set working nf-test for cellranger multi

nf-core · May 1, 2024 · 81650b1 · 81650b1
1 parent 37a9bb6
commit 81650b1
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Showing 2 changed files with 153 additions and 45 deletions.
diff --git a/tests/main_pipeline_cellrangermulti.test b/tests/main_pipeline_cellrangermulti.test
@@ -51,40 +51,104 @@ nextflow_pipeline {
                 //
                 // Check if files were produced
                 //
+                {assert new File( "${outputDir}/results_cellrangermulti/cellrangermulti/mtx_conversions/PBMC_10K/PBMC_10K_raw_matrix.h5ad" ).exists()},
+                {assert new File( "${outputDir}/results_cellrangermulti/cellrangermulti/mtx_conversions/PBMC_10K/PBMC_10K_filtered_matrix.h5ad" ).exists()},
+                {assert new File( "${outputDir}/results_cellrangermulti/cellrangermulti/mtx_conversions/PBMC_10K_CMV/PBMC_10K_CMV_raw_matrix.h5ad" ).exists()},
+                {assert new File( "${outputDir}/results_cellrangermulti/cellrangermulti/mtx_conversions/PBMC_10K_CMV/PBMC_10K_CMV_filtered_matrix.h5ad" ).exists()},
+                {assert new File( "${outputDir}/results_cellrangermulti/cellrangermulti/mtx_conversions/PBMC_10K_CMO/PBMC_10K_CMO_raw_matrix.h5ad" ).exists()},
+                {assert new File( "${outputDir}/results_cellrangermulti/cellrangermulti/mtx_conversions/PBMC_10K_CMO_PBMCs_human_2/PBMC_10K_CMO_PBMCs_human_2_filtered_matrix.h5ad" ).exists()},
                 {assert new File( "${outputDir}/results_cellrangermulti/cellrangermulti/mtx_conversions/4PLEX_HUMAN/4PLEX_HUMAN_raw_matrix.h5ad" ).exists()},
+                {assert new File( "${outputDir}/results_cellrangermulti/cellrangermulti/mtx_conversions/PBMC_10K_CMO_PBMCs_human_1/PBMC_10K_CMO_PBMCs_human_1_filtered_matrix.h5ad" ).exists()},
                 {assert new File( "${outputDir}/results_cellrangermulti/cellrangermulti/mtx_conversions/Colorectal_BC3/Colorectal_BC3_filtered_matrix.h5ad" ).exists()},
                 {assert new File( "${outputDir}/results_cellrangermulti/cellrangermulti/mtx_conversions/Liver_BC1/Liver_BC1_filtered_matrix.h5ad" ).exists()},
                 {assert new File( "${outputDir}/results_cellrangermulti/cellrangermulti/mtx_conversions/Ovarian_BC2/Ovarian_BC2_filtered_matrix.h5ad" ).exists()},
                 {assert new File( "${outputDir}/results_cellrangermulti/cellrangermulti/mtx_conversions/Pancreas_BC4/Pancreas_BC4_filtered_matrix.h5ad" ).exists()},
-                {assert new File( "${outputDir}/results_cellrangermulti/cellrangermulti/mtx_conversions/PBMC_10K_CMO/PBMC_10K_CMO_raw_matrix.h5ad" ).exists()},
-                {assert new File( "${outputDir}/results_cellrangermulti/cellrangermulti/mtx_conversions/PBMC_10K_CMO_PBMCs_human_1/PBMC_10K_CMO_PBMCs_human_1_filtered_matrix.h5ad" ).exists()},
-                {assert new File( "${outputDir}/results_cellrangermulti/cellrangermulti/mtx_conversions/PBMC_10K_CMO_PBMCs_human_2/PBMC_10K_CMO_PBMCs_human_2_filtered_matrix.h5ad" ).exists()},
-                {assert new File( "${outputDir}/results_cellrangermulti/cellrangermulti/mtx_conversions/PBMC_10K_CMV/PBMC_10K_CMV_filtered_matrix.h5ad" ).exists()},
-                {assert new File( "${outputDir}/results_cellrangermulti/cellrangermulti/mtx_conversions/PBMC_10K_CMV/PBMC_10K_CMV_raw_matrix.h5ad" ).exists()},
-                {assert new File( "${outputDir}/results_cellrangermulti/cellrangermulti/mtx_conversions/PBMC_10K/PBMC_10K_filtered_matrix.h5ad" ).exists()},
