Nanoplot output files clobber each other ..

[benbfly]

Description of the bug

When I run 4 samples, I only get one version of the nanoplot output files. It looks like the nanoplot module should use the --prefix command to prefix the generic output file names with the sample IDs or sample names, so that they will be unique and not clobber each other.

Command used and terminal output

No response

Relevant files

No response

System information

Docker/Azure/Tower
Workflow:
Nextflow: 22.10.7
nf-core/nanoseq: 3.1.0

[ktrappe]

Actually, NanoComp https://github.com/wdecoster/nanocomp might be the better option here.

[ktrappe]

nf-core/modules#3110

[Caffeinated-Code]

Following up on this as I have the same issue.
Do we have a newer version of the pipeline that prefixes sample names to Nanoplot outputs or uses Nanocomp?
Version: nf-core/nanoseq v3.1.0 (seems to match with the latest version on github)

[Caffeinated-Code]

Hi,
Hope you are doing well!
Wanted to reach out and check if this bug has been fixed in the current version or when we can expect an update.

Much Thanks!
Swathi

[tamuanand]

If it helps, I got around the clobbering part by changing

https://github.com/nf-core/nanoseq/blob/master/modules/nf-core/nanoplot/main.nf

script:
def input_file = ("$ontfile".endsWith(".fastq.gz")) ? "--fastq ${ontfile}" :
        ("$ontfile".endsWith(".txt")) ? "--summary ${ontfile}" : ''
    """
    NanoPlot \\
        $args \\
        -t $task.cpus \\
        $input_file

to

 script:
    def input_file = ("$ontfile".endsWith(".fastq.gz")) ? "--fastq ${ontfile}" :
        ("$ontfile".endsWith(".txt")) ? "--summary ${ontfile}" : ''
    def prefix = "${meta.id}"
    """
    NanoPlot \\
        --prefix "${prefix}_" \\
        $args \\
        -t $task.cpus \\
        $input_file

[ktrappe]

@tamuanand you can also make use of the existing $args. I added the following to my modules.config

withName: NANOPLOT {
        ext.args = { "--prefix ${meta.id}_" } 
    }

This way, you don't need to change the module but can set the prefix with your custom modules.config. (Took me a while to figure this out...)