microbiomedata/metapro issues and pull requests

#76 - 15 metap documentation

Pull Request - State: closed - Opened by picowatt 2 months ago

#75 - 74 update workflow figure

Pull Request - State: closed - Opened by kaijli 3 months ago

#74 - Update workflow figure

Issue - State: closed - Opened by kaijli 3 months ago

#73 - fix annotation file name

Issue - State: open - Opened by mflynn-lanl 4 months ago

#72 - docker field is an invalid image name

Issue - State: open - Opened by mflynn-lanl 5 months ago
Labels: backlog

#71 - Clean-up inputs

Issue - State: open - Opened by picowatt 6 months ago
Labels: backlog

#70 - Add CI/CD for proteomics workflows

Issue - State: open - Opened by aclum 7 months ago - 2 comments

#69 - 68 update readmemd for 20 release

Pull Request - State: closed - Opened by picowatt 8 months ago

#68 - Update README.md

Issue - State: closed - Opened by picowatt 9 months ago - 3 comments

#67 - Test Kaiko 1.2 with existing WDL

Issue - State: closed - Opened by picowatt 10 months ago - 1 comment
Labels: X Small

#66 - Feature/1.2.1

Pull Request - State: closed - Opened by picowatt 11 months ago

#65 - 58 metap passing in ids for known files and sourcing those files

Pull Request - State: closed - Opened by picowatt 12 months ago - 1 comment

#64 - 62 kaiko wdl file

Pull Request - State: closed - Opened by picowatt over 1 year ago

#63 - add kaiko shared volume to docker submit for local runs only

Pull Request - State: closed - Opened by picowatt over 1 year ago

#62 - Kaiko WDL file

Issue - State: closed - Opened by picowatt over 1 year ago
Labels: Small

#61 - Expose Kaikos Static Files to Its Container Via Cromwell Config

Issue - State: closed - Opened by picowatt over 1 year ago
Labels: X Small

#60 - Implement Annotations File Generation

Issue - State: open - Opened by picowatt over 1 year ago - 1 comment
Labels: Medium, backlog

#59 - Investigate GFF or GFF-like file Generation for Kaiko

Issue - State: closed - Opened by picowatt over 1 year ago - 2 comments
Labels: X Small, backlog

#58 - metaP passing in IDs for known files and sourcing those files

Issue - State: closed - Opened by aclum over 1 year ago - 3 comments

#57 - Automate release packaging using GitHub Actions

Issue - State: open - Opened by picowatt over 1 year ago - 1 comment
Labels: Small, backlog

#56 - 53 make config files inputs

Pull Request - State: closed - Opened by picowatt over 1 year ago

#55 - fix issue with wrong resultant file name being search for

Pull Request - State: closed - Opened by picowatt over 1 year ago

#54 - Incorrect data_object_type for resultant file

Issue - State: closed - Opened by picowatt over 1 year ago - 3 comments
Labels: bug, X Small

#53 - Make config files inputs

Issue - State: closed - Opened by picowatt over 1 year ago - 3 comments
Labels: X Small

#52 - update parent image for postprocessing container

Pull Request - State: closed - Opened by picowatt over 1 year ago

#51 - 47 update dockerfile and wdl for metadata generation

Pull Request - State: closed - Opened by picowatt over 1 year ago

#50 - 48 stop fdr recalculation if no fasta split occurred

Pull Request - State: closed - Opened by picowatt over 1 year ago

#49 - Report generation Dockerfile using unsupported parent image

Issue - State: closed - Opened by picowatt over 1 year ago - 2 comments
Labels: bug, X Small

#48 - Stop FDR recalculation if no FASTA split occurred

Issue - State: closed - Opened by picowatt over 1 year ago
Labels: X Small

#47 - Update Dockerfile and WDL for metadata generation

Issue - State: closed - Opened by picowatt over 1 year ago - 1 comment
Labels: Small

#46 - 45 generate ids using api

Pull Request - State: closed - Opened by picowatt over 1 year ago

#45 - Generate IDs using API

Issue - State: closed - Opened by picowatt almost 2 years ago - 2 comments
Labels: Small

#44 - MASIC Files not found error during masicresultmerge task

Issue - State: open - Opened by Michal-Babins almost 2 years ago
Labels: bug, GSP2023

#43 - 41 integrate schema pkg into wdl pipeline

Pull Request - State: closed - Opened by picowatt almost 2 years ago

#42 - 27 qa execution and evaluation

Pull Request - State: closed - Opened by picowatt almost 2 years ago

#41 - Integrate schema pkg into WDL pipeline

Issue - State: closed - Opened by picowatt almost 2 years ago - 3 comments
Labels: enhancement, Small

#40 - 33 add fdr calculation to processing

Pull Request - State: closed - Opened by picowatt about 2 years ago

#39 - Integrate Kaiko into WDL pipeline

Issue - State: open - Opened by ssarrafan about 2 years ago - 5 comments
Labels: Large, backlog

