uphl-biongs / donut_falls Goto Github PK
View Code? Open in Web Editor NEWBasic workflow for nanopore sequencing data
License: MIT License
Basic workflow for nanopore sequencing data
License: MIT License
Needing updates: staphb/dragonflye from 1.0.14 to 1.1.2 staphb/fastp from 0.23.2 to 0.23.4 staphb/flye from 2.9.2 to 2.9.3 staphb/htslib from 1.17 to 1.19 staphb/nanoplot from 1.40.0 to 1.42.0 staphb/rasusa from 0.7.0 to 0.8.0 staphb/raven from 1.8.1 to 1.8.3
Homopolish uses a similar genome to reduce indel errors. It would be useful to have as an option.
Something like https://github.com/vgl-hub/gfastats or https://github.com/ggonnella/gfapy
If a sequence is closed, send to circlator
Needing updates: staphb/fastp from 0.23.2 to 0.23.4
Needing updates:
dsl1 support will be discontinued in 12-18 months
Needing updates: staphb/dragonflye from 1.0.14 to 1.1.1 staphb/fastp from 0.23.2 to 0.23.4 staphb/flye from 2.9.2 to 2.9.3 staphb/htslib from 1.17 to 1.19 staphb/nanoplot from 1.40.0 to 1.41.6 staphb/raven from 1.8.1 to 1.8.3
This one is going to take some thought since it's like its own workflow, but it should probably get added. The process file is there, but it's not tests.
to resolve discrepencies
Needing updates: staphb/dragonflye from 1.0.14 to 1.1.2 staphb/fastp from 0.23.2 to 0.23.4 staphb/flye from 2.9.2 to 2.9.3 staphb/htslib from 1.17 to 1.19 staphb/nanoplot from 1.40.0 to 1.42.0 staphb/rasusa from 0.7.0 to 0.8.0 staphb/raven from 1.8.1 to 1.8.3
Needing updates: staphb/dragonflye from 1.0.14 to 1.1.1 staphb/fastp from 0.23.2 to 0.23.4 staphb/flye from 2.9.2 to 2.9.3 staphb/htslib from 1.17 to 1.18 staphb/nanoplot from 1.40.0 to 1.41.6 staphb/raven from 1.8.1 to 1.8.3
https://www.biorxiv.org/content/10.1101/2024.03.07.584013v1.full.pdf
"Overall, we recommend the following polishing strategies:
Polypolish-careful alone when depth is very low (<5×), Polypolish-careful and Pypolcacareful when depth is low (5–25×), and Polypolish-default and Pypolca-careful when depth is
sufficient (>25×)."
At least so it mentions the wiki
Needing updates: staphb/dragonflye from 2.9.2 to 1.0.14
Actually get this option working
Needing updates: staphb/fastp from 0.23.2 to 0.23.4
Hi Erin,
I edited the UPHL.config file calling it FBPHL.config
Within the file, I edited the comment portion, replacing it with the path of my Donut_Falls.nf file:
nextflow run /home/bi_fellow/Donut_Falls/Donut_Falls.nf -c /home/bi_fellow/Donut_Falls/configs/FBPHL.config -with-dag donut_falls_$(date +"%y-%m-%d-%H%M%S").png
Was that right?
However, when I run this
nextflow run UPHL-BioNGS/Donut_falls -profile singularity --reads LR_fastqs/barcode01.fastq.gz --reads reads
I got this
UPHL-BioNGS/Donut_falls
currently is sticked on revision: erin-dev -- you need to specify explicitly a revision with the option -r
to use it
What could be the issue?
Thanks,
TJ
Needing updates: staphb/busco from 5.6.1-prok-bacteria_odb10_2024-01-08 to 5.6.1
Needing updates:
Needing updates: staphb/dragonflye from 2.9.2 to 1.0.14
There needs to be an input channel for users to specify their own busco database so it doesn't need to be downloaded at runtime for each sample.
