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Fix samplesheet test failures: add alias column to fixtures and update assertions #90

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Fix samplesheet test failures: add alias column to fixtures and update assertions #90

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2 changes: 1 addition & 1 deletion tests/fixtures/empty_samplesheet.csv
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Original file line number Diff line number Diff line change
@@ -1 +1 @@
sample,patient,timepoint,origin,file
sample,alias,patient,timepoint,origin,file
10 changes: 5 additions & 5 deletions tests/fixtures/valid_samplesheet.csv
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Open in desktop
Original file line number Diff line number Diff line change
@@ -1,5 +1,5 @@
sample,patient,timepoint,origin,file
Patient01_Base,Patient01,Base,tumor,tests/fixtures/data/PD1_Patient01_Base.tsv
Patient02_Base,Patient02,Base,tumor,tests/fixtures/data/PD1_Patient02_Base.tsv
Patient03_Base,Patient03,Base,tumor,tests/fixtures/data/PD1_Patient03_Base.tsv
Patient01_Post,Patient01,Post,tumor,tests/fixtures/data/PD1_Patient01_Post.tsv
sample,alias,patient,timepoint,origin,file
Patient01_Base,Patient01_Base,Patient01,Base,tumor,tests/fixtures/data/PD1_Patient01_Base.tsv
Patient02_Base,Patient02_Base,Patient02,Base,tumor,tests/fixtures/data/PD1_Patient02_Base.tsv
Patient03_Base,Patient03_Base,Patient03,Base,tumor,tests/fixtures/data/PD1_Patient03_Base.tsv
Patient01_Post,Patient01_Post,Patient01,Post,tumor,tests/fixtures/data/PD1_Patient01_Post.tsv
8 changes: 4 additions & 4 deletions tests/modules/local/samplesheet/samplesheet_check.nf.test
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Original file line number Diff line number Diff line change
Expand Up @@ -28,8 +28,8 @@ nextflow_process {
def lines = path(samplesheet_utf8.get(0)).readLines()
assert lines.size() == 5 // Header + 4 data rows
// The output has UTF-8 BOM, so strip it for comparison
assert lines[0].replaceAll("^\uFEFF", "") == "sample,patient,timepoint,origin,file"
assert lines[1].startsWith("Patient01_Base,Patient01,Base,tumor,")
assert lines[0].replaceAll("^\uFEFF", "") == "sample,alias,patient,timepoint,origin,file"
assert lines[1].startsWith("Patient01_Base,Patient01_Base,Patient01,Base,tumor,")
}
}
}
Expand All @@ -55,7 +55,7 @@ nextflow_process {

def lines = path(samplesheet_utf8.get(0)).readLines()
assert lines.size() == 36 // Header + 35 samples
assert lines[0].replaceAll("^\uFEFF", "") == "sample,patient,timepoint,origin,file"
assert lines[0].replaceAll("^\uFEFF", "") == "sample,alias,patient,timepoint,origin,file"
}
}
}
Expand All @@ -79,7 +79,7 @@ nextflow_process {
with(process.out) {
def lines = path(samplesheet_utf8.get(0)).readLines()
assert lines.size() == 1 // Only header
assert lines[0].replaceAll("^\uFEFF", "") == "sample,patient,timepoint,origin,file"
assert lines[0].replaceAll("^\uFEFF", "") == "sample,alias,patient,timepoint,origin,file"
}
}
}
Expand Down