#38 - Unit testing

Issue - State: closed - Opened by ssarrafan about 2 years ago - 3 comments
Labels: Small, backlog

#38 - Unit testing

Issue - State: closed - Opened by ssarrafan about 2 years ago - 3 comments
Labels: Small, backlog

#37 - Add support for filtering taxa

Issue - State: closed - Opened by ssarrafan about 2 years ago - 1 comment
Labels: Small, backlog

#36 - Dockerize Kaiko pipeline

Issue - State: closed - Opened by ssarrafan about 2 years ago - 6 comments
Labels: Small

#35 - Move Kaiko pipeline to Python 3.9

Issue - State: closed - Opened by ssarrafan about 2 years ago - 6 comments
Labels: Small, backlog

#34 - Combine kaiko-denovo and kaiko-taxonomy

Issue - State: closed - Opened by ssarrafan about 2 years ago - 7 comments
Labels: Small

#33 - Add FDR calculation to processing

Issue - State: closed - Opened by picowatt about 2 years ago - 1 comment
Labels: Small

#32 - 31 move data defined in env file to wdl inputs and update processing

Pull Request - State: closed - Opened by picowatt about 2 years ago

#31 - Move data defined in .env file to WDL inputs and update processing

Issue - State: closed - Opened by picowatt about 2 years ago - 5 comments
Labels: Small

#30 - 29 adapt ficus analysis script to conform to latest processing

Pull Request - State: closed - Opened by picowatt over 2 years ago

#29 - Adapt ficus analysis script to conform to latest processing

Issue - State: closed - Opened by picowatt over 2 years ago - 1 comment
Labels: X Small

#28 - 25 wdl generation make sure it matches the metap pipeline

Pull Request - State: closed - Opened by picowatt over 2 years ago

#27 - QA execution and evaluation

Issue - State: closed - Opened by pdpiehowski over 2 years ago - 13 comments

#26 - QA Benchmark specification

Issue - State: closed - Opened by ssarrafan over 2 years ago - 3 comments
Labels: Small

#25 - WDL generation - make sure it matches the metaP pipeline

Issue - State: closed - Opened by ssarrafan over 2 years ago - 3 comments
Labels: Small

#24 - add concat of input FASTA with contaminate file

Pull Request - State: closed - Opened by picowatt over 2 years ago

#23 - 11 adding splitfasta logic to handle fastas 1gb in size

Pull Request - State: closed - Opened by picowatt over 2 years ago

#22 - Concatenating FASTA and contaminate files

Issue - State: closed - Opened by picowatt over 2 years ago

#21 - Preparation Metadata: Proteomics

Issue - State: open - Opened by mslarae13 over 3 years ago - 4 comments
Labels: X Large, backlog

#21 - Preparation Metadata: Proteomics

Issue - State: open - Opened by mslarae13 over 3 years ago - 4 comments
Labels: X Large, backlog

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

Issue - State: closed - Opened by anubhav0fnu almost 3 years ago - 7 comments

#19 - process Prosser uniref dataset.

Issue - State: closed - Opened by anubhav0fnu almost 3 years ago - 2 comments

#18 - Proteomics fixes

Issue - State: closed - Opened by ssarrafan over 3 years ago - 3 comments

#17 - metapro WDL bug fixing and enhancement.

Issue - State: closed - Opened by anubhav0fnu over 3 years ago - 3 comments

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

Issue - State: closed - Opened by anubhav0fnu over 3 years ago - 8 comments

#15 - Update internal_analysis.py

Pull Request - State: open - Opened by yuqiangao over 3 years ago

#14 - update internalAnalysis and integrate with the workflow .

Issue - State: closed - Opened by anubhav0fnu over 3 years ago - 1 comment

#13 - building, testing & integrating kaiko model to the metaPro workflow

Issue - State: closed - Opened by anubhav0fnu over 3 years ago - 2 comments
Labels: backlog

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

Issue - State: closed - Opened by anubhav0fnu over 3 years ago - 2 comments

#11 - adding splitFasta logic to handle Fastas > 1gb in size.

Issue - State: closed - Opened by anubhav0fnu over 3 years ago - 4 comments

#10 - Benchmarking msgf+

Issue - State: closed - Opened by anubhav0fnu over 3 years ago - 5 comments

#9 - Writing Cromwell-WDL to execute commands for multiple containers.

Issue - State: closed - Opened by anubhav0fnu over 3 years ago - 9 comments

#8 - testing code improvements with a few dry runs on our dataset(stegen).

Issue - State: closed - Opened by anubhav0fnu over 3 years ago - 1 comment

#7 - Add example data and example run command

Issue - State: closed - Opened by Michal-Babins over 3 years ago - 5 comments

#6 - Finalize workflow for metaproteomics v2

Issue - State: closed - Opened by ssarrafan over 3 years ago - 4 comments
Labels: Medium

GitHub / microbiomedata/metapro issues and pull requests