Hi, I have some issue with my SAREK pipeline. I have submitted 20 samples but each time I run the pipeline, there's only 1 sample shows variant calling result. Each time, it is different sample. The run was also shown to complete successfully. Does anyone have the same issue? or does anyone knows what could be the reason to this and how I can solve this issue? Interestingly, I also got this error:

ERROR ~ Failed to invoke `workflow.onComplete` event handler

The command that i've used to launch the pipeline is as below:

nextflow run

nf-core/sarek -r 3.4.1 -name "Test_37" -c /rds/general/user/ksheng/home/config.modified -work-dir /rds/general/user/ksheng/ephemeral/SAREK/work -resume -params-file "nf-params.json" Part of the config is as below, the part that I've left out is requesting for available resources:

executor {
    $pbspro {
        queueSize = 49
        submitRateLimit = '10 sec'
        maxForks = 49
    }

    $local {
        cpus = 30
        queueSize = 1
        memory = '920 GB'
    }
}

singularity {
    enabled = true
    autoMounts = true
    runOptions = "-B /rds/,/rds/general/user/$USER/ephemeral/tmp/:/tmp,/rds/general/user/$USER/ephemeral/tmp/:/var/tmp"
}

what is in your params.file?

Why are there

$

in the

executor

scope? In fact, I don't understand the syntax of this section (but I might be missing something). (This is unlikely related to your issue, though.) The sample sheet should get validated by the pipeline, but maybe post it as well, so we can see if there that is set up in the way you intended.

@Rike Hanssen Here is the details of my param.file

{
    "input": "\/rds\/general\/user\/ksheng\/projects\/molecularembryologydata\/live\/Samantha\/Low_Pass_Seq_Batch_2\/sample_sheet.csv",
    "outdir": "\/rds\/general\/user\/ksheng\/projects\/molecularembryologydata\/live\/Samantha\/Low_Pass_Seq_Batch_2\/Test_13",
    "tools": "controlfreec",
    "trim_fastq": true,
    "save_mapped": true,
    "save_output_as_bam": true,
}