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

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

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.

AliNe - v1.1.0

Remove Tophat2
Add bowtie 1
Add kallisto
Add CI
Improve documentation
Add Samtools stats

AliNe - v1.0.1

Deal with remote reads, genome and annotation file.
Simplify how annotation is handled (prepare annotation process removed)

AliNe - v1.0.0

First release of AliNe
Integrate 15 alignment tools [ 'bbmap', 'bowtie2', 'bwaaln', 'bwamem', 'bwasw', 'graphmap2', 'hisat2', 'minimap2', 'novoalign', 'nucmer', 'ngmlr', 'star', 'subread', 'sublong', 'tophat2' ]
Deal with read orintation
Deal with annotation
Deal with sequence scoring system
Deal With short reads (paired or single) and with Long reads (PacBio and ONT)
Trim with fastp (optional)
QC with fastqc (optional)
MultiQC