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microbiomedata
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metaT
Metatranscriptomics workflow
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branch to check http import for nmdc
#38
kaijli
closed
2 weeks ago
0
Metatranscriptome workflow validation
#37
aclum
closed
1 month ago
7
MetaT update to JGI workflows
#36
kaijli
closed
2 weeks ago
4
rfam failing for small sample files
#35
mflynn-lanl
closed
2 months ago
4
replaced "databases" with "${database}"
#34
mflynn-lanl
closed
2 weeks ago
0
remove hard-coded reference database paths
#33
mflynn-lanl
closed
2 weeks ago
1
placeholder ticket for updating annotation version for the metatranscriptome workflow
#32
aclum
closed
2 weeks ago
4
testResults04092024 Assembly make_info_file issues
#31
aclum
closed
3 months ago
1
metat_output [sample]_sorted_features.tsv should be standardized
#30
jzrapp
opened
1 year ago
0
failed workflow runs with different error log. Complete successfully during rerun with same settings.
#29
jzrapp
opened
1 year ago
0
Featurecount is assigning 0 reads to features.
#28
mshakya
opened
1 year ago
0
feature request for rqcfilter implementation - removeribo
#27
jzrapp
closed
2 months ago
2
user reported issue on R script command being invalid
#26
mshakya
closed
1 year ago
7
annotation wdls should point to mg_annotation instead of being copied into this repo
#25
aclum
closed
2 weeks ago
0
create human readable methods readme for metatranscriptome analysis
#24
aclum
opened
1 year ago
1
Finish MetaT Sync & Refactoring
#23
Michal-Babins
closed
6 months ago
4
Update annotation
#22
Michal-Babins
closed
2 years ago
0
Update annotation
#21
Michal-Babins
closed
2 years ago
0
Updated multiple features and merged with JGI
#20
Michal-Babins
closed
2 years ago
0
Add the identifiers for overlapping transcripts from different strands for the MetaT workflow.
#19
ssarrafan
closed
2 years ago
4
Jgi merge
#18
Michal-Babins
closed
2 years ago
0
Fix Sbatch Submission Error for Feature Count
#17
Michal-Babins
opened
3 years ago
1
Adjust metaT workflow with inputs from JGI
#16
hubin-keio
closed
2 years ago
9
Working WDLS
#15
Michal-Babins
closed
3 years ago
1
expose memory requirement parameter for assembly
#14
mshakya
closed
2 months ago
5
Full wdl v1
#13
mshakya
closed
3 years ago
0
Finish end-to-end workflows for MT
#12
ssarrafan
closed
3 years ago
3
copy output.json file from cromwell-executions to an output directory
#11
mflynn-lanl
closed
3 years ago
2
added edgeR as an input to call cs.dockcal_scores and py_pack_path to…
#10
mflynn-lanl
closed
3 years ago
0
tasks not importing correctly when wdl file was being executed from workflows folder
#9
mshakya
closed
3 years ago
2
differentiate metagenome and metatranscriptome annotation and assembly
#8
dehays
closed
2 months ago
1
Workflows - Test small data sets for workflows (metaT)
#7
ssarrafan
closed
3 years ago
3
Workflows - Test large data sets for workflows (metaT)
#6
ssarrafan
closed
3 years ago
11
A good way to import python classes and scripts
#5
mshakya
closed
2 months ago
2
Clean up and discard tasks and scripts that are no longer being used
#4
mshakya
opened
3 years ago
1
Write a task that collects all relevant output files in one place
#3
mshakya
closed
3 years ago
1
Merge hisat2 and samtools docker to single metaT image if possible
#2
mshakya
closed
2 years ago
1
Rename contig names based on the project id
#1
mshakya
closed
3 years ago
1