-                {assert new File( "${outputDir}/results_cellrangermulti/cellrangermulti/mtx_conversions/PBMC_10K/PBMC_10K_raw_matrix.h5ad" ).exists()},
+                {assert new File( "${outputDir}/results_cellrangermulti/cellrangermulti/mtx_conversions/combined_filtered_matrix.h5ad" ).exists()},
+                {assert new File( "${outputDir}/results_cellrangermulti/cellrangermulti/mtx_conversions/combined_raw_matrix.h5ad" ).exists()},
 
                 //
                 // Check if files are the same
                 //
                 {assert snapshot(
                     workflow,
 
-                    // PBMC_10K_CMO_PBMCs_human_1
+                    // barcodes.tsv.gz files
+                    path( "${outputDir}/results_cellrangermulti/cellrangermulti/count/PBMC_10K/outs/multi/count/raw_feature_bc_matrix/barcodes.tsv.gz" ),
+                    path( "${outputDir}/results_cellrangermulti/cellrangermulti/count/PBMC_10K/outs/per_sample_outs/PBMC_10K/count/sample_filtered_feature_bc_matrix/barcodes.tsv.gz" ),
+                    path( "${outputDir}/results_cellrangermulti/cellrangermulti/count/PBMC_10K_CMV/outs/multi/count/raw_feature_bc_matrix/barcodes.tsv.gz" ),
+                    path( "${outputDir}/results_cellrangermulti/cellrangermulti/count/PBMC_10K_CMV/outs/per_sample_outs/PBMC_10K_CMV/count/sample_filtered_feature_bc_matrix/barcodes.tsv.gz" ),
+                    path( "${outputDir}/results_cellrangermulti/cellrangermulti/count/PBMC_10K_CMO/outs/multi/count/raw_feature_bc_matrix/barcodes.tsv.gz" ),
                     path( "${outputDir}/results_cellrangermulti/cellrangermulti/count/PBMC_10K_CMO/outs/per_sample_outs/PBMC_10K_CMO_PBMCs_human_1/count/sample_filtered_feature_bc_matrix/barcodes.tsv.gz" ),
-                    path( "${outputDir}/results_cellrangermulti/cellrangermulti/count/PBMC_10K_CMO/outs/per_sample_outs/PBMC_10K_CMO_PBMCs_human_1/count/sample_filtered_feature_bc_matrix/features.tsv.gz" ),
-                    path( "${outputDir}/results_cellrangermulti/cellrangermulti/count/PBMC_10K_CMO/outs/per_sample_outs/PBMC_10K_CMO_PBMCs_human_1/count/sample_filtered_feature_bc_matrix/matrix.mtx.gz"   ),
-                    path( "${outputDir}/results_cellrangermulti/cellrangermulti/count/PBMC_10K_CMO/outs/per_sample_outs/PBMC_10K_CMO_PBMCs_human_1/metrics_summary.csv" ),
-                    path( "${outputDir}/results_cellrangermulti/cellrangermulti/mtx_conversions/PBMC_10K_CMO_PBMCs_human_1/PBMC_10K_CMO_PBMCs_human_1_filtered_matrix.rds" ),
-
-                    // PBMC_10K_CMO_PBMCs_human_2
                     path( "${outputDir}/results_cellrangermulti/cellrangermulti/count/PBMC_10K_CMO/outs/per_sample_outs/PBMC_10K_CMO_PBMCs_human_2/count/sample_filtered_feature_bc_matrix/barcodes.tsv.gz" ),
+                    path( "${outputDir}/results_cellrangermulti/cellrangermulti/count/4PLEX_HUMAN/outs/multi/count/raw_feature_bc_matrix/barcodes.tsv.gz" ),
+                    path( "${outputDir}/results_cellrangermulti/cellrangermulti/count/4PLEX_HUMAN/outs/per_sample_outs/Colorectal_BC3/count/sample_filtered_feature_bc_matrix/barcodes.tsv.gz" ),
+                    path( "${outputDir}/results_cellrangermulti/cellrangermulti/count/4PLEX_HUMAN/outs/per_sample_outs/Colorectal_BC3/count/sample_raw_feature_bc_matrix/barcodes.tsv.gz" ),
+                    path( "${outputDir}/results_cellrangermulti/cellrangermulti/count/4PLEX_HUMAN/outs/per_sample_outs/Liver_BC1/count/sample_raw_feature_bc_matrix/barcodes.tsv.gz" ),
