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nhoffman / dada2-nf

A Nextflow pipeline for processing 16S rRNA sequences using dada2
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write the input fastq_files.txt to output #20

Closed dhoogest closed 3 years ago

dhoogest commented 3 years ago

Here's a try at #19. I haven't learned details about Channel yet, so useage may be unnecessary. Also would be interested in knowing if there's a more elegant method for moving a file than invoking cp input output as I've done here.

dhoogest commented 3 years ago

You might want to have process read_manifest read from this

Not sure I understand exactly - do you mean that instead of new Channel one of the inputs to process read_manifest is file("fastq_list.csv") like so?:

process read_manifest {

    input:
        file(sample_info) from sample_info
        file(fastq_files) from file("fastq_list.csv")
 ...
dhoogest commented 3 years ago

Maybe this is what you meant - channel split into three rather than invoked multiple times: https://github.com/nhoffman/dada2-nf/pull/20/commits/baeff5a832e72ccb74d0ad131e15d08bd8bc1d7c