microbiomedata/metaPro

Issues

• Add CI/CD for proteomics workflows

  #70 opened 2 months ago by aclum
  1

• Clean-up inputs

  #71 opened a month ago by picowatt
  0

• Update README.md

  #68 opened 3 months ago by picowatt
  3

• Test Kaiko 1.2 with existing WDL

  #67 opened 4 months ago by picowatt
  1

• Implement Annotations File Generation

  #60 opened a year ago by picowatt
  1

• metaP passing in IDs for known files and sourcing those files

  #58 opened 6 months ago by aclum
  3

• Preparation Metadata: Proteomics

  #21 opened 3 years ago by mslarae13
  4

• Integrate Kaiko into WDL pipeline

  #39 opened 2 years ago by ssarrafan
  5

• Investigate GFF or GFF-like file Generation for Kaiko

  #59 opened 10 months ago by picowatt
  2

• Kaiko WDL file

  #62 opened 10 months ago by picowatt
  0

• Expose Kaikos Static Files to Its Container Via Cromwell Config

  #61 opened a year ago by picowatt
  0

• Benchmarking2.0: collect additional stats for newer runs (disk access, memory, N/w bandwidth, cpu time).

  #20 opened a year ago by anubhav0fnu
  7

• building, testing & integrating kaiko model to the metaPro workflow

  #13 opened a year ago by anubhav0fnu
  2

• Automate release packaging using GitHub Actions

  #57 opened a year ago by picowatt
  1

• Make config files inputs

  #53 opened a year ago by picowatt
  3

• Incorrect data_object_type for resultant file

  #54 opened a year ago by picowatt
  3

• Report generation Dockerfile using unsupported parent image

  #49 opened a year ago by picowatt
  2

• Update Dockerfile and WDL for metadata generation

  #47 opened a year ago by picowatt
  1

• Stop FDR recalculation if no FASTA split occurred

  #48 opened a year ago by picowatt
  0

• Add support for filtering taxa

  #37 opened a year ago by ssarrafan
  1

• Generate IDs using API

  #45 opened a year ago by picowatt
  2

• MASIC Files not found error during masicresultmerge task

  #44 opened a year ago by Michal-Babins
  0

• Move Kaiko pipeline to Python 3.9

  #35 opened a year ago by ssarrafan
  6

• Integrate schema pkg into WDL pipeline

  #41 opened 2 years ago by picowatt
  3

• Unit testing

  #38 opened 2 years ago by ssarrafan
  3

• QA execution and evaluation

  #27 opened 2 years ago by pdpiehowski
  13

• Combine kaiko-denovo and kaiko-taxonomy

  #34 opened 2 years ago by ssarrafan
  7

• Dockerize Kaiko pipeline

  #36 opened 2 years ago by ssarrafan
  6

• Add FDR calculation to processing

  #33 opened 2 years ago by picowatt
  1

• Move data defined in .env file to WDL inputs and update processing

  #31 opened 2 years ago by picowatt
  5

• Adapt ficus analysis script to conform to latest processing

  #29 opened 2 years ago by picowatt
  1

• WDL generation - make sure it matches the metaP pipeline

  #25 opened 2 years ago by ssarrafan
  3

• QA Benchmark specification

  #26 opened 2 years ago by ssarrafan
  3

• Concatenating FASTA and contaminate files

  #22 opened 2 years ago by picowatt
  0

• adding splitFasta logic to handle Fastas > 1gb in size.

  #11 opened 2 years ago by anubhav0fnu
  4

• re-process stegen dataset upon getting new genomic ids or attributes from JGI metagenome assembly.

  #12 opened 3 years ago by anubhav0fnu
  2

• process Prosser uniref dataset.

  #19 opened 2 years ago by anubhav0fnu
  2

• test and process spruce dataset on pnnl-MSC(Tahoma).

  #16 opened 3 years ago by anubhav0fnu
  8

• Proteomics fixes

  #18 opened 3 years ago by ssarrafan
  3

• metapro WDL bug fixing and enhancement.

  #17 opened 3 years ago by anubhav0fnu
  3

• Writing Cromwell-WDL to execute commands for multiple containers.

  #9 opened 3 years ago by anubhav0fnu
  9

• Benchmarking msgf+

  #10 opened 3 years ago by anubhav0fnu
  5

• update internalAnalysis and integrate with the workflow .

  #14 opened 3 years ago by anubhav0fnu
  1

• Finalize workflow for metaproteomics v2

  #6 opened 3 years ago by ssarrafan
  4

• Add example data and example run command

  #7 opened 3 years ago by Michal-Babins
  5

• testing code improvements with a few dry runs on our dataset(stegen).

  #8 opened 3 years ago by anubhav0fnu
  1

• Finalize workflow for metaproteomics

  #5 opened 3 years ago by ssarrafan
  2

• Workflows - Test large data sets for workflows (metaPro)

  #2 opened 3 years ago by ssarrafan
  0

• Workflows - Test small data sets for workflows (metaPro)

  #3 opened 3 years ago by ssarrafan
  1

• define cases where blank and QC would be needed

  #4 opened 3 years ago by dehays
  1