+                    path( "${outputDir}/results_cellrangermulti/cellrangermulti/count/4PLEX_HUMAN/outs/per_sample_outs/Liver_BC1/count/sample_filtered_feature_bc_matrix/barcodes.tsv.gz" ),
+                    path( "${outputDir}/results_cellrangermulti/cellrangermulti/count/4PLEX_HUMAN/outs/per_sample_outs/Ovarian_BC2/count/sample_filtered_feature_bc_matrix/barcodes.tsv.gz" ),
+                    path( "${outputDir}/results_cellrangermulti/cellrangermulti/count/4PLEX_HUMAN/outs/per_sample_outs/Ovarian_BC2/count/sample_raw_feature_bc_matrix/barcodes.tsv.gz" ),
+                    path( "${outputDir}/results_cellrangermulti/cellrangermulti/count/4PLEX_HUMAN/outs/per_sample_outs/Pancreas_BC4/count/sample_raw_feature_bc_matrix/barcodes.tsv.gz" ),
+                    path( "${outputDir}/results_cellrangermulti/cellrangermulti/count/4PLEX_HUMAN/outs/per_sample_outs/Pancreas_BC4/count/sample_filtered_feature_bc_matrix/barcodes.tsv.gz" ),
+
+                    // features.tsv.gz files
+                    path( "${outputDir}/results_cellrangermulti/cellrangermulti/count/PBMC_10K/outs/multi/count/raw_feature_bc_matrix/features.tsv.gz" ),
+                    path( "${outputDir}/results_cellrangermulti/cellrangermulti/count/PBMC_10K/outs/per_sample_outs/PBMC_10K/count/sample_filtered_feature_bc_matrix/features.tsv.gz" ),
+                    path( "${outputDir}/results_cellrangermulti/cellrangermulti/count/PBMC_10K_CMV/outs/multi/count/raw_feature_bc_matrix/features.tsv.gz" ),
+                    path( "${outputDir}/results_cellrangermulti/cellrangermulti/count/PBMC_10K_CMV/outs/per_sample_outs/PBMC_10K_CMV/count/sample_filtered_feature_bc_matrix/features.tsv.gz" ),
+                    path( "${outputDir}/results_cellrangermulti/cellrangermulti/count/PBMC_10K_CMO/outs/multi/count/raw_feature_bc_matrix/features.tsv.gz" ),
+                    path( "${outputDir}/results_cellrangermulti/cellrangermulti/count/PBMC_10K_CMO/outs/per_sample_outs/PBMC_10K_CMO_PBMCs_human_1/count/sample_filtered_feature_bc_matrix/features.tsv.gz" ),
                     path( "${outputDir}/results_cellrangermulti/cellrangermulti/count/PBMC_10K_CMO/outs/per_sample_outs/PBMC_10K_CMO_PBMCs_human_2/count/sample_filtered_feature_bc_matrix/features.tsv.gz" ),
-                    path( "${outputDir}/results_cellrangermulti/cellrangermulti/count/PBMC_10K_CMO/outs/per_sample_outs/PBMC_10K_CMO_PBMCs_human_2/count/sample_filtered_feature_bc_matrix/matrix.mtx.gz"   ),
+                    path( "${outputDir}/results_cellrangermulti/cellrangermulti/count/4PLEX_HUMAN/outs/multi/count/raw_feature_bc_matrix/features.tsv.gz" ),
+                    path( "${outputDir}/results_cellrangermulti/cellrangermulti/count/4PLEX_HUMAN/outs/per_sample_outs/Colorectal_BC3/count/sample_filtered_feature_bc_matrix/features.tsv.gz" ),
+                    path( "${outputDir}/results_cellrangermulti/cellrangermulti/count/4PLEX_HUMAN/outs/per_sample_outs/Colorectal_BC3/count/sample_raw_feature_bc_matrix/features.tsv.gz" ),
+                    path( "${outputDir}/results_cellrangermulti/cellrangermulti/count/4PLEX_HUMAN/outs/per_sample_outs/Liver_BC1/count/sample_raw_feature_bc_matrix/features.tsv.gz" ),
+                    path( "${outputDir}/results_cellrangermulti/cellrangermulti/count/4PLEX_HUMAN/outs/per_sample_outs/Liver_BC1/count/sample_filtered_feature_bc_matrix/features.tsv.gz" ),