72 changes: 36 additions & 36 deletions tests/test_data/minimal-example/samplesheet.csv
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Open in desktop
Original file line number Diff line number Diff line change
@@ -1,36 +1,36 @@
sample,patient,timepoint,origin,file
Patient01_Base,Patient01,Base,tumor,https://raw.githubusercontent.com/KarchinLab/TCRtoolkit/refs/heads/main/tests/test_data/minimal-example/PD1_Patient01_Base.tsv
Patient02_Base,Patient02,Base,tumor,https://raw.githubusercontent.com/KarchinLab/TCRtoolkit/refs/heads/main/tests/test_data/minimal-example/PD1_Patient02_Base.tsv
Patient03_Base,Patient03,Base,tumor,https://raw.githubusercontent.com/KarchinLab/TCRtoolkit/refs/heads/main/tests/test_data/minimal-example/PD1_Patient03_Base.tsv
Patient04_Base,Patient04,Base,tumor,https://raw.githubusercontent.com/KarchinLab/TCRtoolkit/refs/heads/main/tests/test_data/minimal-example/PD1_Patient04_Base.tsv
Patient05_Base,Patient05,Base,tumor,https://raw.githubusercontent.com/KarchinLab/TCRtoolkit/refs/heads/main/tests/test_data/minimal-example/PD1_Patient05_Base.tsv
Patient06_Base,Patient06,Base,tumor,https://raw.githubusercontent.com/KarchinLab/TCRtoolkit/refs/heads/main/tests/test_data/minimal-example/PD1_Patient06_Base.tsv
Patient07_Base,Patient07,Base,tumor,https://raw.githubusercontent.com/KarchinLab/TCRtoolkit/refs/heads/main/tests/test_data/minimal-example/PD1_Patient07_Base.tsv
Patient08_Base,Patient08,Base,tumor,https://raw.githubusercontent.com/KarchinLab/TCRtoolkit/refs/heads/main/tests/test_data/minimal-example/PD1_Patient08_Base.tsv
Patient09_Base,Patient09,Base,tumor,https://raw.githubusercontent.com/KarchinLab/TCRtoolkit/refs/heads/main/tests/test_data/minimal-example/PD1_Patient09_Base.tsv
Patient10_Base,Patient10,Base,tumor,https://raw.githubusercontent.com/KarchinLab/TCRtoolkit/refs/heads/main/tests/test_data/minimal-example/PD1_Patient10_Base.tsv
Patient11_Base,Patient11,Base,tumor,https://raw.githubusercontent.com/KarchinLab/TCRtoolkit/refs/heads/main/tests/test_data/minimal-example/PD1_Patient11_Base.tsv
Patient12_Base,Patient12,Base,tumor,https://raw.githubusercontent.com/KarchinLab/TCRtoolkit/refs/heads/main/tests/test_data/minimal-example/PD1_Patient12_Base.tsv
Patient13_Base,Patient13,Base,tumor,https://raw.githubusercontent.com/KarchinLab/TCRtoolkit/refs/heads/main/tests/test_data/minimal-example/PD1_Patient13_Base.tsv
Patient14_Base,Patient14,Base,tumor,https://raw.githubusercontent.com/KarchinLab/TCRtoolkit/refs/heads/main/tests/test_data/minimal-example/PD1_Patient14_Base.tsv
Patient15_Base,Patient15,Base,tumor,https://raw.githubusercontent.com/KarchinLab/TCRtoolkit/refs/heads/main/tests/test_data/minimal-example/PD1_Patient15_Base.tsv
Patient16_Base,Patient16,Base,tumor,https://raw.githubusercontent.com/KarchinLab/TCRtoolkit/refs/heads/main/tests/test_data/minimal-example/PD1_Patient16_Base.tsv
Patient16_Post,Patient16,Post,tumor,https://raw.githubusercontent.com/KarchinLab/TCRtoolkit/refs/heads/main/tests/test_data/minimal-example/PD1_Patient16_Post.tsv
