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Arcadia-Science
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metagenomics
A Nextflow workflow for QC, evaluation, and profiling of metagenomic samples using short- and long-read technologies
MIT License
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Terminal Freeze Issue: Arcadia Bioinformatics Pipeline Hangs at ARCADIASCIENCE_METAGENOMICS Process
#63
ianvalenca
opened
1 year ago
5
Add documentation for accepted DIAMOND columns
#62
elizabethmcd
opened
1 year ago
0
prepare for pub and v1.0.0 release
#61
elizabethmcd
closed
1 year ago
0
Quick code review
#60
mertcelebi
closed
1 year ago
1
updated documentation with DIAMOND information, cleaned up some spots
#59
elizabethmcd
closed
1 year ago
0
Update documentation with sourmash/DIAMOND db instructions
#58
elizabethmcd
closed
1 year ago
1
DIAMOND implementation
#57
elizabethmcd
closed
1 year ago
3
Prodigal addition, small fixes and updates
#56
elizabethmcd
closed
1 year ago
0
Create samplesheet listing files needed for downstream steps
#55
elizabethmcd
opened
1 year ago
0
make subfolders for sourmash commands
#54
elizabethmcd
closed
1 year ago
1
Reports with sourmashconsumr
#53
elizabethmcd
opened
1 year ago
0
Add hifiasm-meta subworkflow
#52
elizabethmcd
opened
1 year ago
0
Eam/docs citations cleanup
#51
elizabethmcd
closed
1 year ago
0
add DIAMOND subworkflow
#50
elizabethmcd
closed
1 year ago
1
Sourmash gather implementation
#49
elizabethmcd
closed
1 year ago
2
Sourmash gather/taxonomy updates
#48
elizabethmcd
closed
1 year ago
1
Swap polishing tool racon for medaka
#47
elizabethmcd
closed
1 year ago
0
Sourmash additions for processing reads and assemblies
#46
elizabethmcd
closed
1 year ago
1
Eam/rename contigs
#45
elizabethmcd
closed
1 year ago
0
Fixes for mapping queues
#44
elizabethmcd
closed
1 year ago
0
Fix mapping queueing for 1:1 mapping
#43
elizabethmcd
closed
1 year ago
1
Move away from nf-core-modified org of modules
#42
elizabethmcd
opened
1 year ago
0
README/docs fixes
#41
elizabethmcd
closed
1 year ago
1
CITATIONS syntax
#40
elizabethmcd
closed
1 year ago
1
Eam/samtools
#39
elizabethmcd
closed
1 year ago
0
Documentation
#38
elizabethmcd
closed
1 year ago
0
Eam/multiqc
#37
elizabethmcd
closed
1 year ago
2
MultiQC Reporting and QC Tools
#36
elizabethmcd
closed
1 year ago
0
nf-core linting
#35
elizabethmcd
closed
1 year ago
1
fix samplesheet input script
#34
elizabethmcd
closed
1 year ago
1
Github CI tests
#33
elizabethmcd
closed
1 year ago
3
Fix schema
#32
elizabethmcd
closed
1 year ago
1
Nanopore depth subworkflow and small organizational modifications
#31
elizabethmcd
closed
1 year ago
0
Taxonomy/element summaries
#30
elizabethmcd
closed
1 year ago
1
Test multiple rounds of polishing for Nanopore workflow
#29
elizabethmcd
closed
1 year ago
2
Add Github CI
#28
elizabethmcd
closed
1 year ago
1
Add multiqc reporting
#27
elizabethmcd
closed
1 year ago
1
Adds a nanopore workflow with long read modules added
#26
elizabethmcd
closed
1 year ago
0
Reconfigure workflow into separate illumina and nanopore workflows
#25
elizabethmcd
closed
1 year ago
0
added illumina test dataset link
#24
elizabethmcd
closed
1 year ago
0
Adds support for samplesheet input
#23
elizabethmcd
closed
1 year ago
0
fix version output
#22
elizabethmcd
closed
1 year ago
1
CPU resource allocation for assembly process
#21
elizabethmcd
closed
1 year ago
1
Time-series reciprocal mapping
#20
elizabethmcd
opened
1 year ago
2
Single copy marker searches to aid manual binning
#19
elizabethmcd
closed
1 year ago
2
Process for downloading databases
#18
elizabethmcd
closed
1 year ago
2
Modification aware basecalling for long read workflow
#17
borgesadair1
closed
1 year ago
4
Test dataset config
#16
elizabethmcd
closed
1 year ago
2
QC: Fastp > MultiQC
#15
elizabethmcd
closed
1 year ago
1
Remove the nf-core SPAdes module and create local metaSPAdes module
#14
elizabethmcd
closed
1 year ago
0
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