{
    "exit_code": null,
    "summary": {
        "num_errors": 1,
        "num_failures": 0,
        "num_skips": 0,
        "num_tests": 1
    },
    "tests": [
        {
            "data": {
                "end_datetime": "2026-09-18T18:41:36.499166",
                "execution_problem": "Unexpected HTTP status code: 400: {\"err_msg\":\"Workflow was not invoked; the following required tools are not installed: toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt (version 5.2+galaxy2), toolshed.g2.bx.psu.edu/repos/iuc/compose_text_param/compose_text_param (version 0.1.1), toolshed.g2.bx.psu.edu/repos/iuc/map_param_value/map_param_value (version 0.2.0), toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc (version 0.74+galaxy1), toolshed.g2.bx.psu.edu/repos/iuc/rgrnastar/rna_star (version 2.7.11b+galaxy1), toolshed.g2.bx.psu.edu/repos/iuc/featurecounts/featurecounts (version 2.1.1+galaxy1), toolshed.g2.bx.psu.edu/repos/iuc/deseq2/deseq2 (version 2.11.40.8+galaxy4)\",\"err_code\":0}",
                "inputs": {
                    "Adjusted p-value threshold": 0.05,
                    "First contrast condition level": "tnSWI1",
                    "Gene annotation GTF": {
                        "class": "File",
                        "decompress": true,
                        "filetype": "gtf",
                        "location": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/002/759/435/GCA_002759435.2_Cand_auris_B8441_V2/GCA_002759435.2_Cand_auris_B8441_V2_genomic.gtf.gz"
                    },
                    "RNA-seq reads (sample sheet)": {
                        "class": "Collection",
                        "collection_type": "sample_sheet:paired",
                        "elements": [
                            {
                                "class": "Collection",
                                "collection_type": "paired",
                                "elements": [
                                    {
                                        "class": "File",
                                        "filetype": "fastqsanger.gz",
                                        "hashes": [
                                            {
                                                "hash_function": "SHA-1",
                                                "hash_value": "7686fa073a0089b0376bbe1d3b819b4ea14e3a67"
                                            }
                                        ],
                                        "identifier": "forward",
                                        "path": "test-data/smoke-25k/AR0382_A_1.fastq.gz"
                                    },
                                    {
                                        "class": "File",
                                        "filetype": "fastqsanger.gz",
                                        "hashes": [
                                            {
                                                "hash_function": "SHA-1",
                                                "hash_value": "f1749c97d907abffd4f5ee36139c22b15376d2af"
                                            }
                                        ],
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                                        "path": "test-data/smoke-25k/AR0382_A_2.fastq.gz"
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                            {
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                                "collection_type": "paired",
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                                                "hash_value": "a120941043541873bd674fc8e5cab4bf7d8dcc37"
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                                        "identifier": "forward",
                                        "path": "test-data/smoke-25k/AR0382_B_1.fastq.gz"
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                                        "filetype": "fastqsanger.gz",
                                        "hashes": [
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                                                "hash_function": "SHA-1",
                                                "hash_value": "8f315372a23e305fc5dc5ee04d31d8a771ccb8f3"
                                            }
                                        ],
                                        "identifier": "reverse",
                                        "path": "test-data/smoke-25k/AR0382_B_2.fastq.gz"
                                    }
                                ],
                                "identifier": "AR0382_B"
                            },
                            {
                                "class": "Collection",
                                "collection_type": "paired",
                                "elements": [
                                    {
                                        "class": "File",
                                        "filetype": "fastqsanger.gz",
                                        "hashes": [
                                            {
                                                "hash_function": "SHA-1",
                                                "hash_value": "d8e170332a2ae20242b8f79c66f287b79fa2c56a"
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                                        ],
                                        "identifier": "forward",
                                        "path": "test-data/smoke-25k/AR0387_A_1.fastq.gz"
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                                    {
                                        "class": "File",
                                        "filetype": "fastqsanger.gz",
                                        "hashes": [
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                                                "hash_function": "SHA-1",
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                                            }
                                        ],
                                        "identifier": "reverse",
                                        "path": "test-data/smoke-25k/AR0387_A_2.fastq.gz"
