/dataprocessing/Ravi_2022/for_quickload/S_lycopersicum_Jun_2022/30-681594536/ 30-681594536 Connected.

Ann Loraine made changes - 21/Aug/23 9:57 AM

Sprint

Summer 6 2023 July 24, Summer 7 2023 Aug 7 [ 175, 176 ]

Summer 6 2023 July 24, Summer 7 2023 Aug 7, Summer 8 2023 Aug 21 [ 175, 176, 177 ]

Ann Loraine made changes - 21/Aug/23 9:57 AM

Rank

Ranked higher

Ann Loraine made changes - 25/Aug/23 2:13 PM

Resolution		Done [ 10000 ]
Status	Post-merge Testing In Progress [ 10003 ]	Closed [ 6 ]

People

Assignee:

Ann Loraine

Reporter:

Molly Davis

Votes:

0 Vote for this issue

Watchers:

2 Start watching this issue

Dates

Created:

19/Jul/23 4:20 PM

Updated:

25/Aug/23 2:13 PM

Resolved:

25/Aug/23 2:13 PM