Uploaded image for project: 'IGB'
  1. IGB
  2. IGBF-4277

Run Nextflow on Polli

        Details

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

          Description



          Once Polli data is in place and we have confirmed data filtered for trimming, run Nextflow.

            Attachments

              Activity

              Ascending order - Click to sort in descending order
              robofjoy Robert Reid created issue -
              robofjoy Robert Reid made changes -
              Field Original Value New Value
              Epic Link IGBF-2993 [ 21429 ]
              robofjoy Robert Reid made changes -
              Status To-Do [ 10305 ] In Progress [ 3 ]
              robofjoy Robert Reid made changes -
              Status In Progress [ 3 ] Needs 1st Level Review [ 10005 ]
              robofjoy Robert Reid made changes -
              Status Needs 1st Level Review [ 10005 ] First Level Review in Progress [ 10301 ]
              robofjoy Robert Reid made changes -
              Status First Level Review in Progress [ 10301 ] To-Do [ 10305 ]
              robofjoy Robert Reid made changes -
              Status To-Do [ 10305 ] In Progress [ 3 ]
              Hide
              Permalink
              bbendick Brandon Bendickson added a comment -

              Nextflow run completed successfully, results found here: /projects/tomato_genome/fnb/dataprocessing/brandon_work/Kelsie_NEXTFLOW/poll

              Show
              bbendick Brandon Bendickson added a comment - Nextflow run completed successfully, results found here: /projects/tomato_genome/fnb/dataprocessing/brandon_work/Kelsie_NEXTFLOW/poll
              Hide
              Permalink
              robofjoy Robert Reid added a comment -

              Next step, summarize the number of reads that align and don't align. (samtools view -F. or -f)

              And then compare these numbers to the previous official nextflow runs. Location in Google slides.

              Show
              robofjoy Robert Reid added a comment - Next step, summarize the number of reads that align and don't align. (samtools view -F. or -f) And then compare these numbers to the previous official nextflow runs. Location in Google slides.
              ann.loraine Ann Loraine made changes -
              Sprint Summer 5 [ 222 ] Summer 5, Summer 6 [ 222, 223 ]
              ann.loraine Ann Loraine made changes -
              Rank Ranked higher
              Hide
              Permalink
              bbendick Brandon Bendickson added a comment -

              Gathered summarized results into this sheet: https://docs.google.com/spreadsheets/d/1pAijbCOI0KUq29KYo4mW2YZj8iE7IW-T2S9p5GhgFMU/edit?gid=1129882996#gid=1129882996

              Show
              bbendick Brandon Bendickson added a comment - Gathered summarized results into this sheet: https://docs.google.com/spreadsheets/d/1pAijbCOI0KUq29KYo4mW2YZj8iE7IW-T2S9p5GhgFMU/edit?gid=1129882996#gid=1129882996
              bbendick Brandon Bendickson made changes -
              Status In Progress [ 3 ] Needs 1st Level Review [ 10005 ]
              Hide
              Permalink
              bbendick Brandon Bendickson added a comment -

              Can you review the results. Which results should we use for Deseq, the new or the original?

              Show
              bbendick Brandon Bendickson added a comment - Can you review the results. Which results should we use for Deseq, the new or the original?
              bbendick Brandon Bendickson made changes -
              Assignee Brandon Bendickson [ bbendick ] Robert Reid [ robertreid ]
              Hide
              Permalink
              robofjoy Robert Reid added a comment -

              We use the original.

              Show
              robofjoy Robert Reid added a comment - We use the original.
              robofjoy Robert Reid made changes -
              Status Needs 1st Level Review [ 10005 ] First Level Review in Progress [ 10301 ]
              robofjoy Robert Reid made changes -
              Status First Level Review in Progress [ 10301 ] Ready for Pull Request [ 10304 ]
              robofjoy Robert Reid made changes -
              Status Ready for Pull Request [ 10304 ] Pull Request Submitted [ 10101 ]
              robofjoy Robert Reid made changes -
              Status Pull Request Submitted [ 10101 ] Reviewing Pull Request [ 10303 ]
              robofjoy Robert Reid made changes -
              Status Reviewing Pull Request [ 10303 ] Merged Needs Testing [ 10002 ]
              robofjoy Robert Reid made changes -
              Status Merged Needs Testing [ 10002 ] Post-merge Testing In Progress [ 10003 ]
              robofjoy Robert Reid made changes -
              Resolution Done [ 10000 ]
              Status Post-merge Testing In Progress [ 10003 ] Closed [ 6 ]

                People

                • Assignee:
                  robofjoy Robert Reid
                  Reporter:
                  robofjoy Robert Reid
                • Votes:
                  0 Vote for this issue
                  Watchers:
                  2 Start watching this issue

                  Dates

                  • Created:
                    Updated:
                    Resolved: