CDCgov/tostadas

Issues

• [External] [Bug] Error when running a submission that does not require fasta file

  #239 opened 12 days ago by Alan-Collins
  0

• [Internal] [Bug] Submission code is not checking locally for report.xml

  #237 opened 21 days ago by jessicarowell
  0

• [Internal] [Bug] User config plugins will be ignored: nf-schema@2.1.1 and invalid input values

  #234 opened 22 days ago by jessicarowell
  0

• [Internal] [Bug] UnboundLocalError: local variable 'sra_submission' referenced before assignment

  #231 opened a month ago by jessicarowell
  1

• [Internal] [Feature] Refactor to bulk-submit samples

  #213 opened 2 months ago by jessicarowell
  0

• [Internal] [Feature] Fix tests (for Github Actions)

  #220 opened 2 months ago by jessicarowell
  0

• [Internal] [Bug] "DataFrame columns are not unique" in BioSample

  #230 opened 21 days ago by jessicarowell
  1

• [Internal] [Feature] Incorporate AST and other optional bacteria BioSample attributes to submission.xml

  #219 opened 21 days ago by jessicarowell
  0

• [Internal] [Bug] Conflicts running TOSTADAS on AWS

  #235 opened 22 days ago by jessicarowell
  0

• [External] [Bug] Docker profile bug for submission

  #233 opened 22 days ago by kyleoconnell
  1

• [Internal] [Bug] 'Not a valid path value:' for relative paths on command line

  #227 opened a month ago by jessicarowell
  1

• Bug: Discrepancies in nextflow.config and test.config Files

  #226 opened 23 days ago by RamiyapriyaS
  0

• [Internal] [Bug] Conda environment on scicomp: RepeatMasker::createLib(): Error

  #216 opened 23 days ago by jessicarowell
  0

• [Internal] [Bug] Conda on Scicomp: Issue with cache clearing

  #224 opened 23 days ago by RamiyapriyaS
  0

• [Internal] [Feature] Make these custom field validations "smarter"

  #198 opened 9 months ago by jessicarowell
  0

• [Internal] [Bug] Nextflow version 24.04.2 and nextflow.config tower configuration incompatibility

  #210 opened a month ago by jessicarowell
  1

• [Internal] [Feature] Refactor to support nanopore data

  #172 opened 10 months ago by jessicarowell
  0

• [External] [Bug] Pandas 'host_age' KeyError in Test Profile

  #225 opened a month ago by nrminor
  1

• [Internal] [Feature] Cloud support for submissions

  #204 opened 3 months ago by jessicarowell
  0

• [Internal] [Bug] Implement logging after the batch submission code is written

  #212 opened 2 months ago by jessicarowell
  0

• [Internal] [Feature] Support for GEO submissions

  #229 opened a month ago by jessicarowell
  0

• [Internal] [Bug] Vadr missing from conda profile

  #222 opened 2 months ago by jessicarowell
  1

• [External] [Bug] test fails at validation step

  #201 opened 2 months ago by ammaraziz
  1

• [Internal] [Bug] Change age to host_age in metadata template

  #223 opened 2 months ago by jessicarowell
  1

• [Internal] [Feature] Accommodate additional biosample metadata templates starting with wastewater

  #189 opened 2 months ago by kyleoconnell
  1

• [Internal] [Bug] RepeatMasker GFF "IndexError: list index out of range"

  #221 opened 2 months ago by RamiyapriyaS
  1

• [Internal] [Feature] Build submission process directly into pipeline

  #203 opened 2 months ago by jessicarowell
  0

• [Internal] [Bug] Table2asn error on test data user-provided annotations: duplicate Bioseq id

  #217 opened 2 months ago by jessicarowell
  0

• [Internal] [Bug] GenBank folder not showing up in outdir/submission_outputs

  #214 opened 2 months ago by jessicarowell
  1

• [External] [Feature] Clarify Conda Requirement

  #199 opened 2 months ago by garfinjm
  1

• [Internal] [Feature] Recode SeqSender to modify data validation

  #181 opened 2 months ago by kyleoconnell
  1

• [Internal] [Feature] Write a new update_submission.py script

  #211 opened 2 months ago by jessicarowell
  0

• [Internal] [Feature] Change name of fastq files before SRA upload

  #209 opened 2 months ago by jessicarowell
  1

• [Internal] [Feature] SRA Publication Delay Release

  #206 opened 2 months ago by jessicarowell
  1

• [Internal] [Bug] New code not generating report.xml after submission

  #205 opened 2 months ago by jessicarowell
  1

• [Internal] [Feature] Ensure metadata validation is checking all fields required for NCBI submission

  #183 opened 3 months ago by kyleoconnell
  1

• [Internal] [Feature] Check metadata date format

  #154 opened 3 months ago by kyleoconnell
  1

• [External] [Bug] CWE-798 Security Vulnerability - Plain Text Password

  #202 opened 3 months ago by thomasphung
  0

• [Internal] [Feature] Refactor submission scripts so that each python script from seqsender is a separate local nf process

  #147 opened 3 months ago by kyleoconnell
  1

• [Internal] [Bug] fasta_path cannot be empty (sra-only submissions)

  #191 opened 9 months ago by jessicarowell
  0

• [Internal] [Feature] Make bakta db download occur if user doesn't provide path to bakta db

  #151 opened 10 months ago by kyleoconnell
  0

• [Internal] [Feature] Evaluate if we need Run_utility or not

  #176 opened 10 months ago by kyleoconnell
  1

• [Internal] [Feature] Evaluate if we need 'Check Files' Module.

  #169 opened 10 months ago by kyleoconnell
  1

• [Internal] [Bug] Won't accept any 'dots' in sample file names

  #173 opened 10 months ago by jessicarowell
  0

• [Internal] [Bug] Remove fasta file name from metadata excel sheet.

  #148 opened 10 months ago by kyleoconnell
  1

• [Internal] [Feature] Convert param validation to nf-core validation plugin

  #158 opened a year ago by kyleoconnell
  1

• [Internal] [Feature] Move viral and bacterial annotation to subworkflows

  #155 opened a year ago by kyleoconnell
  0

• [Internal] [Test] Refactor BAKTA to a single subworkflow instead of calling the processes in the main workflow.

  #161 opened a year ago by kyleoconnell
  0

• [Internal] [Bug] **Installation for CDC**

  #160 opened a year ago by lskatz
  1

• [Internal] [Feature] For Bacteria / Bakta, align submission outputs with Bakta native submission capabilities

  #149 opened a year ago by kyleoconnell
  1