+                    path( "${outputDir}/results_cellrangermulti/cellrangermulti/count/4PLEX_HUMAN/outs/per_sample_outs/Ovarian_BC2/count/sample_filtered_feature_bc_matrix/features.tsv.gz" ),
+                    path( "${outputDir}/results_cellrangermulti/cellrangermulti/count/4PLEX_HUMAN/outs/per_sample_outs/Ovarian_BC2/count/sample_raw_feature_bc_matrix/features.tsv.gz" ),
+                    path( "${outputDir}/results_cellrangermulti/cellrangermulti/count/4PLEX_HUMAN/outs/per_sample_outs/Pancreas_BC4/count/sample_raw_feature_bc_matrix/features.tsv.gz" ),
+                    path( "${outputDir}/results_cellrangermulti/cellrangermulti/count/4PLEX_HUMAN/outs/per_sample_outs/Pancreas_BC4/count/sample_filtered_feature_bc_matrix/features.tsv.gz" ),
+
+                    // matrix.mtx.gz files
+                    path( "${outputDir}/results_cellrangermulti/cellrangermulti/count/PBMC_10K/outs/multi/count/raw_feature_bc_matrix/matrix.mtx.gz" ),
+                    path( "${outputDir}/results_cellrangermulti/cellrangermulti/count/PBMC_10K/outs/per_sample_outs/PBMC_10K/count/sample_filtered_feature_bc_matrix/matrix.mtx.gz" ),
+                    path( "${outputDir}/results_cellrangermulti/cellrangermulti/count/PBMC_10K_CMV/outs/multi/count/raw_feature_bc_matrix/matrix.mtx.gz" ),
+                    path( "${outputDir}/results_cellrangermulti/cellrangermulti/count/PBMC_10K_CMV/outs/per_sample_outs/PBMC_10K_CMV/count/sample_filtered_feature_bc_matrix/matrix.mtx.gz" ),
+                    path( "${outputDir}/results_cellrangermulti/cellrangermulti/count/PBMC_10K_CMO/outs/multi/count/raw_feature_bc_matrix/matrix.mtx.gz" ),
+                    path( "${outputDir}/results_cellrangermulti/cellrangermulti/count/PBMC_10K_CMO/outs/per_sample_outs/PBMC_10K_CMO_PBMCs_human_1/count/sample_filtered_feature_bc_matrix/matrix.mtx.gz" ),
+                    path( "${outputDir}/results_cellrangermulti/cellrangermulti/count/PBMC_10K_CMO/outs/per_sample_outs/PBMC_10K_CMO_PBMCs_human_2/count/sample_filtered_feature_bc_matrix/matrix.mtx.gz" ),
+                    path( "${outputDir}/results_cellrangermulti/cellrangermulti/count/4PLEX_HUMAN/outs/multi/count/raw_feature_bc_matrix/matrix.mtx.gz" ),
+                    path( "${outputDir}/results_cellrangermulti/cellrangermulti/count/4PLEX_HUMAN/outs/per_sample_outs/Colorectal_BC3/count/sample_filtered_feature_bc_matrix/matrix.mtx.gz" ),
+                    path( "${outputDir}/results_cellrangermulti/cellrangermulti/count/4PLEX_HUMAN/outs/per_sample_outs/Colorectal_BC3/count/sample_raw_feature_bc_matrix/matrix.mtx.gz" ),
+                    path( "${outputDir}/results_cellrangermulti/cellrangermulti/count/4PLEX_HUMAN/outs/per_sample_outs/Liver_BC1/count/sample_raw_feature_bc_matrix/matrix.mtx.gz" ),
+                    path( "${outputDir}/results_cellrangermulti/cellrangermulti/count/4PLEX_HUMAN/outs/per_sample_outs/Liver_BC1/count/sample_filtered_feature_bc_matrix/matrix.mtx.gz" ),
+                    path( "${outputDir}/results_cellrangermulti/cellrangermulti/count/4PLEX_HUMAN/outs/per_sample_outs/Ovarian_BC2/count/sample_filtered_feature_bc_matrix/matrix.mtx.gz" ),
+                    path( "${outputDir}/results_cellrangermulti/cellrangermulti/count/4PLEX_HUMAN/outs/per_sample_outs/Ovarian_BC2/count/sample_raw_feature_bc_matrix/matrix.mtx.gz" ),
+                    path( "${outputDir}/results_cellrangermulti/cellrangermulti/count/4PLEX_HUMAN/outs/per_sample_outs/Pancreas_BC4/count/sample_raw_feature_bc_matrix/matrix.mtx.gz" ),