Needing updates: staphb/busco from 5.6.1-prok-bacteria_odb10_2024-01-08 to 5.6.1
Take https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0060204 into consideration
Needing updates: staphb/busco from 5.6.1-prok-bacteria_odb10_2024-01-08 to 5.6.1
Needing updates: staphb/busco from 5.6.1-prok-bacteria_odb10_2024-01-08 to 5.6.1
Needing updates:
Needing updates: staphb/fastp from 0.23.2 to 0.23.4
Needing updates: staphb/dragonflye from 1.0.14 to 1.1.2 staphb/fastp from 0.23.2 to 0.23.4 staphb/flye from 2.9.2 to 2.9.3 staphb/htslib from 1.17 to 1.19 staphb/nanoplot from 1.40.0 to 1.42.0 staphb/polypolish from 0.5.0 to 0.6.0 staphb/rasusa from 0.7.0 to 0.8.0 staphb/raven from 1.8.1 to 1.8.3
Needing updates:
Fix
>1 circ=false len=1653372 gc=30.47 cov=1251.36 asmb=unicycler stp=False
Most bacteria that "we" sequence have a 5M genome. It'd be faster if filtlong used that instead of keeping 95%.
Needing updates: staphb/busco from 5.6.1-prok-bacteria_odb10_2024-01-08 to 5.6.1
First. Genome size (see fanagislab/kmerfreq#2 from some tips on how to use kmerfreq)
This is what fails 99% of the time.
I'd like to use dnaapler instead.
Needing updates: staphb/fastp from 0.23.2 to 0.23.4
Needing updates: staphb/fastp from 0.23.2 to 0.23.4
Needing updates: staphb/dragonflye from 1.0.14 to 1.1.1 staphb/fastp from 0.23.2 to 0.23.4 staphb/flye from 2.9.2 to 2.9.3 staphb/htslib from 1.17 to 1.19 staphb/nanoplot from 1.40.0 to 1.41.6 staphb/raven from 1.8.1 to 1.8.3
Another hybrid assembler, but it's very fast
Kraken2 has "issues" with long-reads, but perhaps something like Melon would help.
Add a version check so that tools don't go out of date
Needing updates:
Needing updates: staphb/dragonflye from 1.0.14 to 1.1.2 staphb/fastp from 0.23.2 to 0.23.4 staphb/flye from 2.9.2 to 2.9.3 staphb/htslib from 1.17 to 1.19 staphb/nanoplot from 1.40.0 to 1.42.0 staphb/polypolish from 0.5.0 to 0.6.0 staphb/rasusa from 0.7.0 to 0.8.0 staphb/raven from 1.8.1 to 1.8.3
Fails due to github actions as opposed to something in the script wrong
Needing updates: staphb/dragonflye from 1.0.14 to 1.1.2 staphb/fastp from 0.23.2 to 0.23.4 staphb/flye from 2.9.2 to 2.9.3 staphb/htslib from 1.17 to 1.19 staphb/nanoplot from 1.40.0 to 1.42.0 staphb/rasusa from 0.7.0 to 0.8.0 staphb/raven from 1.8.1 to 1.8.3
Without all the nf-core scripts in bin :D
The following example shows how use a closure to collect and sort all sequences in a FASTA file from shortest to longest:
Channel
.fromPath('/data/sequences.fa')
.splitFasta( record: [id: true, sequence: true] )
.collectFile( name:'result.fa', sort: { it.size() } ) {
it.sequence
}
.view { it.text }
Needing updates: staphb/dragonflye from 1.0.14 to 1.1.2 staphb/fastp from 0.23.2 to 0.23.4 staphb/flye from 2.9.2 to 2.9.3 staphb/htslib from 1.17 to 1.19 staphb/nanoplot from 1.40.0 to 1.42.0 staphb/rasusa from 0.7.0 to 0.8.0 staphb/raven from 1.8.1 to 1.8.3
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