Channel question on result file in directory result of programe

[biowang]

I don`t know how do I put file into channel, the file lie in a directory.
while directory is a parameter rather than a file.

such as programe "tophat ".
the command line like following:
$ tophat -o tophat_out genome_index R1.fq R2.fq

the result like this

tophat_out/:
accepted_hits.bam deletions.bed junctions.bed prep_reads.info

align_summary.txt insertions.bed logs unmapped.bam

then I want pass the file "accepted_hits.bam" into a Channel, How should I do?

hearing from you!

[pprieto]

Hi
If you want to pass "accepted_hits.bam" through an output Channel within a process you have to define it in the output declarations as in this example where the acceptem_hits.bam is going to be sent through channel bam

process mapping {
input:
...
output:
file "tophat_out/accepted_hits.bam" into bam

"""
tophat2 -p ${task.cpus} --GTF $annotation_file genome.index ${read1} ${read2}
"""
}

[pditommaso]

There's no distinction between regular files and directories. They can be managed in the same identical manner by Nextflow channels.

You may want to have a look to this RNA-Seq example, that uses Tophat, at this link:
https://github.com/nextflow-io/rnatoy/blob/master/main.nf

Feel free to continue the discussion in the Nextflow forum:
https://groups.google.com/forum/#!forum/nextflow