ERROR ~ Error executing process > 'pipeline:makeReport'

[laurenlansdowne]

Operating System

Windows 10

Other Linux

No response

Workflow Version

23.04.2

Workflow Execution

EPI2ME Desktop (Local)

Other workflow execution

No response

EPI2ME Version

v5.2.1

CLI command run

No response

Workflow Execution - CLI Execution Profile

None

What happened?

Stopped with error

Relevant log output

Core Nextflow options
  runName        : flamboyant_connor
  containerEngine: docker
  launchDir      : /mnt/c/Users/lansdole/epi2melabs/instances/wf-flu_01JA5H4KHSX80W2WP3VQSSNTWM
  workDir        : /mnt/c/Users/lansdole/epi2melabs/instances/wf-flu_01JA5H4KHSX80W2WP3VQSSNTWM/work
  projectDir     : /mnt/c/Users/lansdole/epi2melabs/workflows/epi2me-labs/wf-flu
  userName       : epi2mewsl
  profile        : standard
  configFiles    : /mnt/c/Users/lansdole/epi2melabs/workflows/epi2me-labs/wf-flu/nextflow.config
Input Options
  fastq          : /mnt/c/Users/lansdole/Desktop/Sequencing Data/LL_flu_and_plant_test_10_10_24/fastq_pass/barcode04/FBA62538_pass_barcode04_b32a4180_8dbdcf08_10.fastq.gz
Output Options
  out_dir        : /mnt/c/Users/lansdole/epi2melabs/instances/wf-flu_01JA5H4KHSX80W2WP3VQSSNTWM/output
!! Only displaying parameters that differ from the pipeline defaults !!
--------------------------------------------------------------------------------
If you use epi2me-labs/wf-flu for your analysis please cite:
* The nf-core framework
  https://doi.org/10.1038/s41587-020-0439-x
--------------------------------------------------------------------------------
This is epi2me-labs/wf-flu v1.2.3.
--------------------------------------------------------------------------------
Searching input for [.fastq, .fastq.gz, .fq, .fq.gz] files.
NOT Downsampling!!!
[11/7f191f] Submitted process > fastcat (1)
[7a/486e2a] Submitted process > pipeline:getParams
[23/623ef6] Submitted process > pipeline:getVersions
[fb/7411e2] Submitted process > pipeline:alignReads (1)
[88/487b14] Submitted process > pipeline:coverageCalc (1)
[86/1c2422] Submitted process > pipeline:medakaVariants (1)
[1d/ec2ea3] Submitted process > pipeline:makeConsensus (1)
[2a/c5df56] Submitted process > pipeline:typeFlu (1)
[e2/0d5b68] Submitted process > pipeline:processType (1)
[c7/27bf21] Submitted process > pipeline:prepNextclade (1)
[c1/e1e843] Submitted process > pipeline:collectFilesInDir (1)
[c2/9b9a6b] Submitted process > pipeline:nextclade (1)
[a5/a6e745] Submitted process > pipeline:nextclade (2)
[74/0e28c5] Submitted process > pipeline:makeReport
ERROR ~ Error executing process > 'pipeline:makeReport'
Caused by:
  Process `pipeline:makeReport` terminated with an error exit status (1)
Command executed:
  echo '[
      {
          "barcode": null,
          "type": "test_sample",
          "run_ids": [
              "8dbdcf08518f045d5dc8f9f5e393a714691a1d5a"
          ],
          "basecall_models": [
              "dna_r10.4.1_e8.2_400bps_hac@v4.3.0"
          ],
          "alias": "FBA62538_pass_barcode04_b32a4180_8dbdcf08_10",
          "group_key": {
              "groupTarget": "FBA62538_pass_barcode04_b32a4180_8dbdcf08_10",
              "groupSize": 1
          },
          "n_fastq": 1,
          "group_index": "FBA62538_pass_barcode04_b32a4180_8dbdcf08_10_0",
          "n_seqs": 9617
      }
  ]' > metadata.json
      workflow-glue report "wf-flu-report.html"        --data data         --stats stats_         --versions versions         --params params.json         --nextclade_files nextclade/*         --nextclade_datasets "nextclade.csv"         --metadata metadata.json         --workflow_version v1.2.3
Command exit status:
  1
Command output:
  (empty)
Command error:
  [12:50:16 - workflow_glue] Bootstrapping CLI.
  [12:50:25 - matplotlib.font_manager] generated new fontManager
  [12:50:26 - workflow_glue] Starting entrypoint.
  Traceback (most recent call last):
    File "/mnt/c/Users/lansdole/epi2melabs/workflows/epi2me-labs/wf-flu/bin/workflow-glue", line 7, in <module>
      cli()
    File "/mnt/c/Users/lansdole/epi2melabs/workflows/epi2me-labs/wf-flu/bin/workflow_glue/__init__.py", line 82, in cli
      args.func(args)
    File "/mnt/c/Users/lansdole/epi2melabs/workflows/epi2me-labs/wf-flu/bin/workflow_glue/report.py", line 128, in main
      get_row_format(row)
    File "/mnt/c/Users/lansdole/epi2melabs/workflows/epi2me-labs/wf-flu/bin/workflow_glue/report.py", line 85, in get_row_format
      cell.add(td(span(row)))
    File "/opt/custflow/epi2meuser/conda/lib/python3.8/site-packages/dominate/tags.py", line 63, in __init__
      super(html_tag, self).__init__(*args, **kwargs)
    File "/opt/custflow/epi2meuser/conda/lib/python3.8/site-packages/dominate/dom_tag.py", line 129, in __init__
      self.add(*args)
    File "/opt/custflow/epi2meuser/conda/lib/python3.8/site-packages/dominate/dom_tag.py", line 237, in add
      raise ValueError('%r not a tag or string.' % obj)
  ValueError: None not a tag or string.
Work dir:
  /mnt/c/Users/lansdole/epi2melabs/instances/wf-flu_01JA5H4KHSX80W2WP3VQSSNTWM/work/74/0e28c5cfc4887d38285dae09e1c970
Tip: view the complete command output by changing to the process work dir and entering the command `cat .command.out`
 -- Check '/mnt/c/Users/lansdole/epi2melabs/instances/wf-flu_01JA5H4KHSX80W2WP3VQSSNTWM/nextflow.log' file for details

Application activity log entry

No response

Were you able to successfully run the latest version of the workflow with the demo data?

other (please describe below)

Other demo data information

No response

[BioWilko]

@SamStudio8 @cjw85 :)

[cjalder]

Hi @laurenlansdowne - this issue has been identified internally and we should have a fix in the next release cycle.