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chanzuckerberg
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idseq-workflows
Portable WDL workflows for IDseq production pipelines
https://idseq.net/
MIT License
31
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12
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fix fasta writing bug
#93
morsecodist
closed
3 years ago
4
adding provenance documentation for cg files
#92
katrinakalantar
closed
3 years ago
1
automating short-read-mngs full-size benchmarks
#91
mlin
closed
3 years ago
0
Update ivar trim to address issues with trimming in SWIFT/SNAP protocol
#90
katrinakalantar
closed
3 years ago
0
Updates to address gaps identified in initial ont validation
#89
katrinakalantar
closed
3 years ago
1
simplify pytest fixture scheme
#88
mlin
closed
3 years ago
0
Generalized CG updates
#87
kislyuk
closed
3 years ago
0
Update Consensus Genomes workflow to handle Oxford Nanopore data
#86
kislyuk
closed
3 years ago
4
retire idseq-dag step status JSON
#85
mlin
closed
3 years ago
0
Update CG Dockerfile
#84
kislyuk
closed
3 years ago
3
short-read-mngs auto_benchmark: measure precision/recall wrt taxa truth sets
#83
mlin
closed
3 years ago
1
Phylo Refactor
#82
morsecodist
closed
3 years ago
1
Fix typo in RemoveHost no reads left check
#81
jshoe
closed
3 years ago
0
Migrate status JSON files out of idseq-dag
#80
mlin
closed
3 years ago
3
Add utility functions to read truth files, compute AUPR
#79
kislyuk
closed
3 years ago
3
Add benchmark truth files to manifest
#78
kislyuk
closed
3 years ago
0
Question - workflow language selection evaluation?
#77
tfmorris
opened
3 years ago
2
added host genome generation wdl
#76
morsecodist
closed
3 years ago
1
increase sj collapsed limit
#75
morsecodist
closed
3 years ago
0
Create update-run.wdl
#74
lynnlangit
closed
3 years ago
8
Filter taxids out of hit summaries
#73
morsecodist
closed
3 years ago
2
Update Entrez contact address
#72
kislyuk
closed
3 years ago
0
enable the ability to create generic consensus genomes
#71
katrinakalantar
closed
3 years ago
1
Size of VMs needed for full metagenomics test
#70
lynnlangit
opened
3 years ago
0
Switch to stricter schema and simpler inheritence
#69
morsecodist
closed
3 years ago
0
Parsing Refactor
#68
morsecodist
closed
3 years ago
5
[CH-27791] Add check for "No reads after MakeConsensus"
#67
jshoe
closed
3 years ago
2
Fail if kSNP3 produces empty output
#66
morsecodist
closed
3 years ago
0
Low hanging fruit optimization of cluster file parsing
#65
morsecodist
closed
3 years ago
0
Added logs to deduplication step
#64
morsecodist
closed
3 years ago
0
idseq_dag/util/fasta.py: don't mangle FASTQ read names with pipe characters (second attempt)
#63
mlin
closed
3 years ago
0
idseq_dag/util/fasta.py: don't mangle FASTQ read names with pipe characters
#62
mlin
closed
3 years ago
2
Fix count for simple file truncation (no full check)
#61
tfrcarvalho
closed
3 years ago
0
Stop filtering short reads in validate input and make count more reliable
#60
tfrcarvalho
closed
3 years ago
0
short-read-mngs auto benchmarking framework
#59
mlin
closed
3 years ago
0
Add instructions to run CG locally
#58
tfrcarvalho
closed
3 years ago
0
Fix glob on trim reads that would not catch all output files
#57
tfrcarvalho
closed
3 years ago
0
Bug Fix: fixes logical condition when applying length correction
#56
tfrcarvalho
closed
3 years ago
0
Fix file reference to use miniwdl download caching logic
#55
tfrcarvalho
closed
3 years ago
1
local alignment: extract db to temp space instead of output dir
#54
mlin
closed
3 years ago
1
github CI: upgrade deprecated set-env
#53
mlin
closed
3 years ago
0
fix reading header bug
#52
morsecodist
closed
3 years ago
1
Compute and export alignment results from combining NT and NR hits
#51
tfrcarvalho
closed
3 years ago
0
Replace cdhit-dup with idseq-dedup
#50
morsecodist
closed
3 years ago
3
Add samtools_depth.txt to the output zip
#49
jshoe
closed
3 years ago
0
Add support for single-end fastqs
#48
tfrcarvalho
closed
3 years ago
0
Remove dag_branch from consensus-genome
#47
jshoe
closed
3 years ago
0
short-read-mngs unit tests v2
#46
mlin
closed
3 years ago
0
Emit depths file for consensus genome.
#45
tfrcarvalho
closed
4 years ago
0
add short-read-mngs end-to-end test to CI (using viral databases)
#44
mlin
closed
4 years ago
1
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