Patient17_Base,Patient17,Base,tumor,https://raw.githubusercontent.com/KarchinLab/TCRtoolkit/refs/heads/main/tests/test_data/minimal-example/PD1_Patient17_Base.tsv
Patient17_Post,Patient17,Post,tumor,https://raw.githubusercontent.com/KarchinLab/TCRtoolkit/refs/heads/main/tests/test_data/minimal-example/PD1_Patient17_Post.tsv
Patient18_Base,Patient18,Base,tumor,https://raw.githubusercontent.com/KarchinLab/TCRtoolkit/refs/heads/main/tests/test_data/minimal-example/PD1_Patient18_Base.tsv
Patient18_Post,Patient18,Post,tumor,https://raw.githubusercontent.com/KarchinLab/TCRtoolkit/refs/heads/main/tests/test_data/minimal-example/PD1_Patient18_Post.tsv
Patient19_Base,Patient19,Base,tumor,https://raw.githubusercontent.com/KarchinLab/TCRtoolkit/refs/heads/main/tests/test_data/minimal-example/PD1_Patient19_Base.tsv
Patient19_Post,Patient19,Post,tumor,https://raw.githubusercontent.com/KarchinLab/TCRtoolkit/refs/heads/main/tests/test_data/minimal-example/PD1_Patient19_Post.tsv
Patient20_Base,Patient20,Base,tumor,https://raw.githubusercontent.com/KarchinLab/TCRtoolkit/refs/heads/main/tests/test_data/minimal-example/PD1_Patient20_Base.tsv
Patient20_Post,Patient20,Post,tumor,https://raw.githubusercontent.com/KarchinLab/TCRtoolkit/refs/heads/main/tests/test_data/minimal-example/PD1_Patient20_Post.tsv
Patient21_Base,Patient21,Base,tumor,https://raw.githubusercontent.com/KarchinLab/TCRtoolkit/refs/heads/main/tests/test_data/minimal-example/PD1_Patient21_Base.tsv
Patient21_Post,Patient21,Post,tumor,https://raw.githubusercontent.com/KarchinLab/TCRtoolkit/refs/heads/main/tests/test_data/minimal-example/PD1_Patient21_Post.tsv
Patient22_Base,Patient22,Base,tumor,https://raw.githubusercontent.com/KarchinLab/TCRtoolkit/refs/heads/main/tests/test_data/minimal-example/PD1_Patient22_Base.tsv
Patient22_Post,Patient22,Post,tumor,https://raw.githubusercontent.com/KarchinLab/TCRtoolkit/refs/heads/main/tests/test_data/minimal-example/PD1_Patient22_Post.tsv
Patient23_Base,Patient23,Base,tumor,https://raw.githubusercontent.com/KarchinLab/TCRtoolkit/refs/heads/main/tests/test_data/minimal-example/PD1_Patient23_Base.tsv
Patient23_Post,Patient23,Post,tumor,https://raw.githubusercontent.com/KarchinLab/TCRtoolkit/refs/heads/main/tests/test_data/minimal-example/PD1_Patient23_Post.tsv
Patient24_Base,Patient24,Base,tumor,https://raw.githubusercontent.com/KarchinLab/TCRtoolkit/refs/heads/main/tests/test_data/minimal-example/PD1_Patient24_Base.tsv
Patient24_Post,Patient24,Post,tumor,https://raw.githubusercontent.com/KarchinLab/TCRtoolkit/refs/heads/main/tests/test_data/minimal-example/PD1_Patient24_Post.tsv
Patient25_Base,Patient25,Base,tumor,https://raw.githubusercontent.com/KarchinLab/TCRtoolkit/refs/heads/main/tests/test_data/minimal-example/PD1_Patient25_Base.tsv
Patient25_Post,Patient25,Post,tumor,https://raw.githubusercontent.com/KarchinLab/TCRtoolkit/refs/heads/main/tests/test_data/minimal-example/PD1_Patient25_Post.tsv
sample,alias,patient,timepoint,origin,file
Patient01_Base,Patient01_Base,Patient01,Base,tumor,https://raw.githubusercontent.com/KarchinLab/TCRtoolkit/refs/heads/main/tests/test_data/minimal-example/PD1_Patient01_Base.tsv
