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isugifNF
/
polishCLR
A nextflow pipeline for polishing CLR assemblies
https://isugifnf.github.io/polishCLR/
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error exit status (139) during ARROW_02:merge_consensus in the Case I run
#65
junesk9
opened
1 year ago
0
docs: Document params with test data files
#64
j23414
closed
1 year ago
0
Doc step2
#63
j23414
closed
1 year ago
1
add default parameter documentation
#62
j23414
closed
1 year ago
0
update figure 01
#61
j23414
closed
1 year ago
0
reformat: publishDir
#60
j23414
closed
1 year ago
0
Generalizable split
#59
j23414
closed
1 year ago
1
nextflow conda launcher can pick the wrong java version
#58
cement-head
opened
1 year ago
5
Remove old input code
#57
j23414
closed
1 year ago
0
defaultBranch: changed to main
#56
j23414
closed
1 year ago
0
add: more descriptive input file msgs
#55
j23414
closed
1 year ago
0
Drop templates
#54
j23414
closed
1 year ago
0
archive canu trio input
#53
j23414
closed
1 year ago
0
Update Pipeline Diagram
#52
j23414
closed
1 year ago
0
Bug: Singularity image with get_seqs returning segfault
#51
j23414
closed
1 year ago
1
reformat: remove any module load calls
#50
j23414
closed
1 year ago
1
test: singularity
#49
Sivanandan
closed
1 year ago
1
reformat: readability
#48
j23414
closed
1 year ago
2
Update: Dockerfile
#47
j23414
closed
1 year ago
1
update bwa-mem2 version command
#46
j23414
closed
1 year ago
0
feat: throw an error on invalid flags
#45
j23414
closed
1 year ago
2
feat: check software dependencies
#44
j23414
closed
1 year ago
0
feat: surface customized parameters for sub programs
#43
j23414
closed
1 year ago
0
Bring in QUAST?
#42
Astahlke
closed
1 year ago
1
Mitogenome missing error
#41
Astahlke
closed
1 year ago
3
What's up with the java install?
#40
Astahlke
closed
1 year ago
2
Stahlke wip
#39
Astahlke
closed
1 year ago
0
add: smaller dataset
#38
j23414
closed
1 year ago
9
Add an “unrecognized parameter” catch-all kind of error
#37
j23414
closed
1 year ago
0
Rebuild new image for DockerHub and test on singularity (HPC)
#36
j23414
closed
2 years ago
4
workaround for singularity not activating micromamba env
#35
j23414
closed
2 years ago
0
Add jekyll read-the-docs
#34
j23414
closed
1 year ago
4
setup ci
#33
j23414
closed
2 years ago
0
Turn on nextflow ci
#32
j23414
closed
2 years ago
1
docs: docker image
#31
j23414
closed
2 years ago
0
Alt edits
#30
j23414
closed
2 years ago
0
Possible example data
#29
Astahlke
closed
2 years ago
1
Require PacBio CLR data to be bam files
#28
j23414
opened
2 years ago
1
Final QV Report
#27
j23414
opened
2 years ago
1
Atlas issues
#26
Astahlke
closed
1 year ago
1
Flag renaming for clarity
#25
Astahlke
closed
2 years ago
1
SLURM fails when there are too many contigs
#24
Astahlke
opened
2 years ago
0
Module refactor
#23
j23414
closed
2 years ago
0
log software versions
#22
j23414
closed
1 year ago
2
Purge dups
#21
j23414
closed
2 years ago
0
TrioCanu assembly input
#20
j23414
closed
2 years ago
3
Temporary method of splitting pipeline
#19
j23414
closed
2 years ago
0
Add an `--alternative_assembly` flag
#18
j23414
closed
2 years ago
2
latest
#17
j23414
closed
2 years ago
0
revert combineVCF to avoid "duplicate sample name error"
#16
j23414
closed
2 years ago
0
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