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                                ],
                                "identifier": "AR0387_A"
                            },
                            {
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                                "elements": [
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                                        "class": "File",
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                                        "path": "test-data/smoke-25k/AR0387_B_1.fastq.gz"
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                                        "filetype": "fastqsanger.gz",
                                        "hashes": [
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                                        ],
                                        "identifier": "reverse",
                                        "path": "test-data/smoke-25k/AR0387_B_2.fastq.gz"
                                    }
                                ],
                                "identifier": "AR0387_B"
                            },
                            {
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                                        ],
                                        "identifier": "forward",
                                        "path": "test-data/smoke-25k/AR0382_tnSWI1_A_1.fastq.gz"
                                    },
                                    {
                                        "class": "File",
                                        "filetype": "fastqsanger.gz",
                                        "hashes": [
                                            {
                                                "hash_function": "SHA-1",
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                                            }
                                        ],
                                        "identifier": "reverse",
                                        "path": "test-data/smoke-25k/AR0382_tnSWI1_A_2.fastq.gz"
                                    }
                                ],
                                "identifier": "AR0382_tnSWI1_A"
                            },
                            {
                                "class": "Collection",
                                "collection_type": "paired",
                                "elements": [
                                    {
                                        "class": "File",
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                                        "hashes": [
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                                        "identifier": "forward",
                                        "path": "test-data/smoke-25k/AR0382_tnSWI1_B_1.fastq.gz"
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                                    {
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                                        "filetype": "fastqsanger.gz",
                                        "hashes": [
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                                        "identifier": "reverse",
                                        "path": "test-data/smoke-25k/AR0382_tnSWI1_B_2.fastq.gz"
                                    }
                                ],
                                "identifier": "AR0382_tnSWI1_B"
                            }
                        ],
                        "rows": {
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                                "AR0382",
                                "A"
                            ],
                            "AR0382_B": [
                                "AR0382",
                                "B"
                            ],
                            "AR0382_tnSWI1_A": [
                                "tnSWI1",
                                "A"
                            ],
                            "AR0382_tnSWI1_B": [
                                "tnSWI1",
                                "B"
                            ],
                            "AR0387_A": [
                                "AR0387",
                                "A"
                            ],
                            "AR0387_B": [
                                "AR0387",
                                "B"
                            ]
                        }
                    },
                    "Reference condition level": "AR0382",
                    "Reference genome FASTA": {
                        "class": "File",
                        "decompress": true,
                        "filetype": "fasta",
                        "location": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/002/759/435/GCA_002759435.2_Cand_auris_B8441_V2/GCA_002759435.2_Cand_auris_B8441_V2_genomic.fna.gz"
                    },
                    "Second contrast condition level": "AR0387",
                    "Strandedness": "stranded - reverse",
                    "log2 fold change threshold": 1.0
                },
                "invocation_details": null,
                "job": null,
                "output_problems": [],
                "problem_log": null,
                "start_datetime": "2026-09-18T18:40:32.111040",
                "status": "error"
            },
            "doc": "Fast structural smoke test over the same six samples at 25,000 read pairs each (~7 MB compressed total). Makes NO biological claim: at that depth SCF1 falls to roughly 50 fragments in AR0382 and near zero elsewhere, and the significance tables may legitimately be empty. What it does exercise is everything that can silently break without erroring - the sample_sheet:paired input shape, the flatten side-branch, the six-element map-over identifier space, both condition-split joins, both DESeq2 reductions, and both cross-step invariants. Every assertion here is a subset of case 1's, with the depth constant changed and the biological claims removed.",
            "has_data": true,
            "id": "galaxy-workflow.gxwf.yml_1",
            "test_type": "galaxy_workflow"
        }
    ],
    "version": "0.1"
}