Patient02_Base,Patient02_Base,Patient02,Base,tumor,https://raw.githubusercontent.com/KarchinLab/TCRtoolkit/refs/heads/main/tests/test_data/minimal-example/PD1_Patient02_Base.tsv
Patient03_Base,Patient03_Base,Patient03,Base,tumor,https://raw.githubusercontent.com/KarchinLab/TCRtoolkit/refs/heads/main/tests/test_data/minimal-example/PD1_Patient03_Base.tsv
Patient04_Base,Patient04_Base,Patient04,Base,tumor,https://raw.githubusercontent.com/KarchinLab/TCRtoolkit/refs/heads/main/tests/test_data/minimal-example/PD1_Patient04_Base.tsv
Patient05_Base,Patient05_Base,Patient05,Base,tumor,https://raw.githubusercontent.com/KarchinLab/TCRtoolkit/refs/heads/main/tests/test_data/minimal-example/PD1_Patient05_Base.tsv
Patient06_Base,Patient06_Base,Patient06,Base,tumor,https://raw.githubusercontent.com/KarchinLab/TCRtoolkit/refs/heads/main/tests/test_data/minimal-example/PD1_Patient06_Base.tsv
Patient07_Base,Patient07_Base,Patient07,Base,tumor,https://raw.githubusercontent.com/KarchinLab/TCRtoolkit/refs/heads/main/tests/test_data/minimal-example/PD1_Patient07_Base.tsv
Patient08_Base,Patient08_Base,Patient08,Base,tumor,https://raw.githubusercontent.com/KarchinLab/TCRtoolkit/refs/heads/main/tests/test_data/minimal-example/PD1_Patient08_Base.tsv
Patient09_Base,Patient09_Base,Patient09,Base,tumor,https://raw.githubusercontent.com/KarchinLab/TCRtoolkit/refs/heads/main/tests/test_data/minimal-example/PD1_Patient09_Base.tsv
Patient10_Base,Patient10_Base,Patient10,Base,tumor,https://raw.githubusercontent.com/KarchinLab/TCRtoolkit/refs/heads/main/tests/test_data/minimal-example/PD1_Patient10_Base.tsv
Patient11_Base,Patient11_Base,Patient11,Base,tumor,https://raw.githubusercontent.com/KarchinLab/TCRtoolkit/refs/heads/main/tests/test_data/minimal-example/PD1_Patient11_Base.tsv
Patient12_Base,Patient12_Base,Patient12,Base,tumor,https://raw.githubusercontent.com/KarchinLab/TCRtoolkit/refs/heads/main/tests/test_data/minimal-example/PD1_Patient12_Base.tsv
Patient13_Base,Patient13_Base,Patient13,Base,tumor,https://raw.githubusercontent.com/KarchinLab/TCRtoolkit/refs/heads/main/tests/test_data/minimal-example/PD1_Patient13_Base.tsv
Patient14_Base,Patient14_Base,Patient14,Base,tumor,https://raw.githubusercontent.com/KarchinLab/TCRtoolkit/refs/heads/main/tests/test_data/minimal-example/PD1_Patient14_Base.tsv
Patient15_Base,Patient15_Base,Patient15,Base,tumor,https://raw.githubusercontent.com/KarchinLab/TCRtoolkit/refs/heads/main/tests/test_data/minimal-example/PD1_Patient15_Base.tsv
Patient16_Base,Patient16_Base,Patient16,Base,tumor,https://raw.githubusercontent.com/KarchinLab/TCRtoolkit/refs/heads/main/tests/test_data/minimal-example/PD1_Patient16_Base.tsv
Patient16_Post,Patient16_Post,Patient16,Post,tumor,https://raw.githubusercontent.com/KarchinLab/TCRtoolkit/refs/heads/main/tests/test_data/minimal-example/PD1_Patient16_Post.tsv
Patient17_Base,Patient17_Base,Patient17,Base,tumor,https://raw.githubusercontent.com/KarchinLab/TCRtoolkit/refs/heads/main/tests/test_data/minimal-example/PD1_Patient17_Base.tsv
