uphl-biongs / donut_falls Goto Github PK

Needing updates: staphb/busco from 5.6.1-prok-bacteria_odb10_2024-01-08 to 5.6.1

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: 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/busco from 5.6.1-prok-bacteria_odb10_2024-01-08 to 5.6.1

Needing updates: staphb/dragonflye from 2.9.2 to 1.0.14

Unicycler is supposed to be rotating finished assemblies, but for some reason is not.

Take https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0060204 into consideration

This is what fails 99% of the time.

I'd like to use dnaapler instead.

Kraken2 has "issues" with long-reads, but perhaps something like Melon would help.

https://github.com/xinehc/melon

Needing updates:

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/fastp from 0.23.2 to 0.23.4

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

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×)."

Needing updates: staphb/dragonflye from 2.9.2 to 1.0.14

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 }

Actually get this option working

Most bacteria that "we" sequence have a 5M genome. It'd be faster if filtlong used that instead of keeping 95%.

Fails due to github actions as opposed to something in the script wrong

• flye assembly
• masurca hybrid assembly
• raven assembly from directory
• raven assembly with polishing

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/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 1.19 staphb/nanoplot from 1.40.0 to 1.41.6 staphb/raven from 1.8.1 to 1.8.3

Needing updates: staphb/fastp from 0.23.2 to 0.23.4

Without all the nf-core scripts in bin :D

Needing updates: staphb/busco from 5.6.1-prok-bacteria_odb10_2024-01-08 to 5.6.1

Homopolish uses a similar genome to reduce indel errors. It would be useful to have as an option.

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.

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/fastp from 0.23.2 to 0.23.4

Needing updates: staphb/fastp from 0.23.2 to 0.23.4

Needing updates:

Needing updates:

First. Genome size (see fanagislab/kmerfreq#2 from some tips on how to use kmerfreq)

to resolve discrepencies

Fix

>1 circ=false len=1653372 gc=30.47 cov=1251.36 asmb=unicycler stp=False

Needing updates:

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/fastp from 0.23.2 to 0.23.4

Needing updates: staphb/busco from 5.6.1-prok-bacteria_odb10_2024-01-08 to 5.6.1

https://github.com/UPHL-BioNGS/Donut_Falls/actions/runs/4895749315/jobs/8741720315

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

Another hybrid assembler, but it's very fast

https://github.com/vpc-ccg/haslr

Needing updates:

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

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

At least so it mentions the wiki

https://github.com/rrwick/Perfect-bacterial-genome-tutorial/wiki

Needing updates: staphb/busco from 5.6.1-prok-bacteria_odb10_2024-01-08 to 5.6.1

Add a version check so that tools don't go out of date