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AVR-biosecurity-bioinformatics
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freyr
A Nextflow-based metabarcoding pipeline for agricultural biosecurity and biosurveillance
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bug fixes with Nanopore code
#29
jackscanlan
closed
2 weeks ago
0
Nanopore handling
#28
jackscanlan
closed
2 weeks ago
0
Adjustments to DADA2 parameters when using Nanopore data
#27
jackscanlan
opened
3 weeks ago
1
Handle when ASV is longer than reference database sequence (BLAST)
#26
jackscanlan
opened
3 weeks ago
1
Handle extra process time needed for the first pull of a container
#25
jackscanlan
opened
3 weeks ago
1
Basic handling of Nanopore-derived `.fastq(.gz)` files as data input
#24
jackscanlan
closed
2 weeks ago
0
Workflow structure converted one that contains subworkflows + preliminary single-end read support
#22
jackscanlan
closed
4 weeks ago
0
Investigate `tronko` for taxonomic assignment via phylogenetic placement
#21
jackscanlan
opened
4 weeks ago
0
update subworkflow-conversion branch
#20
jackscanlan
closed
1 month ago
0
Informative error when samplesheet contains incorrect primer sequences
#19
jackscanlan
opened
1 month ago
0
Group modules into subworkflows
#17
jackscanlan
closed
4 weeks ago
0
Chunk `TAX_IDTAXA` input to speed up taxonomic assignment
#16
jackscanlan
opened
1 month ago
0
Train taxonomic assignment models from FASTA within freyr
#15
alexpiper
opened
1 month ago
1
Add a licence
#14
alexpiper
opened
1 month ago
1
Add OTU clustering functionality
#13
alexpiper
opened
1 month ago
4
Rework `output` directory
#12
jackscanlan
opened
1 month ago
0
Read tracking might be broken at FILTER_SEQTAB and beyond
#11
jackscanlan
opened
1 month ago
0
Add multithreading to R-based processes
#9
jackscanlan
closed
2 weeks ago
0
Add template `samplesheet.csv` and `loci_params.csv` to respository
#8
jackscanlan
opened
1 month ago
0
Resolve duplicated functions.R files
#7
alexpiper
closed
1 month ago
2
Make process resource requirements depend dynamically on input file properties
#6
jackscanlan
opened
1 month ago
0
Rareplot error causes pipeline failure at process PHYLOSEQ_UNFILTERED
#5
alexpiper
closed
1 month ago
1
Add ability to override specific values in the `loci_params.csv` input file via pipeline parameters
#4
jackscanlan
closed
1 month ago
3
Handle case where no samples exceed `min_sample_reads` loci parameter
#3
jackscanlan
opened
1 month ago
2
Containerisation of processes, and Shifter profile
#2
jackscanlan
closed
3 months ago
0
Direct package loading
#1
jackscanlan
closed
4 months ago
0