Patient17_Post,Patient17_Post,Patient17,Post,tumor,https://raw.githubusercontent.com/KarchinLab/TCRtoolkit/refs/heads/main/tests/test_data/minimal-example/PD1_Patient17_Post.tsv
Patient18_Base,Patient18_Base,Patient18,Base,tumor,https://raw.githubusercontent.com/KarchinLab/TCRtoolkit/refs/heads/main/tests/test_data/minimal-example/PD1_Patient18_Base.tsv
Patient18_Post,Patient18_Post,Patient18,Post,tumor,https://raw.githubusercontent.com/KarchinLab/TCRtoolkit/refs/heads/main/tests/test_data/minimal-example/PD1_Patient18_Post.tsv
Patient19_Base,Patient19_Base,Patient19,Base,tumor,https://raw.githubusercontent.com/KarchinLab/TCRtoolkit/refs/heads/main/tests/test_data/minimal-example/PD1_Patient19_Base.tsv
Patient19_Post,Patient19_Post,Patient19,Post,tumor,https://raw.githubusercontent.com/KarchinLab/TCRtoolkit/refs/heads/main/tests/test_data/minimal-example/PD1_Patient19_Post.tsv
Patient20_Base,Patient20_Base,Patient20,Base,tumor,https://raw.githubusercontent.com/KarchinLab/TCRtoolkit/refs/heads/main/tests/test_data/minimal-example/PD1_Patient20_Base.tsv
Patient20_Post,Patient20_Post,Patient20,Post,tumor,https://raw.githubusercontent.com/KarchinLab/TCRtoolkit/refs/heads/main/tests/test_data/minimal-example/PD1_Patient20_Post.tsv
Patient21_Base,Patient21_Base,Patient21,Base,tumor,https://raw.githubusercontent.com/KarchinLab/TCRtoolkit/refs/heads/main/tests/test_data/minimal-example/PD1_Patient21_Base.tsv
Patient21_Post,Patient21_Post,Patient21,Post,tumor,https://raw.githubusercontent.com/KarchinLab/TCRtoolkit/refs/heads/main/tests/test_data/minimal-example/PD1_Patient21_Post.tsv
Patient22_Base,Patient22_Base,Patient22,Base,tumor,https://raw.githubusercontent.com/KarchinLab/TCRtoolkit/refs/heads/main/tests/test_data/minimal-example/PD1_Patient22_Base.tsv
Patient22_Post,Patient22_Post,Patient22,Post,tumor,https://raw.githubusercontent.com/KarchinLab/TCRtoolkit/refs/heads/main/tests/test_data/minimal-example/PD1_Patient22_Post.tsv
Patient23_Base,Patient23_Base,Patient23,Base,tumor,https://raw.githubusercontent.com/KarchinLab/TCRtoolkit/refs/heads/main/tests/test_data/minimal-example/PD1_Patient23_Base.tsv
Patient23_Post,Patient23_Post,Patient23,Post,tumor,https://raw.githubusercontent.com/KarchinLab/TCRtoolkit/refs/heads/main/tests/test_data/minimal-example/PD1_Patient23_Post.tsv
Patient24_Base,Patient24_Base,Patient24,Base,tumor,https://raw.githubusercontent.com/KarchinLab/TCRtoolkit/refs/heads/main/tests/test_data/minimal-example/PD1_Patient24_Base.tsv
Patient24_Post,Patient24_Post,Patient24,Post,tumor,https://raw.githubusercontent.com/KarchinLab/TCRtoolkit/refs/heads/main/tests/test_data/minimal-example/PD1_Patient24_Post.tsv
Patient25_Base,Patient25_Base,Patient25,Base,tumor,https://raw.githubusercontent.com/KarchinLab/TCRtoolkit/refs/heads/main/tests/test_data/minimal-example/PD1_Patient25_Base.tsv
Patient25_Post,Patient25_Post,Patient25,Post,tumor,https://raw.githubusercontent.com/KarchinLab/TCRtoolkit/refs/heads/main/tests/test_data/minimal-example/PD1_Patient25_Post.tsv