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  1. IGB
  2. IGBF-3127

Version control nf-core configuration files used for rna-seq analysis

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        • Type: Task
        • Status: Closed (View Workflow)
        • Priority: Major
        • Resolution: Done
        • Affects Version/s: None
        • Fix Version/s: None
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          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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              Task - A task that needs to be done. IGBF-3143 Run RNA-Seq data processing pipeline on positive splicing control and experimental samples

              • Major - Major loss of function.
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              Task - A task that needs to be done. IGBF-3143 Run RNA-Seq data processing pipeline on positive splicing control and experimental samples

              • Major - Major loss of function.
              • Closed

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                ann.loraine Ann Loraine added a comment -

                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 Ann Loraine added a comment - 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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                  • Assignee:
                    ann.loraine Ann Loraine
                    Reporter:
                    ann.loraine Ann Loraine
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