Releases | Open Source Science

AliNe - AliNe - v1.5.2

Fix issue using annotation introduced in v1.5.0. val => path (annotation was not usable) Fix issue for Graphmap2 when using annotation (https://github.com/sq line duplicated) Add annotation in test Update multiqc version and remove pdf output (html only)Fix issue using annotation introduced in v1.5.0. val => path (annotation was not usable) Fix issue for Graphmap2 when using annotation (https://github.com/sq line duplicated) Add annotation in test Update multiqc version and remove pdf output (html only) Improve parameter visibility

Scientific Software - Peer-reviewed - Nextflow
Published by Juke34 11 months ago

AliNe - AliNe - v1.5.1

Update strandedness to handle null for daisy chaining case Update read_type to handle null for daisy chaining case Filter bam file among csv input (useful for daisy chaining with RAIN)

Scientific Software - Peer-reviewed - Nextflow
Published by Juke34 12 months ago

AliNe - AliNe - v1.5.1

Update strandedness to handle null for daisy chaining case Update read_type to handle null for daisy chaining case

Scientific Software - Peer-reviewed - Nextflow
Published by Juke34 12 months ago

AliNe - AliNe - v1.5.0

use of meta (dictionary) as first item in channels (see nf-core concept)
add csv input possibility + test
add AlineUtils to add functions (e.g. for name cleaning)
params added by AliNe are now handled by sample (not globally. So ait was in main.nf header now it is a process) => All is saved in a new output file
warn for best aligner according to data type is now a dedicated process
remove skip-strandedness parameters (now strandedness empty is equivalent )
new route for guessing strandedness and read length to avoid to redo the subsampling.
now AliNe can handle several types of data_type in a single run (via csv)
centralise all aligner parameters auto handling by Aline into process checkalignerparams (except single/pair commands)
use realpath when doing ln -s to avoid some issues
update hpc config
add data_type parameter (rna / dna) some tools (e.g. subread) need that information.

Full Changelog: https://github.com/Juke34/AliNe/compare/v1.4.0...v1.5.0

Scientific Software - Peer-reviewed - Nextflow
Published by Juke34 12 months ago

AliNe - AliNe - v1.4.0

What's Changed

Now input reference/genome can be compressed
Remove option to deal with patterns. Now pattern are fixed. file extension expected : <.fastq.gz>, <.fq.gz>, <.fastq> or <.fq> for paired reads extra <R1001> or <R2001> is expected where and <001> are optional. e.g. <sampleid1.fastq.gz>, <sampleidR1.fastq.gz>, <sampleidR1001.fastq.gz>) )
Now we can provide a list of file (coma separated) as input. Before it was only for remote files.
refer to reference instead of genome by @Juke34 in https://github.com/Juke34/AliNe/pull/37
add time to DAG file name to avoid to have to remove it at every run
add tag in some modules where it was missing for nicer output
add test for remote files
fix path to hpc.config when the iTrop profile is loaded

Full Changelog: https://github.com/Juke34/AliNe/compare/v1.3.0...v1.4.0

Scientific Software - Peer-reviewed - Nextflow
Published by Juke34 about 1 year ago

AliNe - AliNe - v1.3.0

add last aligner
salmon: fixes file name output (add salmon suffix)
graphmap2: standardize way of handling paired-end. Instead to concat and align, align R1 and R2 independently then merge.
Update README

Scientific Software - Peer-reviewed - Nextflow
Published by Juke34 about 1 year ago

AliNe - AliNe - v1.2.0

Add bwa-mem2 Add salmon ngmlr and sublong can now works with paired-en reads Standardize information and user interaction at the beginning of Aline when checking tools and params Fix error when using long reads with bwasw, options "-x ont2d" and "-x pacbio" not usable (only for bwamem) Update tests and Readme

Scientific Software - Peer-reviewed - Nextflow
Published by Juke34 about 1 year ago

AliNe - AliNe: A Flexible and Efficient Nextflow Pipeline for Read Alignment

Latest changes from the review (Improve paper and documentation). This is the version that will be used in the JOSS paper.