Uploaded image for project: 'IGB'
  1. IGB
  2. IGBF-3043

Align and process rice RNA-Seq data using nf-core/rnaseq pipeline

    Details

    • Type: Task
    • Status: Closed (View Workflow)
    • Priority: Major
    • Resolution: Done
    • Affects Version/s: None
    • Fix Version/s: None
    • Labels:
      None
    • Story Points:
      2
    • Sprint:
      Spring 1 2022 Jan 3 - Jan 14, Spring 2 2022 Jan 18 - Jan 28, Spring 3 2022 Jan 31 - Feb 11, Spring 4 2022 Feb 14 - Feb 25, Spring 5 2022 Feb 28 - Mar 11

      Description

      Align and process RNA-Seq data using nf-core/rnaseq pipeline

        Attachments

          Issue Links

            Activity

            ann.loraine Ann Loraine created issue -
            ann.loraine Ann Loraine made changes -
            Field Original Value New Value
            Epic Link IGBF-3039 [ 21553 ]
            ann.loraine Ann Loraine made changes -
            Sprint Spring 1 2022 Jan 3 - Jan 14 [ 136 ] Spring 1 2022 Jan 3 - Jan 14, Spring 2 2022 Jan 18 - Jan 28 [ 136, 137 ]
            ann.loraine Ann Loraine made changes -
            Rank Ranked higher
            ann.loraine Ann Loraine made changes -
            Status To-Do [ 10305 ] In Progress [ 3 ]
            ann.loraine Ann Loraine made changes -
            Assignee Ann Loraine [ aloraine ]
            ann.loraine Ann Loraine made changes -
            Status In Progress [ 3 ] To-Do [ 10305 ]
            ann.loraine Ann Loraine made changes -
            Status To-Do [ 10305 ] In Progress [ 3 ]
            ann.loraine Ann Loraine made changes -
            Comment [ More errors:

            {code}
              >>>>> Now validing the length of the 2 paired-end infiles: A.C.Y.S.3_1_trimmed.fq.gz and A.C.Y.S.3_2_trimmed.fq.gz <<<<<
              Writing validated paired-end Read 1 reads to A.C.Y.S.3_1_val_1.fq.gz
              Writing validated paired-end Read 2 reads to A.C.Y.S.3_2_val_2.fq.gz
              
              Read 2 output is truncated at sequence count: 23469680, please check your paired-end input files! Terminating...
              
              INFO: Cleaning up image...

            Work dir:
              /nobackup/lorainelab/salty_rice/rna-seq/work/c7/25844b7fa5600e4c60222407461493

            Tip: you can replicate the issue by changing to the process work dir and entering the command `bash .command.run`
            {code}

            ]
            ann.loraine Ann Loraine made changes -
            Description Align and process RNA-Seq data using nf-core/rnaseq pipeline Align and process RNA-Seq data using nf-core/rnaseq pipeline
            ann.loraine Ann Loraine made changes -
            Assignee Ann Loraine [ aloraine ]
            ann.loraine Ann Loraine made changes -
            Assignee Ann Loraine [ aloraine ]
            ann.loraine Ann Loraine made changes -
            Status In Progress [ 3 ] To-Do [ 10305 ]
            ann.loraine Ann Loraine made changes -
            Status To-Do [ 10305 ] In Progress [ 3 ]
            ann.loraine Ann Loraine made changes -
            Status In Progress [ 3 ] To-Do [ 10305 ]
            ann.loraine Ann Loraine made changes -
            Sprint Spring 1 2022 Jan 3 - Jan 14, Spring 2 2022 Jan 18 - Jan 28 [ 136, 137 ] Spring 1 2022 Jan 3 - Jan 14, Spring 2 2022 Jan 18 - Jan 28, Spring 3 2022 Jan 31 - Feb 11 [ 136, 137, 138 ]
            ann.loraine Ann Loraine made changes -
            Rank Ranked higher
            ann.loraine Ann Loraine made changes -
            Status To-Do [ 10305 ] In Progress [ 3 ]
            ann.loraine Ann Loraine made changes -
            Status In Progress [ 3 ] To-Do [ 10305 ]
            ann.loraine Ann Loraine made changes -
            Sprint Spring 1 2022 Jan 3 - Jan 14, Spring 2 2022 Jan 18 - Jan 28, Spring 3 2022 Jan 31 - Feb 11 [ 136, 137, 138 ] Spring 1 2022 Jan 3 - Jan 14, Spring 2 2022 Jan 18 - Jan 28, Spring 3 2022 Jan 31 - Feb 11, Spring 4 2022 Feb 14 - Feb 25 [ 136, 137, 138, 139 ]
            ann.loraine Ann Loraine made changes -
            Rank Ranked higher
            ann.loraine Ann Loraine made changes -
            Status To-Do [ 10305 ] In Progress [ 3 ]
            ann.loraine Ann Loraine made changes -
            Status In Progress [ 3 ] To-Do [ 10305 ]
            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 -
            Assignee Ann Loraine [ aloraine ] Nowlan Freese [ nfreese ]
            nfreese Nowlan Freese made changes -
            Status Needs 1st Level Review [ 10005 ] First Level Review in Progress [ 10301 ]
            nfreese Nowlan Freese made changes -
            Assignee Nowlan Freese [ nfreese ] Ann Loraine [ aloraine ]
            nfreese Nowlan Freese made changes -
            Status First Level Review in Progress [ 10301 ] To-Do [ 10305 ]
            ann.loraine Ann Loraine made changes -
            Sprint Spring 1 2022 Jan 3 - Jan 14, Spring 2 2022 Jan 18 - Jan 28, Spring 3 2022 Jan 31 - Feb 11, Spring 4 2022 Feb 14 - Feb 25 [ 136, 137, 138, 139 ] Spring 1 2022 Jan 3 - Jan 14, Spring 2 2022 Jan 18 - Jan 28, Spring 3 2022 Jan 31 - Feb 11, Spring 4 2022 Feb 14 - Feb 25, Spring 5 2022 Feb 28 - Mar 11 [ 136, 137, 138, 139, 140 ]
            ann.loraine Ann Loraine made changes -
            Rank Ranked higher
            ann.loraine Ann Loraine made changes -
            Status To-Do [ 10305 ] In Progress [ 3 ]
            ann.loraine Ann Loraine made changes -
            Status In Progress [ 3 ] To-Do [ 10305 ]
            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 -
            Assignee Ann Loraine [ aloraine ]
            nfreese Nowlan Freese made changes -
            Status Needs 1st Level Review [ 10005 ] First Level Review in Progress [ 10301 ]
            nfreese Nowlan Freese made changes -
            Assignee Nowlan Freese [ nfreese ]
            nfreese Nowlan Freese made changes -
            Assignee Nowlan Freese [ nfreese ]
            nfreese Nowlan Freese 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 ]
            ann.loraine Ann Loraine made changes -
            Assignee Ann Loraine [ aloraine ]
            nfreese Nowlan Freese made changes -
            Link This issue relates to IGBF-3099 [ IGBF-3099 ]
            ann.loraine Ann Loraine made changes -
            Summary Align and process RNA-Seq data using nf-core/rnaseq pipeline Align and process rice RNA-Seq data using nf-core/rnaseq pipeline

              People

              • Assignee:
                ann.loraine Ann Loraine
                Reporter:
                ann.loraine Ann Loraine
              • Votes:
                0 Vote for this issue
                Watchers:
                Start watching this issue

                Dates

                • Created:
                  Updated:
                  Resolved: