nanoporetech / epi2me-api Goto Github PK

It started the analysis but we have an issue with uploading the files.

LIVE INSTANCE STATE { download: { progress: { bytes: 0, total: 0, niceSize: 0 }, success: { files: 0, bytes: 0, reads: 0, niceReads: 0, niceSize: 0 }, types: {}, fail: 0, niceTypes: '' }, upload: { progress: { bytes: -8655034949, total: 0, niceSize: '-8655034949' }, success: { files: 0, bytes: 0, reads: 0, niceReads: '0', niceSize: '0' }, types: {}, filesCount: 29, niceTypes: '', failure: { 'NoSuchBucket: The specified bucket does not exist': 28 } }, warnings: [] }

When we try to upload files, it give the above error. Can you help us with how to specify the files to the api?

Originally posted by @youssefabadir in #2 (comment)

I am trying to run fastq custom alignment workflow and it download this file instead of the output files.

telemetry-252547.log

Is this a problem from my side?

I am trying to run epi2me on an HPC but keep running into nextflow trying to run through docker instead of apptainer. I added apptainer to the profile list (see below) but it will not run
profiles {
// the "standard" profile is used implicitly by nextflow
// if no other profile is given on the CLI
standard {
docker {
enabled = true
// this ensures the container is run as the host user and group, but
// also adds the host user to the within-container group
runOptions = "--user $(id -u):$(id -g) --group-add 100"
}
}

// using singularity instead of docker
singularity {
singularity {
enabled = true
autoMounts = true
}
}

// using Apptainer instead of Docker
apptainer {
apptainer {
enabled = true
autoMounts = true
container = "/path to /nextflow_latest.sif"
}
}

router.post('/fastqref', function (req, res, next) {
  const EPI2ME = new API({
    url: 'https://epi2me.nanoporetech.com',
    apikey: 'apikeyhere',
    apisecret: 'secretkeyhere',
    inputFolder: req.body['inputFolder'],
    outputFolder: req.body['outputFolder'],
  });

  const factory = new Factory(API);
  const workflowId = 1825;
  EPI2ME.REST.startWorkflow({ variables: { idWorkflowInstance: workflowId }})
  .then(console.info)
  .catch(console.error);

Error is attached below.

We want to run other workflows other than Fastq custom alignment (id: 1825). We want to know when will the documentation be ready? As, we are on a tight schedule to integrate epi2me-api with our program. If the documentation won't be ready soon, Can you help us with syntax?