Get file list from directory channel nexflow

Question

Is there a way to specify the folder name and then create a channel with the file names inside it in nextflow?

And yes I could make a file with the contents of the directory, that's not what i'm asking.

Thanks

Answer 1

I think you can just use the fromPath factory method for this. If you want all files in the directory and in all sub-directories, you can use the double asterisk to cross directory boundaries:

params.search_dir = './directory'


workflow {

    Channel
        .fromPath( "${params.search_dir}/**" )
        .view()
}

Otherwise, a single asterisk will match only files in the top-level directory. Append hidden: true if you also need your output to include hidden files. Note that multiple paths or glob patterns can also be specified using a list, for example:

params.search_dir = './directory'
params.another_dir = './another/directory'


workflow {

    Channel
        .fromPath( [ "${params.search_dir}/**", "${params.another_dir}/*" ) ]
        .view()
}