veg flea-pipeline issues

veg / flea-pipeline

A pipeline for long-read sequencing data.

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issues

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Request for a test case and clarification on reference and DB paths

#89 jong3 opened 1 month ago
0
Remove groovy meta declaration

#88 pditommaso closed 6 years ago
0
Failing tests

#87 stevenweaver closed 1 year ago
0
Compute JS divergence for earliest time point.

#86 kemaleren closed 6 years ago
0
bootstrap multiselect doesn't work anymore due to Ember version upgrade

#85 kemaleren closed 7 years ago
0
evo_history is missing time points

#84 kemaleren opened 7 years ago
1
Use all time points for inframe database

#83 kemaleren closed 7 years ago
0
Update config to default to local

#82 kemaleren closed 7 years ago
0
Deal with -1 coordinates when there is an insertion before the first reference coord

#81 kemaleren opened 7 years ago
1
Rotate MDS to maximize date variance along x axis

#80 kemaleren closed 7 years ago
1
Re-implement the 'pause to edit alignment' feature

#79 kemaleren opened 7 years ago
2
Check that <X% of reads are identified as contaminants.

#78 kemaleren opened 7 years ago
1
Check that error rate cutoff is consistent with contaminant identity

#77 kemaleren opened 7 years ago
0
Cannot do multiple concurrent runs on silverback

#76 kemaleren closed 7 years ago
3
Break Nextflow pipeline into sub-pipelines

#75 kemaleren opened 7 years ago
0
Build a Singularity container.

#74 kemaleren opened 7 years ago
0
Parallelize obtainEvolutionaryHistory.bf

#73 kemaleren closed 7 years ago
0
Dynamic directives for production and development

#72 kemaleren opened 7 years ago
0
Fix Viterbi length when trimming heads/tails.

#71 kemaleren closed 7 years ago
0
optionally remove HQCS with copynumber 0

#70 kemaleren closed 7 years ago
0
Keep high-probability out-of-frame sequences

#69 kemaleren opened 8 years ago
0
Better git branch structure

#68 kemaleren opened 8 years ago
1
Put time point labels in job names

#67 kemaleren closed 7 years ago
1
Tasks with unknown number of output files look for wrong leftover files

#66 kemaleren closed 7 years ago
1
Use quality scores in poly head/tail trimming model

#65 kemaleren opened 8 years ago
0
Use drmaa module for managing remote tasks

#64 kemaleren closed 7 years ago
0
Checkpointing does not work with sample_clusters task

#63 kemaleren closed 8 years ago
1
Support multithreading

#62 kemaleren closed 7 years ago
0
Report discarded sequences

#61 kemaleren opened 8 years ago
0
max length parameter interferes with copy number computation

#60 kemaleren opened 8 years ago
0
Disable FUBAR caching

#59 kemaleren closed 7 years ago
1
Better statistics for phenotope metrics

#58 kemaleren opened 8 years ago
0
User-settable parameters

#57 kemaleren closed 7 years ago
1
Allow user-specified clustering method

#56 kemaleren closed 7 years ago
1
usearch options: disallow gaps at the end

#55 kemaleren opened 8 years ago
0
Refactor CCS/HQCS pair tasks to reduce code duplication

#54 kemaleren closed 7 years ago
1
Compute copynumbers after editing alignment

#53 kemaleren closed 7 years ago
0
adding python gitignore file

#52 stevenweaver closed 6 years ago
1
adding installation requirements to setup.py file

#51 stevenweaver closed 9 years ago
0
Prepare package for release

#50 kemaleren closed 7 years ago
1
two-state HMM trims too much of the sequences

#49 kemaleren closed 7 years ago
1
usearch cannot handle long filenames

#48 kemaleren closed 9 years ago
1
test command line scripts

#47 kemaleren closed 7 years ago
0
break alignment pipeline into smaller subpipelines

#46 kemaleren closed 7 years ago
0
Quantify and summarize results of shift correction

#45 kemaleren closed 7 years ago
1
alignment diagnosis task not running on cluster

#44 kemaleren closed 9 years ago
2
Use custom exception types

#43 kemaleren closed 7 years ago
1
Unable to copy errors on silverback

#42 kemaleren closed 7 years ago
2
Parse logfile and get task running times

#41 kemaleren closed 7 years ago
1
More complete logs

#40 kemaleren closed 9 years ago
1