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Adding Assembly Stub Output and Generating IRIDA Next-Compliant JSON Output #9

Merged
merged 18 commits into from
Nov 8, 2023
Merged

Adding Assembly Stub Output and Generating IRIDA Next-Compliant JSON Output #9

merged 18 commits into from
Nov 8, 2023

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emarinier
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@emarinier emarinier commented Nov 2, 2023 •
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  • Adds stub assembly output.
  • Generates a JSON file that is compatible with IRIDA Next.

Example single JSON output:

{
    "files": {
        "samples": {
            "SAMPLE1": [
                {
                    "path": "assembly/SAMPLE1.assembly.fa.gz"
                }
            ]
        }
    },
    "metadata": {
        "samples": {
            "SAMPLE1": {
                "reads": ["sample1_R1.fastq.gz", "sample1_R2.fastq.gz"]
            }
        }
    }
}

Example combined, flattened, and IRIDA-compliant JSON output:

{
    "files": {
        "global": [
            {
                "path": "summary/summary.txt.gz"
            }
        ],
        "samples": {
            "SAMPLE1": [
                {
                    "path": "assembly/SAMPLE1.assembly.fa.gz"
                }
            ],
            "SAMPLE2": [
                {
                    "path": "assembly/SAMPLE2.assembly.fa.gz"
                }
            ],
            "SAMPLE3": [
                {
                    "path": "assembly/SAMPLE3.assembly.fa.gz"
                }
            ]
        }
    },
    "metadata": {
        "samples": {
            "SAMPLE1": {
                "reads.1": "sample1_R1.fastq.gz",
                "reads.2": "sample1_R2.fastq.gz"
            },
            "SAMPLE2": {
                "reads.1": "sample2_R1.fastq.gz",
                "reads.2": "sample2_R2.fastq.gz"
            },
            "SAMPLE3": {
                "reads.1": "sample1_R1.fastq.gz",
                "reads.2": "null"
            }
        }
    }
}

Example summary file:

IRIDANEXT-EXAMPLE-NF Pipeline Summary

SUCCESS!

SAMPLE1:
    reads.1: /nf-core/test-datasets/viralrecon/illumina/amplicon/sample1_R1.fastq.gz
    reads.2: /nf-core/test-datasets/viralrecon/illumina/amplicon/sample1_R2.fastq.gz
    assembly: /nextflow-scratch/debeb133b9824ba8883d17261ce70f2f/a4/f892f61e24b5f7eaec584b044ce953/SAMPLE1.assembly.fa.gz

SAMPLE2:
    reads.1: /nf-core/test-datasets/viralrecon/illumina/amplicon/sample2_R1.fastq.gz
    reads.2: /nf-core/test-datasets/viralrecon/illumina/amplicon/sample2_R2.fastq.gz
    assembly: /nextflow-scratch/debeb133b9824ba8883d17261ce70f2f/cd/a2659b9486a06df86fbfa5ce8269bc/SAMPLE2.assembly.fa.gz

SAMPLE3:
    reads.1: /nf-core/test-datasets/viralrecon/illumina/amplicon/sample1_R1.fastq.gz
    reads.2: null
    assembly: /nextflow-scratch/debeb133b9824ba8883d17261ce70f2f/4a/d37e827094eb9c060c4c0be1a440af/SAMPLE3.assembly.fa.gz

Will very likely need to change how the summary file is written to avoid code injection: #10

@emarinier emarinier self-assigned this Nov 2, 2023
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github-actions bot commented Nov 2, 2023 •
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nf-core lint overall result: Passed ✅ ⚠️

Posted for pipeline commit bfdb364

+| ✅ 156 tests passed       |+
#| ❔   2 tests were ignored |#
!| ❗  15 tests had warnings |!

❗ Test warnings:

  • readme - README did not have a Nextflow minimum version badge.
  • pipeline_todos - TODO string in nextflow.config: Specify your pipeline's command line flags
  • pipeline_todos - TODO string in ci.yml: You can customise CI pipeline run tests as required
  • pipeline_todos - TODO string in awsfulltest.yml: You can customise AWS full pipeline tests as required
  • pipeline_todos - TODO string in methods_description_template.yml: #Update the HTML below to your preferred methods description, e.g. add publication citation for this pipeline
  • pipeline_todos - TODO string in test_full.config: Specify the paths to your full test data ( on nf-core/test-datasets or directly in repositories, e.g. SRA)
  • pipeline_todos - TODO string in test_full.config: Give any required params for the test so that command line flags are not needed
  • pipeline_todos - TODO string in test.config: Specify the paths to your test data on nf-core/test-datasets
  • pipeline_todos - TODO string in test.config: Give any required params for the test so that command line flags are not needed
  • pipeline_todos - TODO string in base.config: Check the defaults for all processes
  • pipeline_todos - TODO string in base.config: Customise requirements for specific processes.
  • pipeline_todos - TODO string in output.md: Write this documentation describing your workflow's output
  • pipeline_todos - TODO string in usage.md: Add documentation about anything specific to running your pipeline. For general topics, please point to (and add to) the main nf-core website.
  • pipeline_todos - TODO string in WorkflowIridanext.groovy: Optionally add in-text citation tools to this list.
  • pipeline_todos - TODO string in WorkflowMain.groovy: Add Zenodo DOI for pipeline after first release

❔ Tests ignored:

  • files_unchanged - File ignored due to lint config: assets/sendmail_template.txt
  • files_unchanged - File ignored due to lint config: lib/NfcoreTemplate.groovy

✅ Tests passed:

Run details

  • nf-core/tools version 2.10
  • Run at 2023-11-08 19:23:31

@emarinier emarinier changed the title WIP: Adding Assembly Stub Output and Generating IRIDA Next-Compliant JSON Output Adding Assembly Stub Output and Generating IRIDA Next-Compliant JSON Output Nov 7, 2023
@emarinier emarinier requested a review from apetkau November 7, 2023 20:28
apetkau
apetkau requested changes Nov 8, 2023
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This looks amazing. Thanks so much for all you work on this Eric 😄. There are just a few suggestions I have.

@emarinier emarinier mentioned this pull request Nov 8, 2023
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I've made the changes and it's working as expected locally and on Azure.

apetkau
apetkau approved these changes Nov 8, 2023
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Awesome. Thanks so much Eric. This looks great. Merging.

@apetkau apetkau merged commit d230c4d into dev Nov 8, 2023
@apetkau apetkau deleted the assembly branch November 8, 2023 20:24
@emarinier emarinier mentioned this pull request Nov 9, 2023
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