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

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)

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 check_aligner_params (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: v1.4.0...v1.5.0

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 <_R1_001> or <_R2_001> is expected where and <_001> are optional. e.g. <sample_id_1.fastq.gz>, <sample_id_R1.fastq.gz>, <sample_id_R1_001.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 #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: v1.3.0...v1.4.0

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