Channel question on result file in directory result of programe about nextflow HOT 2 CLOSED

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}
"""
}

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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

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