h3abionet HPCBio-Refgraph_pipeline issues

h3abionet / HPCBio-Refgraph_pipeline

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Adding Bowtie to Assemblie

#39 NeginValizadegan opened 1 year ago
1
updated the cdhit_test script automated new cdhit file

#38 NeginValizadegan closed 2 years ago
0
Add threading for process

#37 cjfields opened 2 years ago
0
Filtering & Annotation workflow

#36 cjfields opened 3 years ago
15
Merge MaSURCA code

#35 cjfields closed 3 years ago
0
Merge forks back into main branch

#34 cjfields closed 3 years ago
4
Extraction of discordant, splitter and unmapped reads

#33 yuantianhpc closed 3 years ago
1
Implement parameter summary output at beginning of pipeline run

#32 kkowalden opened 3 years ago
0
Test assemblies from bowtie2 alignment

#31 cjfields closed 3 years ago
1
Add updated extraction step to the workflow

#30 cjfields closed 3 years ago
1
Test sga

#29 cjfields closed 3 years ago
2
Small README.md update

#28 cjfields closed 3 years ago
0
Move assembly stats to new process

#27 cjfields closed 3 years ago
5
Get workflow warnings ironed out

#26 cjfields closed 3 years ago
3
Revert single line back

#25 cjfields closed 3 years ago
0
Update README

#24 cjfields closed 3 years ago
0
Allow queue to be configurable

#23 cjfields closed 3 years ago
0
Small spelling error

#22 cjfields closed 3 years ago
0
Implement location placement

#21 cjfields opened 3 years ago
0
Add step to extract mapped mates

#20 cjfields closed 3 years ago
1
Add back Kraken2 step

#19 cjfields closed 2 years ago
3
Prepare data for shipping from UIUC to ilifu

#18 grendon closed 3 years ago
8
Basic documentation

#17 cjfields closed 3 years ago
4
Implement contig coverage

#16 cjfields opened 3 years ago
1
Implement basic annotation

#15 cjfields closed 2 years ago
1
Implement contig filtering

#14 cjfields opened 3 years ago
1
Implement CI

#13 cjfields opened 3 years ago
0
Trimming optimization

#12 yuantianhpc closed 3 years ago
7
QC outputs

#11 cjfields opened 3 years ago
2
QC inputs

#10 cjfields closed 3 years ago
6
Generation of new 1000g data

#9 cjfields closed 3 years ago
9
Test updated master

#8 cjfields closed 3 years ago
0
Merge dev into master

#7 cjfields closed 3 years ago
1
masurca - generating config file on the fly

#6 grendon closed 3 years ago
5
Containerization of tools

#5 cjfields closed 3 years ago
3
assembly tool as input parameter

#4 grendon opened 4 years ago
3
in bamtofastq process: add option for single reads

#3 grendon closed 3 years ago
3
move module from the body to the directives of the process

#2 grendon closed 4 years ago
1
Add README.md file

#1 grendon closed 3 years ago
2