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Adds Program Outputs to Irida Next JSON Output File #5

Merged
merged 2 commits into from
Dec 13, 2024
Merged

Adds Program Outputs to Irida Next JSON Output File #5

merged 2 commits into from
Dec 13, 2024

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emarinier
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@emarinier emarinier commented Dec 13, 2024 •
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I added both TSV and XLSX, because it's a pain trying to use XLSX when you don't have Excel or something that opens those files.

Output:

{
    "files": {
        "global": [
            {
                "path": "process/results.xlsx"
            },
            {
                "path": "process/results.tsv"
            },
            {
                "path": "distances/profile_dists.run.json"
            },
            {
                "path": "distances/profile_dists.results.text"
            },
            {
                "path": "distances/profile_dists.ref_profile.text"
            },
            {
                "path": "distances/profile_dists.query_profile.text"
            },
            {
                "path": "distances/profile_dists.allele_map.json"
            },
            {
                "path": "merged/locidex.merge.profile.tsv"
            }
        ],
        "samples": {
            
        }
    },
    "metadata": {
        "samples": {
            
        }
    }
}

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github-actions bot commented Dec 13, 2024 •
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nf-core pipelines lint overall result: Passed ✅ ⚠️

Posted for pipeline commit 6b3fa13

+| ✅ 143 tests passed       |+
#| ❔  28 tests were ignored |#
!| ❗   4 tests had warnings |!

❗ Test warnings:

❔ Tests ignored:

  • files_exist - File is ignored: assets/nf-core-fastmatchirida_logo_light.png
  • files_exist - File is ignored: docs/images/nf-core-fastmatchirida_logo_light.png
  • files_exist - File is ignored: docs/images/nf-core-fastmatchirida_logo_dark.png
  • files_exist - File is ignored: .github/workflows/awstest.yml
  • files_exist - File is ignored: .github/workflows/awsfulltest.yml
  • files_exist - File is ignored: lib/Utils.groovy
  • files_exist - File is ignored: lib/WorkflowMain.groovy
  • files_exist - File is ignored: lib/NfcoreTemplate.groovy
  • files_exist - File is ignored: lib/Workflowfastmatchirida.groovy
  • nextflow_config - Config variable ignored: manifest.name
  • nextflow_config - Config variable ignored: manifest.homePage
  • nextflow_config - Config variable ignored: params.max_cpus
  • files_unchanged - File ignored due to lint config: LICENSE or LICENSE.md or LICENCE or LICENCE.md
  • files_unchanged - File ignored due to lint config: .github/CONTRIBUTING.md
  • files_unchanged - File ignored due to lint config: .github/ISSUE_TEMPLATE/bug_report.yml
  • files_unchanged - File ignored due to lint config: .github/PULL_REQUEST_TEMPLATE.md
  • files_unchanged - File ignored due to lint config: .github/workflows/branch.yml
  • files_unchanged - File ignored due to lint config: assets/email_template.html
  • files_unchanged - File ignored due to lint config: assets/email_template.txt
  • files_unchanged - File ignored due to lint config: assets/sendmail_template.txt
  • files_unchanged - File does not exist: assets/nf-core-fastmatchirida_logo_light.png
  • files_unchanged - File does not exist: docs/images/nf-core-fastmatchirida_logo_light.png
  • files_unchanged - File does not exist: docs/images/nf-core-fastmatchirida_logo_dark.png
  • files_unchanged - File ignored due to lint config: docs/README.md
  • files_unchanged - File ignored due to lint config: .gitignore or .prettierignore
  • actions_awstest - 'awstest.yml' workflow not found: /home/runner/work/fastmatchirida/fastmatchirida/.github/workflows/awstest.yml
  • actions_awsfulltest - actions_awsfulltest
  • pipeline_name_conventions - pipeline_name_conventions

✅ Tests passed:

Run details

  • nf-core/tools version 3.0.1
  • Run at 2024-12-13 15:50:45

@emarinier emarinier self-assigned this Dec 13, 2024
apetkau
apetkau approved these changes Dec 13, 2024
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This looks great. Thanks so much Eric 😄

@sgsutcliffe
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sgsutcliffe commented Dec 13, 2024 •
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Looks good!

@emarinier emarinier merged commit 8c43747 into dev Dec 13, 2024
4 checks passed
@emarinier emarinier deleted the update-json branch January 17, 2025 19:31
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@sgsutcliffe sgsutcliffe sgsutcliffe approved these changes

@apetkau apetkau apetkau approved these changes

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@emarinier @sgsutcliffe @apetkau