Public-Health-Bioinformatics cpo-pipeline issues

Public-Health-Bioinformatics / cpo-pipeline

An analysis pipeline for the purpose of investigating Carbapenemase-Producing Organisms.

MIT License

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issues

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Bash script edits

#51 DiDigsDNA closed 5 years ago
1
added 'sample_id' to headers for 'final_plasmid.tsv' and 'custom_plas…

#50 DiDigsDNA closed 5 years ago
0
Provide header for plasmid output

#49 dfornika closed 5 years ago
8
updated path to abricate_cpo_plasmid_db

#48 DiDigsDNA closed 5 years ago
2
Configuration error: databases/abricate_cpo_plasmid_db

#47 dfornika closed 5 years ago
3
Retry downloads if they fail due to NCBI rate-limit

#46 dfornika closed 5 years ago
0
Concurrent NCBI Refseq Downloads

#45 dfornika closed 5 years ago
0
Cleanup

#44 dfornika closed 5 years ago
0
Code Cleanup

#43 dfornika opened 5 years ago
15
Filter plasmids

#42 dfornika closed 5 years ago
0
Additional output

#41 dfornika closed 5 years ago
0
Update tree module

#40 dfornika closed 5 years ago
0
Add structured logging using 'structlog' library

#39 dfornika closed 5 years ago
0
Plasmid analysis

#38 dfornika closed 5 years ago
0
Plasmid Analysis

#37 dfornika opened 5 years ago
2
Add functions to collect and write final outputs table

#36 dfornika closed 5 years ago
1
Collect Relevant Outputs

#35 dfornika closed 5 years ago
0
Quast 5

#34 dfornika closed 5 years ago
0
Use Quast-5.* (includes BUSCO)

#33 dfornika closed 5 years ago
1
Merge pipelines

#32 dfornika closed 5 years ago
0
Split resistance from typing

#31 dfornika closed 5 years ago
0
Split out 'resistance' from 'typing' module.

#30 dfornika closed 5 years ago
0
Use drmaa-python library to submit jobs from pipeline scripts.

#29 dfornika closed 5 years ago
0
Output dir structure

#28 dfornika closed 5 years ago
0
Split qsub files

#27 dfornika closed 5 years ago
0
Use drmaa python library to submit qsub jobs from pipeline.py scripts

#26 dfornika closed 5 years ago
0
Split qsub job scripts into one script per tool

#25 dfornika closed 5 years ago
0
Collect Provenance Data

#24 dfornika opened 5 years ago
2
New assembly parser tests

#23 dfornika closed 5 years ago
0
Tree parsers testing

#22 dfornika closed 5 years ago
0
Complete testing for Tree Result Parsers

#21 dfornika closed 5 years ago
0
check for external program completion

#20 bfjia closed 5 years ago
2
Testing for parsers in 'typing' phase of pipeline.

#19 dfornika closed 5 years ago
0
Post assembly qc

#18 bfjia closed 5 years ago
0
Complete Testing for Typing Result Parsers

#17 dfornika closed 5 years ago
0
Better error handling

#16 bfjia opened 5 years ago
1
QC Logic for post assembly quality controls

#15 bfjia closed 5 years ago
2
Assembly parsers

#14 dfornika closed 5 years ago
0
Complete Testing for Assembly Result Parsers

#13 dfornika closed 5 years ago
1
Genome coverage estimation

#12 bfjia closed 5 years ago
1
Produce a report that summarizes Pass/Fail for each QC check for each sample

#11 dfornika opened 5 years ago
1
Ensure that a tree is still produced even if some samples fail

#10 dfornika opened 5 years ago
0
Decide on output directory structure

#9 dfornika closed 5 years ago
3
Merge Pipeline Phases Into One Unified Pipeline

#8 dfornika closed 5 years ago
2
Complete Testing for All Result Parsers

#7 dfornika closed 5 years ago
0
Improved logging

#6 dfornika closed 5 years ago
0
Remove 'pipeline_assembly_contaminant.sh' script

#5 dfornika closed 5 years ago
1
Determine 'Expected species' automatically

#4 dfornika closed 5 years ago
3
Remove dependency on pandas in pipeline script

#3 dfornika closed 5 years ago
0
Verify integrity and identity of databases

#2 dfornika opened 5 years ago
1