microbiomedata/metat issues and pull requests

#41 - Enable "Edit on GitHub" link by defining `:github_url:` in `index.rst`

Pull Request - State: closed - Opened by eecavanna about 2 months ago

#40 - Enable "Edit on GitHub" link by defining `:github_url:` in `index.rst`

Issue - State: closed - Opened by eecavanna about 2 months ago - 1 comment

#39 - Update documentation

Pull Request - State: closed - Opened by kaijli 3 months ago - 2 comments

#38 - branch to check http import for nmdc

Pull Request - State: closed - Opened by kaijli 5 months ago

#37 - Metatranscriptome workflow validation

Issue - State: closed - Opened by aclum 7 months ago - 7 comments

#36 - MetaT update to JGI workflows

Pull Request - State: closed - Opened by kaijli 7 months ago - 4 comments

#35 - rfam failing for small sample files

Issue - State: closed - Opened by mflynn-lanl 7 months ago - 4 comments

#34 - replaced "databases" with "${database}"

Pull Request - State: closed - Opened by mflynn-lanl 8 months ago

#33 - remove hard-coded reference database paths

Issue - State: closed - Opened by mflynn-lanl 8 months ago - 1 comment

#32 - placeholder ticket for updating annotation version for the metatranscriptome workflow

Issue - State: closed - Opened by aclum 9 months ago - 4 comments

#31 - testResults04092024 Assembly make_info_file issues

Issue - State: closed - Opened by aclum 9 months ago - 1 comment

#30 - metat_output [sample]_sorted_features.tsv should be standardized

Issue - State: open - Opened by jzrapp over 1 year ago

#29 - failed workflow runs with different error log. Complete successfully during rerun with same settings.

Issue - State: open - Opened by jzrapp over 1 year ago

#28 - Featurecount is assigning 0 reads to features.

Issue - State: open - Opened by mshakya over 1 year ago

#28 - Featurecount is assigning 0 reads to features.

Issue - State: open - Opened by mshakya over 1 year ago

#27 - feature request for rqcfilter implementation - removeribo

Issue - State: closed - Opened by jzrapp over 1 year ago - 2 comments
Labels: enhancement

#26 - user reported issue on R script command being invalid

Issue - State: closed - Opened by mshakya over 1 year ago - 7 comments

#26 - user reported issue on R script command being invalid

Issue - State: closed - Opened by mshakya over 1 year ago - 7 comments

#25 - annotation wdls should point to mg_annotation instead of being copied into this repo

Issue - State: closed - Opened by aclum almost 2 years ago

#24 - create human readable methods readme for metatranscriptome analysis

Issue - State: open - Opened by aclum about 2 years ago - 1 comment

#23 - Finish MetaT Sync & Refactoring

Issue - State: closed - Opened by Michal-Babins over 2 years ago - 4 comments
Labels: workflows, backlog

#22 - Update annotation

Pull Request - State: closed - Opened by Michal-Babins almost 3 years ago

#21 - Update annotation

Pull Request - State: closed - Opened by Michal-Babins almost 3 years ago

#20 - Updated multiple features and merged with JGI

Pull Request - State: closed - Opened by Michal-Babins almost 3 years ago

#19 - Add the identifiers for overlapping transcripts from different strands for the MetaT workflow.

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

#18 - Jgi merge

Pull Request - State: closed - Opened by Michal-Babins over 3 years ago

#17 - Fix Sbatch Submission Error for Feature Count

Issue - State: open - Opened by Michal-Babins over 3 years ago - 1 comment

#16 - Adjust metaT workflow with inputs from JGI

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

#15 - Working WDLS

Pull Request - State: closed - Opened by Michal-Babins over 3 years ago - 1 comment

#14 - expose memory requirement parameter for assembly

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

#13 - Full wdl v1

Pull Request - State: closed - Opened by mshakya over 3 years ago

#12 - Finish end-to-end workflows for MT

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

#11 - copy output.json file from cromwell-executions to an output directory

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

#10 - added edgeR as an input to call cs.dockcal_scores and py_pack_path to…

Pull Request - State: closed - Opened by mflynn-lanl almost 4 years ago

#9 - tasks not importing correctly when wdl file was being executed from workflows folder

Issue - State: closed - Opened by mshakya almost 4 years ago - 2 comments

#8 - differentiate metagenome and metatranscriptome annotation and assembly

Issue - State: closed - Opened by dehays almost 4 years ago - 1 comment

#7 - Workflows - Test small data sets for workflows (metaT)

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

#6 - Workflows - Test large data sets for workflows (metaT)

Issue - State: closed - Opened by ssarrafan almost 4 years ago - 11 comments
Labels: workflows

#5 - A good way to import python classes and scripts

Issue - State: closed - Opened by mshakya about 4 years ago - 2 comments
Labels: enhancement

#4 - Clean up and discard tasks and scripts that are no longer being used

Issue - State: open - Opened by mshakya about 4 years ago - 1 comment
Labels: enhancement

#3 - Write a task that collects all relevant output files in one place

Issue - State: closed - Opened by mshakya about 4 years ago - 1 comment
Labels: enhancement

#2 - Merge hisat2 and samtools docker to single metaT image if possible

Issue - State: closed - Opened by mshakya about 4 years ago - 1 comment
Labels: bug, enhancement

#1 - Rename contig names based on the project id

Issue - State: closed - Opened by mshakya about 4 years ago - 1 comment
Labels: enhancement

GitHub / microbiomedata/metat issues and pull requests