Uploaded image for project: 'IGB'
  1. IGB
  2. IGBF-3735

Run the latest version of the nf-core/rnaseq pipeline with tardigrade data

        Details

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

          Description

          Task: Continue the workflow started in IGBF-3708 by running the latest version of the nf-core/rnaseq pipeline with the downloaded fastq files. Continue to document the commands used to run this pipeline (see IGBF-3721).

          For reference, here is that workflow once again:

          1. Run prefetch.sh to get .sra files for the list of SRR accessions.
          2. Check that the .sra files got downloaded correctly.
          3. Run fasterq-dump to make fastq files from the .sra files.
          4. Compress the fastq files with gzip using gzip.sh and submit to slurm queue using sbatch-doIt.sh
          5. Run nf-core/rnaseq pipeline latest version. For this, you have to make a "parameter" file and provide gene annotations (.gtf file), genome annotations (.bed file), and genome assembly (.fasta file).
          6. Check that the pipeline ran correctly.

            Attachments

              Issue Links

              relates to

              Task - A task that needs to be done. IGBF-3790 Run nf-core/rnaseq v 3.14 on SRP484252 (2024 Goldstein Lab)

              • Major - Major loss of function.
              • Closed

              Task - A task that needs to be done. IGBF-3708 Download tardigrade RNA-Seq data onto cluster

              • Major - Major loss of function.
              • Closed

              Task - A task that needs to be done. IGBF-3721 Document Tardigrade RNA-Seq Pipeline

              • Major - Major loss of function.
              • Closed

                Activity

                Ascending order - Click to sort in descending order
                pkulzer Paige Kulzer created issue -
                pkulzer Paige Kulzer made changes -
                Field Original Value New Value
                Epic Link IGBF-1395 [ 17470 ]
                pkulzer Paige Kulzer made changes -
                Link This issue relates to IGBF-3708 [ IGBF-3708 ]
                pkulzer Paige Kulzer made changes -
                Link This issue relates to IGBF-3721 [ IGBF-3721 ]
                nfreese Nowlan Freese made changes -
                Sprint Summer 1 [ 195 ]
                nfreese Nowlan Freese made changes -
                Sprint Summer 2 [ 196 ]
                nfreese Nowlan Freese made changes -
                Rank Ranked higher
                ann.loraine Ann Loraine made changes -
                Epic Link IGBF-1395 [ 17470 ] IGBF-3778 [ 22997 ]
                ann.loraine Ann Loraine made changes -
                Sprint Summer 2 [ 196 ] Summer 2, Summer 3 [ 196, 197 ]
                ann.loraine Ann Loraine made changes -
                Rank Ranked higher
                ann.loraine Ann Loraine made changes -
                Sprint Summer 2, Summer 3 [ 196, 197 ] Summer 2, Summer 3, Summer 4 [ 196, 197, 198 ]
                ann.loraine Ann Loraine made changes -
                Rank Ranked higher
                ann.loraine Ann Loraine made changes -
                Sprint Summer 2, Summer 3, Summer 4 [ 196, 197, 198 ] Summer 2, Summer 3, Summer 4, Summer 5 [ 196, 197, 198, 199 ]
                ann.loraine Ann Loraine made changes -
                Rank Ranked higher
                pkulzer Paige Kulzer made changes -
                Sprint Summer 2, Summer 3, Summer 4, Summer 5 [ 196, 197, 198, 199 ] Summer 2, Summer 3, Summer 4, Summer 6 [ 196, 197, 198, 200 ]
                Hide
                Permalink
                ann.loraine Ann Loraine added a comment - - edited

                This is now done. AL ran the latest, most accurate version of the pipeline as part of a linked ticket IGBF-3790, and described the experience.

                Show
                ann.loraine Ann Loraine added a comment - - edited This is now done. AL ran the latest, most accurate version of the pipeline as part of a linked ticket IGBF-3790 , and described the experience.
                ann.loraine Ann Loraine made changes -
                Link This issue relates to IGBF-3790 [ IGBF-3790 ]
                ann.loraine Ann Loraine made changes -
                Status To-Do [ 10305 ] In Progress [ 3 ]
                ann.loraine Ann Loraine made changes -
                Status In Progress [ 3 ] Needs 1st Level Review [ 10005 ]
                ann.loraine Ann Loraine made changes -
                Status Needs 1st Level Review [ 10005 ] First Level Review in Progress [ 10301 ]
                ann.loraine Ann Loraine made changes -
                Status First Level Review in Progress [ 10301 ] Ready for Pull Request [ 10304 ]
                ann.loraine Ann Loraine made changes -
                Status Ready for Pull Request [ 10304 ] Pull Request Submitted [ 10101 ]
                ann.loraine Ann Loraine made changes -
                Status Pull Request Submitted [ 10101 ] Reviewing Pull Request [ 10303 ]
                ann.loraine Ann Loraine made changes -
                Status Reviewing Pull Request [ 10303 ] Merged Needs Testing [ 10002 ]
                ann.loraine Ann Loraine made changes -
                Status Merged Needs Testing [ 10002 ] Post-merge Testing In Progress [ 10003 ]
                ann.loraine Ann Loraine made changes -
                Resolution Done [ 10000 ]
                Status Post-merge Testing In Progress [ 10003 ] Closed [ 6 ]

                  People

                  • Assignee:
                    pkulzer Paige Kulzer
                    Reporter:
                    pkulzer Paige Kulzer
                  • Votes:
                    0 Vote for this issue
                    Watchers:
                    2 Start watching this issue

                    Dates

                    • Created:
                      Updated:
                      Resolved: