Set up channel to loop through multi location (?)

[Tuan Nguyen]

Hi there, 

Maybe a novice question. I'm not sure how to describe my situation, but long story short, I have a few files to run my analysis, each batches are stored in a Chr based folder (Chr1, Chr2...Chr23). How can I set up another channel for Nextflow to loop through 23 Chr ?

Below is my current script that work with 1 folder. 

vcf_ch = Channel

        .fromPath( '/result/Chr1/*.gz' )

        .toSortedList()

        .collect()

tabix_ch = Channel

        .fromPath( '/result/Chr1/*.gz.tbi' )

        .collect()

process VCF_SUBSET {

        publishDir "$baseDir/result/ALL_CHR", mode: 'copy', overwrite: true

        input:

        path file from vcf_ch

        path tabix_file from tabix_ch

        output:

        file "*.vcf.gz" 

        script:

        """

        bcftools merge -i AF:avg,MAF:avg,R2:avg ${file} --threads 20 -Oz  -o test.vcf.gz

        """

}

Many thanks,

Tuan

[Xin Gong]

I think you can use wildcard character in fromPath, see doc here