Issues

• feat(Summary workflow): additional annotation dependent metrics

  enhancementlow priority
  iRNA-COSI/APAeval#468 · Filter by author ninsch3000 opened on Aug 18, 2023

• chore: migrate containers from dockerhub.io/apaeval to biocontainers

  iRNA-COSI/APAeval#467 · Filter by author ninsch3000 opened on Aug 17, 2023

• feat(Summary workflow): check that PAS are reported as single nucleotide in input bed

  enhancement
  iRNA-COSI/APAeval#458 · Filter by author ninsch3000 opened on Jan 10, 2023

• feat(Execution workflows / Utils): making RefSeq annotations work for QAPA and PAQR.

  blockedenhancement
  iRNA-COSI/APAeval#457 · Filter by author mrgazzara opened on Dec 20, 2022
  3

• chore: remove unnecessary requirement in identification swf

  low priority
  iRNA-COSI/APAeval#456 · Filter by author dominikburri opened on Nov 29, 2022

• refactor: Singularity from conda environment might cause errors

  low priority
  iRNA-COSI/APAeval#418 · Filter by author dominikburri opened on Sep 7, 2022
  1

• feat(Execution workflow): LABRAT feature to reuse previous makeTFfasta output

  enhancementlow priority
  iRNA-COSI/APAeval#406 · Filter by author mrgazzara opened on Aug 9, 2022
  2

• fix(Summary workflows): don't overwrite previous results on new run

  buglow prioritynextflow
  iRNA-COSI/APAeval#400 · Filter by author ninsch3000 opened on Aug 5, 2022
  2

• docs(Summary Workflows): Logging

  documentationgood first issuelow priority
  iRNA-COSI/APAeval#394 · Filter by author ninsch3000 opened on Jul 28, 2022

• feat(Execution workflow): CSI-UTR - report Format 04 BED file in workflow (per-PAS fractional relative usage)

  iRNA-COSI/APAeval#388 · Filter by author SamBryce-Smith opened on Jul 18, 2022
  4

  

• docs(Execution workflow): update output file specifications for reporting region-level 'polyA site usage scores'

  documentation
  iRNA-COSI/APAeval#380 · Filter by author SamBryce-Smith opened on Jul 13, 2022
  

• feat(Summary workflows): new SWF for relative usage quantification

  meta
  iRNA-COSI/APAeval#371 · Filter by author ninsch3000 opened on Jul 7, 2022

• chore(CommBench): Meta issue

  manuscriptsmeta
  iRNA-COSI/APAeval#335 · Filter by author uniqueg opened on Jul 6, 2022 · Community benchmarking manuscript

• feat(Summary workflow): Utils script/module to filter and convert ground truth TPM data to be compatible with relative quantification benchmark

  high priority
  iRNA-COSI/APAeval#301 · Filter by author faricazjj opened on Jun 12, 2022
  3

  

• feat(Summary workflows): Differential summary workflow

  low priority
  iRNA-COSI/APAeval#294 · Filter by author faricazjj opened on Jun 12, 2022
  1

• feat(Publication): Plot outside of OpenEBench

  duplicate
  iRNA-COSI/APAeval#290 · Filter by author faricazjj opened on Jun 12, 2022
  2

• feat(Execution workflow):Time and memory usage

  iRNA-COSI/APAeval#270 · Filter by author faricazjj opened on Jun 12, 2022
  1

  

• fix(Execution workflow): APAtrap input parameter boolean check

  bug
  iRNA-COSI/APAeval#244 · Filter by author faricazjj opened on May 6, 2022
  

• refactor: update Snakemake version in apaeval_env.yaml

  enhancementlow priority
  iRNA-COSI/APAeval#223 · Filter by author ninsch3000 opened on Apr 1, 2022

• feat(Utils): BAM to FASTQ

  iRNA-COSI/APAeval#209 · Filter by author dominikburri opened on Jan 11, 2022
  3

  

• docs: prefer relative paths if possible

  documentationgood first issuelow priority
  iRNA-COSI/APAeval#192 · Filter by author dominikburri opened on Nov 10, 2021

• feat(Utils): add tool to convert reference PAS bed to gtf

  enhancement
  iRNA-COSI/APAeval#190 · Filter by author ninsch3000 opened on Nov 10, 2021

• feat(Utils): Add utilility to sort a BED file by chromosome and coordinate

  iRNA-COSI/APAeval#186 · Filter by author SamBryce-Smith opened on Oct 13, 2021
  

• test: Add genome fasta file to test_data directory

  iRNA-COSI/APAeval#178 · Filter by author SamBryce-Smith opened on Sep 23, 2021
  

• docs: update participant contributions

  documentationquestion
  iRNA-COSI/APAeval#111 · Filter by author FitzsimmonsCM opened on Jun 3, 2021
  72