kallisto|bustools 0.28.2 update

.nf-test.log

@@ -0,0 +1,17 @@
+Feb-27 21:54:16.881 [main] INFO  com.askimed.nf.test.App - nf-test 0.8.4
+Feb-27 21:54:16.895 [main] INFO  com.askimed.nf.test.App - Arguments: [test, tests/main_pipeline_kallisto.test, --update-snapshot]
+Feb-27 21:54:17.590 [main] INFO  com.askimed.nf.test.App - Nextflow Version: 23.10.1
+Feb-27 21:54:17.592 [main] INFO  com.askimed.nf.test.commands.RunTestsCommand - Load config from file /home/ec2-user/scrnaseq/nf-test.config...
+Feb-27 21:54:17.887 [main] INFO  com.askimed.nf.test.commands.RunTestsCommand - Detected 1 test files.
+Feb-27 21:54:18.162 [main] INFO  com.askimed.nf.test.config.FileStaging - Copy directory '/home/ec2-user/scrnaseq/bin' to '/home/ec2-user/scrnaseq/.nf-test/tests/72e0d0f6b834ab79755c0f97ef8c4ca8/meta/bin'
+Feb-27 21:54:18.164 [main] INFO  com.askimed.nf.test.config.FileStaging - Copy directory '/home/ec2-user/scrnaseq/lib' to '/home/ec2-user/scrnaseq/.nf-test/tests/72e0d0f6b834ab79755c0f97ef8c4ca8/meta/lib'
+Feb-27 21:54:18.164 [main] INFO  com.askimed.nf.test.config.FileStaging - Copy directory '/home/ec2-user/scrnaseq/assets' to '/home/ec2-user/scrnaseq/.nf-test/tests/72e0d0f6b834ab79755c0f97ef8c4ca8/meta/assets'
+Feb-27 21:54:18.171 [main] DEBUG com.askimed.nf.test.core.AbstractTest - Stage 0 user provided files...
+Feb-27 21:54:18.174 [main] INFO  com.askimed.nf.test.core.TestExecutionEngine - Started test plan
+Feb-27 21:54:18.174 [main] INFO  com.askimed.nf.test.core.TestExecutionEngine - Running testsuite 'Test Workflow main.nf' from file '/home/ec2-user/scrnaseq/tests/main_pipeline_kallisto.test'.
+Feb-27 21:54:18.174 [main] INFO  com.askimed.nf.test.core.TestExecutionEngine - Run test '72e0d0f6: test-dataset_kallisto_aligner'. type: com.askimed.nf.test.lang.pipeline.PipelineTest
+Feb-27 21:55:36.281 [main] DEBUG com.askimed.nf.test.lang.extensions.SnapshotFile - Load snapshots from file '/home/ec2-user/scrnaseq/tests/main_pipeline_kallisto.test.snap'
+Feb-27 21:55:36.305 [main] DEBUG com.askimed.nf.test.lang.extensions.Snapshot - Snapshots 'test-dataset_kallisto_aligner' match.
+Feb-27 21:55:36.306 [main] INFO  com.askimed.nf.test.core.TestExecutionEngine - Test '72e0d0f6: test-dataset_kallisto_aligner' finished. status: PASSED
+Feb-27 21:55:36.308 [main] INFO  com.askimed.nf.test.core.TestExecutionEngine - Testsuite 'Test Workflow main.nf' finished. snapshot file: true, skipped tests: false, failed tests: false
+Feb-27 21:55:36.308 [main] INFO  com.askimed.nf.test.core.TestExecutionEngine - Executed 1 tests. 0 tests failed. Done!

modules.json

@@ -57,12 +57,12 @@
                     },
                     "kallistobustools/count": {
                         "branch": "master",
-                        "git_sha": "3f5420aa22e00bd030a2556dfdffc9e164ec0ec5",
+                        "git_sha": "de8215983defba48cd81961d620a9e844f11c7e7",
                         "installed_by": ["modules"]
                     },
                     "kallistobustools/ref": {
                         "branch": "master",
-                        "git_sha": "3f5420aa22e00bd030a2556dfdffc9e164ec0ec5",
+                        "git_sha": "de8215983defba48cd81961d620a9e844f11c7e7",
                         "installed_by": ["modules"]
                     },
                     "multiqc": {

modules/local/mtx_to_h5ad.nf

@@ -27,7 +27,7 @@ process MTX_TO_H5AD {
     if (params.aligner == 'kallisto') {
         mtx_matrix   = "*count/counts_unfiltered/*.mtx"
         barcodes_tsv = "*count/counts_unfiltered/*.barcodes.txt"
-        features_tsv = "*count/counts_unfiltered/*.genes.txt"
+        features_tsv = "*count/counts_unfiltered/*.genes.names.txt"
     } else if (params.aligner == 'alevin') {
         mtx_matrix   = "*_alevin_results/af_quant/alevin/quants_mat.mtx"
         barcodes_tsv = "*_alevin_results/af_quant/alevin/quants_mat_rows.txt"
@@ -54,13 +54,13 @@ process MTX_TO_H5AD {
     else if (params.aligner == 'kallisto' && params.kb_workflow != 'standard')
     """
     # convert file types
-    for input_type in spliced unspliced ; do
+    for input_type in nascent ambiguous mature ; do
         mtx_to_h5ad.py \\
             --aligner ${params.aligner} \\
             --sample ${meta.id} \\
-            --input *count/counts_unfiltered/\${input_type}.mtx \\
-            --barcode *count/counts_unfiltered/\${input_type}.barcodes.txt \\
-            --feature *count/counts_unfiltered/\${input_type}.genes.txt \\
+            --input *count/counts_unfiltered/cells_x_genes.\${input_type}.mtx \\
+            --barcode $barcodes_tsv \\
+            --feature $features_tsv \\
             --txp2gene ${txp2gene} \\
             --star_index ${star_index} \\
             --out ${meta.id}/${meta.id}_\${input_type}_matrix.h5ad ;

modules/local/mtx_to_seurat.nf

@@ -26,7 +26,7 @@ process MTX_TO_SEURAT {
     } else if (params.aligner == "kallisto") {
         matrix   = "*count/counts_unfiltered/*.mtx"
         barcodes = "*count/counts_unfiltered/*.barcodes.txt"
-        features = "*count/counts_unfiltered/*.genes.txt"
+        features = "*count/counts_unfiltered/*.genes.names.txt"
     } else if (params.aligner == "alevin") {
         matrix   = "*_alevin_results/af_quant/alevin/quants_mat.mtx"
         barcodes = "*_alevin_results/af_quant/alevin/quants_mat_rows.txt"
@@ -43,11 +43,11 @@ process MTX_TO_SEURAT {
     if (params.aligner == 'kallisto' && params.kb_workflow != 'standard')
     """
     # convert file types
-    for input_type in spliced unspliced ; do
+    for input_type in nascent ambiguous mature ; do
         mtx_to_seurat.R \\
-            *count/counts_unfiltered/\${input_type}.mtx \\
-            *count/counts_unfiltered/\${input_type}.barcodes.txt \\
-            *count/counts_unfiltered/\${input_type}.genes.txt \\
+            *count/counts_unfiltered/cells_x_genes.\${input_type}.mtx \\
+            $barcodes \\
+            $features \\
             ${meta.id}/${meta.id}_\${input_type}_matrix.rds \\
             ${aligner}
     done