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nf-core
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fastquorum
Pipeline to produce consensus reads using unique molecular indexes/barcodes (UMIs)
https://nf-co.re/fastquorum
MIT License
20
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9
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fix: output bai from ALIGN_CONSENSUS_BAM
#79
znorgaard
closed
1 week ago
2
Output bai when using ht mode
#78
SPPearce
closed
1 week ago
4
chore: bump dev version
#77
znorgaard
closed
3 weeks ago
5
chore: bump dev version
#76
znorgaard
closed
3 weeks ago
3
chore: correct date
#75
znorgaard
closed
3 weeks ago
1
mapped BAM index not produced in high-throughput (ht) mode
#74
lauren-tjoeka
closed
1 week ago
5
The retry strategy used for memory / cpu usage in FastQC and consensus reads is brittle
#73
lbeltrame
opened
4 weeks ago
0
Remove double image in the README
#72
SPPearce
opened
4 weeks ago
1
Add stubs to all local modules
#71
SPPearce
closed
4 weeks ago
4
chore: release 1.0.1
#70
znorgaard
closed
3 weeks ago
2
chore: prepare for 1.0.1 release
#69
znorgaard
closed
4 weeks ago
1
bugfix: merging lanes would result in an error
#68
nh13
closed
2 months ago
5
Allow igenomes to work
#67
SPPearce
closed
2 months ago
2
fix: support when multiple value args can be a number or a comma-delimited string
#66
nh13
closed
2 months ago
2
Update the validation* arguments as per the nf-schema migration guide
#65
nh13
opened
2 months ago
0
igenomes does not currently work
#64
SPPearce
closed
2 months ago
1
Enable validation lenient mode to allow filter_min_reads to be an integer or string
#63
SPPearce
closed
2 months ago
4
Fix passing filter_min_reads as int
#62
prot-devin
closed
2 months ago
2
Add KAPA to the list of Vendors/Kits
#61
nh13
opened
2 months ago
1
Allow escalation of memory for FilterConsensusReads
#60
SPPearce
closed
2 months ago
3
fix: add error retry for fgbio's FilterConsensusReads
#59
nh13
closed
2 months ago
2
Add when conditions to prepare
#58
SPPearce
closed
2 months ago
4
Hardcoded 8GB limit in the FilterConsensusReads processes
#57
lbeltrame
closed
2 months ago
6
Cannot skip BWA index generation
#56
lbeltrame
closed
2 months ago
2
RFE: Quality trimming in the pipeline
#55
lbeltrame
opened
4 months ago
1
bugfix: merging lanes would result in an error
#54
nh13
closed
2 months ago
2
GroupReadsByUmi failing on one sample
#53
SPPearce
closed
2 months ago
10
Error at GroupReadsByUmi due to read order?
#52
davidmasp
opened
4 months ago
5
docs: update subway diagrams
#51
nh13
closed
4 months ago
2
updates post 1.0.0 release
#50
nh13
closed
2 months ago
4
1.0.0 redux
#49
nh13
closed
4 months ago
1
release 1.0.0 post fixes
#48
nh13
closed
4 months ago
1
Improve the output usage
#47
nh13
opened
4 months ago
0
Add additional metrics to MultiQC
#46
nh13
opened
4 months ago
1
Use updated fgbio modules in nf-core/modules
#45
nh13
opened
4 months ago
0
Suggestions
#44
SPPearce
closed
4 months ago
1
ci: update snapshots with 1.0.0 release
#43
nh13
closed
4 months ago
1
Release 1.0.0
#42
nh13
closed
4 months ago
4
Bump version to 1.0
#41
nh13
closed
4 months ago
1
Use fgbio-slim when not producing plots
#40
nh13
opened
4 months ago
0
Alternative specification of FASTQs and read structures
#39
nh13
opened
4 months ago
0
add support for samples to have multiple runs or lanes
#38
nh13
closed
4 months ago
4
Support for third UMI read
#37
adamrtalbot
closed
4 months ago
2
doc: update docs with more explanations
#36
nh13
closed
4 months ago
1
Cat fastq
#35
SPPearce
closed
4 months ago
5
doc: add fastquorum subway diagram
#34
nh13
closed
4 months ago
5
High throughput version of the best practices
#33
nh13
closed
4 months ago
1
Fix duplicate line README.md
#32
nh13
closed
4 months ago
1
Important! Template update for nf-core/tools v2.14.1
#31
nf-core-bot
closed
4 months ago
1
Template update for nf-core/tools version 2.14.1
#30
nh13
closed
4 months ago
1
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