Ecosyste.ms: Issues

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GitHub / microbiomedata/workflowplanning issues and pull requests

#38 - monitor the health status for NMDC EDGE

Issue - State: closed - Opened by ssarrafan over 2 years ago - 4 comments

#37 - Add mongoDB and validation to automation workflow

Issue - State: closed - Opened by ssarrafan over 2 years ago - 6 comments
Labels: Backlog

#35 - Processing of GROW data

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

#33 - Proposal: include GO functional annotation in annotation workflows

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

#32 - MetaG update from JGI

Issue - State: closed - Opened by hubin-keio almost 3 years ago - 5 comments
Labels: Backlog

#31 - Create a script for JSON object generation without GOLD ID.

Issue - State: closed - Opened by hubin-keio almost 3 years ago - 4 comments

#30 - Post 2022 GSP Cleanup

Issue - State: closed - Opened by scanon about 3 years ago - 1 comment

#29 - Process Bioscales data in preparation for release to portal

Issue - State: closed - Opened by ssarrafan about 3 years ago - 4 comments
Labels: April2022 Release

#28 - Process EMP500 data in preparation for release to portal

Issue - State: closed - Opened by ssarrafan about 3 years ago - 6 comments
Labels: April2022 Release

#27 - Process MPI data in preparation for release to portal

Issue - State: closed - Opened by ssarrafan about 3 years ago - 1 comment

#26 - Edge - Install Condor for UCSD instance

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

#25 - Document process and requirements needed to test workflows

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

#24 - Finish end-to-end workflows for MG going from raw reads to all data products.

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

#23 - GFF3 outputs

Issue - State: open - Opened by hubin-keio about 4 years ago - 4 comments

#22 - (WIP) Add annotation WDL files

Pull Request - State: open - Opened by scanon almost 5 years ago

#21 - First pull request for MVP metatranscriptomic pipeline

Pull Request - State: closed - Opened by mshakya almost 5 years ago

#20 - Consolidate assembly pipelines

Issue - State: closed - Opened by scanon almost 5 years ago - 1 comment
Labels: enhancement

#19 - fix bug: bbmap array variable cannot be using as ${} File/String in c…

Pull Request - State: closed - Opened by chienchi almost 5 years ago

#19 - fix bug: bbmap array variable cannot be using as ${} File/String in c…

Pull Request - State: closed - Opened by chienchi almost 5 years ago

#18 - Cromwell does not "infile" as variable. It is a bug. Use input_files …

Pull Request - State: closed - Opened by chienchi almost 5 years ago

#17 - Update assembly output to _contigs.fna

Pull Request - State: closed - Opened by chienchi almost 5 years ago

#16 - assembly input json use array File for fastq

Pull Request - State: closed - Opened by chienchi almost 5 years ago

#15 - Update MAGs and Assembly workflow

Pull Request - State: closed - Opened by chienchi almost 5 years ago

#14 - Update Assembly and MAGs workflow to support JTM dynamic worker

Pull Request - State: closed - Opened by chienchi almost 5 years ago

#13 - supported JTM dynamic worker

Pull Request - State: closed - Opened by poeli almost 5 years ago

#12 - Updated planning for Meta-proteomics workflow

Pull Request - State: closed - Opened by anubhav0fnu almost 5 years ago - 1 comment

#11 - Create Task-2.1.5-2.md

Pull Request - State: closed - Opened by ghost almost 5 years ago

#10 - Update Assembly workflow to JGI version

Pull Request - State: closed - Opened by chienchi about 5 years ago

#9 - read-based analysis pipeline

Pull Request - State: closed - Opened by poeli about 5 years ago - 1 comment

#8 - The workflow for Task2.1.2

Pull Request - State: closed - Opened by poeli about 5 years ago - 1 comment

#7 - Adding WDL and Docker files and run example for Task 2.1.1 and 2.1.3

Pull Request - State: closed - Opened by chienchi about 5 years ago - 1 comment

#6 - Update

Pull Request - State: closed - Opened by chienchi over 5 years ago

#5 - Update Task-2.1.1.md

Pull Request - State: closed - Opened by mhuntemann over 5 years ago

#4 - Cornwell v44

Pull Request - State: closed - Opened by poeli over 5 years ago - 2 comments

#3 - Task 2.1.2

Pull Request - State: closed - Opened by poeli over 5 years ago

#1 - Adding requirements and brief desc for Task2.1.1 and Task2.1.3

Pull Request - State: closed - Opened by chienchi over 5 years ago