[IGBF-3127] Version control nf-core configuration files used for rna-seq analysis - JIRA UNCC

Details

Type: Task
Status: Closed (View Workflow)
Priority: Major
Resolution: Done
Affects Version/s: None
Fix Version/s: None
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Story Points:
0.5
Epic Link:
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Sprint:
Summer 1 2022 May 23

Description

From Cedar W:

Hi Ann and Robert,

Could you please let me know where the configuration file you're using to run the nf-core rnaseq pipeline is located as well as any additional info I'd need to replicate your methods? Kelsey and I would like to process our data in parallel with Rob so that we can see how the pipeline works and make sure it's reproducible. Also, is it worthwhile to make a separate pipelines repo for this project, or is that unnecessarily complicated? I'm happy to use the file from an existing repo if that makes more sense.

Thanks!

Cedar

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IGBF-3143 Run RNA-Seq data processing pipeline on positive splicing control and experimental samples

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IGBF-3143 Run RNA-Seq data processing pipeline on positive splicing control and experimental samples

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Ann Loraine created issue - 26/May/22 10:50 AM

Ann Loraine made changes - 26/May/22 10:50 AM

Field	Original Value	New Value
Epic Link		IGBF-2993 [ 21429 ]

Ann Loraine made changes - 26/May/22 10:50 AM

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To-Do [ 10305 ]

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Ann Loraine added a comment - 26/May/22 6:15 PM

Scripts and configurations were already version-controlled. Replied to above email with:

Hello Cedar,
Sorry for the late reply!
Here is the information you requested. If you have any questions please let me know!
Configuration file I used to run nf-core/rnaseq on the "ARE" RNA-Seq data from Gloria's lab: https://bitbucket.org/hotpollen/flavonoid-rnaseq/src/main/ExternalDataSets/tomato.config To run nf-core/rna-seq, you also need a sample file describing your experiment. For the ARE data set, I used this:https://bitbucket.org/hotpollen/flavonoid-rnaseq/src/main/ExternalDataSets/samples.csv
When I ran nf-core/rnaseq, I had to launch the nextflow program. To make this easier, I created and modified the following script:https://bitbucket.org/hotpollen/flavonoid-rnaseq/src/main/src/doIt.sh
When working on this, I had to learn how to use nextflow and nf-core/rnaseq. I used my lab's Jira system to keep track of information I found helpful, and describe what I did. Here are some links to my notes:https://jira.bioviz.org/browse/IGBF-2947 - "Investigate using nf-core/rnaseq pipeline"
https://jira.bioviz.org/browse/IGBF-2970 - "Re-run nf-core/rnaseq using proper strand designation and better sample prefix"

Best wishes,
Ann

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Ann Loraine added a comment - 26/May/22 6:15 PM Scripts and configurations were already version-controlled. Replied to above email with: Hello Cedar, Sorry for the late reply! Here is the information you requested. If you have any questions please let me know! Configuration file I used to run nf-core/rnaseq on the "ARE" RNA-Seq data from Gloria's lab: https://bitbucket.org/hotpollen/flavonoid-rnaseq/src/main/ExternalDataSets/tomato.config To run nf-core/rna-seq, you also need a sample file describing your experiment. For the ARE data set, I used this: https://bitbucket.org/hotpollen/flavonoid-rnaseq/src/main/ExternalDataSets/samples.csv When I ran nf-core/rnaseq, I had to launch the nextflow program. To make this easier, I created and modified the following script: https://bitbucket.org/hotpollen/flavonoid-rnaseq/src/main/src/doIt.sh When working on this, I had to learn how to use nextflow and nf-core/rnaseq. I used my lab's Jira system to keep track of information I found helpful, and describe what I did. Here are some links to my notes: https://jira.bioviz.org/browse/IGBF-2947 - "Investigate using nf-core/rnaseq pipeline" https://jira.bioviz.org/browse/IGBF-2970 - "Re-run nf-core/rnaseq using proper strand designation and better sample prefix" Best wishes, Ann