AliNe: A Flexible and Efficient Nextflow Pipeline for Read Alignment

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 <R> 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 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