+                    path( "${outputDir}/results_cellrangermulti/cellrangermulti/count/4PLEX_HUMAN/outs/per_sample_outs/Pancreas_BC4/count/sample_filtered_feature_bc_matrix/matrix.mtx.gz" ),
+
+                    // metrics_summary.csv files
+                    path( "${outputDir}/results_cellrangermulti/cellrangermulti/count/PBMC_10K/outs/per_sample_outs/PBMC_10K/metrics_summary.csv" ),
+                    path( "${outputDir}/results_cellrangermulti/cellrangermulti/count/PBMC_10K_CMV/outs/per_sample_outs/PBMC_10K_CMV/metrics_summary.csv" ),
+                    path( "${outputDir}/results_cellrangermulti/cellrangermulti/count/PBMC_10K_CMO/outs/per_sample_outs/PBMC_10K_CMO_PBMCs_human_1/metrics_summary.csv" ),
                     path( "${outputDir}/results_cellrangermulti/cellrangermulti/count/PBMC_10K_CMO/outs/per_sample_outs/PBMC_10K_CMO_PBMCs_human_2/metrics_summary.csv" ),
-
-                    // RDS
-                    path( "${outputDir}/results_cellrangermulti/cellrangermulti/mtx_conversions/*/*.rds" ),
+                    path( "${outputDir}/results_cellrangermulti/cellrangermulti/count/4PLEX_HUMAN/outs/per_sample_outs/Colorectal_BC3/metrics_summary.csv" ),
+                    path( "${outputDir}/results_cellrangermulti/cellrangermulti/count/4PLEX_HUMAN/outs/per_sample_outs/Liver_BC1/metrics_summary.csv" ),
+                    path( "${outputDir}/results_cellrangermulti/cellrangermulti/count/4PLEX_HUMAN/outs/per_sample_outs/Ovarian_BC2/metrics_summary.csv" ),
+                    path( "${outputDir}/results_cellrangermulti/cellrangermulti/count/4PLEX_HUMAN/outs/per_sample_outs/Pancreas_BC4/metrics_summary.csv" ),
+
+                    // RDS files
+                    path( "${outputDir}/results_cellrangermulti/cellrangermulti/mtx_conversions/PBMC_10K/PBMC_10K_raw_matrix.rds" ),
+                    path( "${outputDir}/results_cellrangermulti/cellrangermulti/mtx_conversions/PBMC_10K/PBMC_10K_filtered_matrix.rds" ),
+                    path( "${outputDir}/results_cellrangermulti/cellrangermulti/mtx_conversions/PBMC_10K_CMV/PBMC_10K_CMV_raw_matrix.rds" ),
+                    path( "${outputDir}/results_cellrangermulti/cellrangermulti/mtx_conversions/PBMC_10K_CMV/PBMC_10K_CMV_filtered_matrix.rds" ),
+                    path( "${outputDir}/results_cellrangermulti/cellrangermulti/mtx_conversions/PBMC_10K_CMO/PBMC_10K_CMO_raw_matrix.rds" ),
+                    path( "${outputDir}/results_cellrangermulti/cellrangermulti/mtx_conversions/PBMC_10K_CMO_PBMCs_human_2/PBMC_10K_CMO_PBMCs_human_2_filtered_matrix.rds" ),
+                    path( "${outputDir}/results_cellrangermulti/cellrangermulti/mtx_conversions/4PLEX_HUMAN/4PLEX_HUMAN_raw_matrix.rds" ),
+                    path( "${outputDir}/results_cellrangermulti/cellrangermulti/mtx_conversions/PBMC_10K_CMO_PBMCs_human_1/PBMC_10K_CMO_PBMCs_human_1_filtered_matrix.rds" ),
+                    path( "${outputDir}/results_cellrangermulti/cellrangermulti/mtx_conversions/Colorectal_BC3/Colorectal_BC3_filtered_matrix.rds" ),
+                    path( "${outputDir}/results_cellrangermulti/cellrangermulti/mtx_conversions/Liver_BC1/Liver_BC1_filtered_matrix.rds" ),
+                    path( "${outputDir}/results_cellrangermulti/cellrangermulti/mtx_conversions/Ovarian_BC2/Ovarian_BC2_filtered_matrix.rds" ),
+                    path( "${outputDir}/results_cellrangermulti/cellrangermulti/mtx_conversions/Pancreas_BC4/Pancreas_BC4_filtered_matrix.rds" )
 
                 ).match()}