cerebis meta-sweeper issues

cerebis / meta-sweeper

Parametric sweep of simulated microbial communities and metagenomic sequencing.

GNU General Public License v3.0

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A5 use of Unix "file" command is tricked by symbolic links

#79 cerebis closed 7 years ago
2
Low coverage assemblies can return non-zero exit

#78 cerebis opened 7 years ago
0
More recent versions of Nextflow throw exceptions with MetaSweeper.java

#77 cerebis closed 7 years ago
1
Check sort order on contact_map.py

#76 cerebis opened 7 years ago
0
Organisation of shared dependent modules

#75 cerebis opened 7 years ago
0
Unintended rescaling of trans-rate

#74 cerebis closed 7 years ago
0
Possible extension of profiles to include more definition.

#73 cerebis opened 7 years ago
0
Implement free shearing simulation

#72 cerebis opened 7 years ago
0
Multi-chrom genomes with procedural abundances

#71 cerebis opened 7 years ago
0
Fine-tuning simple structure simulation by nested intervals

#70 cerebis opened 7 years ago
1
Treatment of sparse sites and wgs read-pair noise

#69 cerebis closed 7 years ago
4
Specifying a few resource limits might be useful.

#68 cerebis opened 7 years ago
0
Facility for fixed, user defined tree

#67 cerebis closed 7 years ago
2
Occasional occurence of java.util.ConcurrentModificationException

#66 cerebis opened 7 years ago
0
Unintended continuation when single clade timeseries is given a multiple clade community

#65 cerebis opened 7 years ago
0
snvbpnmft.py throws an error when there are no reliable variant sites.

#64 cerebis closed 7 years ago
0
Use of JavaSE8 Map.putIfAbsent()

#63 cerebis opened 7 years ago
0
nextflow hangs rather than exiting after workflow termination

#62 koadman opened 7 years ago
3
params.debug undefined

#61 koadman closed 7 years ago
5
Only two clades are used in multi-clade configurations

#60 koadman closed 7 years ago
0
Random sampling of parameter space

#59 cerebis opened 7 years ago
1
pipeline_utils.py is not used

#58 cerebis closed 7 years ago
0
bash_configure not setting environment variables

#57 koadman closed 7 years ago
3
Add documentation for satisfying beagle-lib dependency of timeseries workflow.

#56 cerebis closed 7 years ago
1
wait_on jiffy only works for single files.

#55 cerebis opened 7 years ago
0
test profile table no long correct format

#54 cerebis closed 7 years ago
0
JNI_LIB_PATH should not be an explicit absolute path

#53 cerebis closed 7 years ago
1
sim3C: consider exposing more parameters controlling empirical distribution to users

#52 cerebis opened 7 years ago
0
3-way channel cross in multisample

#51 koadman opened 7 years ago
1
Merge multisample into master

#50 koadman closed 7 years ago
0
Validate poly-chromosomal genomes in sim3C

#49 cerebis closed 7 years ago
1
Validate treatment of sim3C site duplication

#48 cerebis closed 7 years ago
2
Adopt a space efficient graph interchange format

#47 cerebis opened 7 years ago
4
Some naive operations possess poor time complexity.

#46 cerebis closed 7 years ago
0
Longer read-pairs (250bp) can lead to read-through problems. Add a warning.

#45 cerebis closed 7 years ago
5
Read creation rate of ART could be improved.

#44 cerebis closed 7 years ago
1
sim3C should make use of a observer pattern

#43 cerebis opened 7 years ago
0
SimForward must gracefully handle templates without cutsites

#42 cerebis closed 7 years ago
2
Simulating sequencing reads

#41 cerebis closed 7 years ago
0
BWA MEM mapping can produce no mapped reads to some contigs

#40 cerebis opened 7 years ago
6
Ability to simulate simple 3D structure in Hi-C/3C reads

#39 koadman opened 8 years ago
17
Add procedural tree and profile support to workflow

#38 cerebis closed 7 years ago
1
simForward.py appears to have a minor defect in sample from distributions

#37 cerebis closed 7 years ago
1
Assigning profiles within and across trees.

#36 cerebis closed 7 years ago
3
Procedural abundance profiles

#35 cerebis closed 8 years ago
2
Non-deterministic cache misses

#34 cerebis closed 8 years ago
4
Cached custom objects rely on weak hash codes

#33 cerebis closed 7 years ago
6
Nextflow resume is broken by the NamedValue helper class

#32 cerebis closed 8 years ago
1
phylogenetic tree generation

#31 cerebis closed 8 years ago
8
support a 'local' config outside the repo

#30 koadman closed 7 years ago
0