diff --git a/tests/fixtures/empty_samplesheet.csv b/tests/fixtures/empty_samplesheet.csv
index ed11825..ae9164a 100644
--- a/tests/fixtures/empty_samplesheet.csv
+++ b/tests/fixtures/empty_samplesheet.csv
@@ -1 +1 @@
-sample,patient,timepoint,origin,file
+sample,alias,patient,timepoint,origin,file
diff --git a/tests/fixtures/valid_samplesheet.csv b/tests/fixtures/valid_samplesheet.csv
index 92bee94..b3d34d9 100644
--- a/tests/fixtures/valid_samplesheet.csv
+++ b/tests/fixtures/valid_samplesheet.csv
@@ -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
diff --git a/tests/modules/local/samplesheet/samplesheet_check.nf.test b/tests/modules/local/samplesheet/samplesheet_check.nf.test
index f405c4f..f7e67ea 100644
--- a/tests/modules/local/samplesheet/samplesheet_check.nf.test
+++ b/tests/modules/local/samplesheet/samplesheet_check.nf.test
@@ -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,")
             }
         }
     }
@@ -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"
             }
         }
     }
@@ -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"
             }
         }
     }
diff --git a/tests/test_data/minimal-example/samplesheet.csv b/tests/test_data/minimal-example/samplesheet.csv
index 79d1b0f..5f89b10 100644
--- a/tests/test_data/minimal-example/samplesheet.csv
+++ b/tests/test_data/minimal-example/samplesheet.csv
@@ -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