Remove problematic workflow snapshotting

nf-core · Oct 18, 2024 · 4a71603 · 4a71603
1 parent a6ed155
commit 4a71603
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Showing 10 changed files with 3 additions and 104 deletions.
diff --git a/tests/main_pipeline_alevin.nf.test b/tests/main_pipeline_alevin.nf.test
@@ -45,7 +45,6 @@ nextflow_pipeline {
                 // Check if files are the same
                 //
                 {assert snapshot(
-                    workflow,
                     path( "${outputDir}/results_alevin/alevin/Sample_X_alevin_results/af_quant/alevin/quants_mat_cols.txt" ),
                     path( "${outputDir}/results_alevin/alevin/Sample_X_alevin_results/af_quant/alevin/quants_mat.mtx" ),
                     path( "${outputDir}/results_alevin/alevin/Sample_X_alevin_results/af_quant/alevin/quants_mat_rows.txt" ),

diff --git a/tests/main_pipeline_alevin.nf.test.snap b/tests/main_pipeline_alevin.nf.test.snap
@@ -1,25 +1,6 @@
 {
     "test-dataset_alevin_aligner": {
         "content": [
-            {
-                "stderr": [
-
-                ],
-                "errorReport": "",
-                "exitStatus": 0,
-                "failed": false,
-                "stdout": [
-
-                ],
-                "errorMessage": "",
-                "trace": {
-                    "tasksFailed": 0,
-                    "tasksCount": 14,
-                    "tasksSucceeded": 14
-                },
-                "name": "workflow",
-                "success": true
-            },
             "quants_mat_cols.txt:md5,e9868982c17a330392e38c2a5933cf97",
             "quants_mat.mtx:md5,b8aa7b3c488fd8923de50a3621d4991f",
             "quants_mat_rows.txt:md5,6227df5a13127b71c71fb18cd8574857",

diff --git a/tests/main_pipeline_cellranger.nf.test b/tests/main_pipeline_cellranger.nf.test
@@ -47,7 +47,6 @@ nextflow_pipeline {
                 // Check if files are the same
                 //
                 {assert snapshot(
-                    workflow,
                     path( "${outputDir}/results_cellranger/cellranger/count/Sample_X/outs/filtered_feature_bc_matrix/barcodes.tsv.gz" ),
                     path( "${outputDir}/results_cellranger/cellranger/count/Sample_X/outs/filtered_feature_bc_matrix/features.tsv.gz" ),
                     path( "${outputDir}/results_cellranger/cellranger/count/Sample_X/outs/filtered_feature_bc_matrix/matrix.mtx.gz" ),

diff --git a/tests/main_pipeline_cellranger.nf.test.snap b/tests/main_pipeline_cellranger.nf.test.snap
@@ -1,25 +1,6 @@
 {
     "test-dataset_cellranger_aligner": {
         "content": [
-            {
-                "stderr": [
-
-                ],
-                "errorReport": "",
-                "exitStatus": 0,
-                "failed": false,
-                "stdout": [
-
-                ],
-                "errorMessage": "",
-                "trace": {
-                    "tasksFailed": 0,
-                    "tasksCount": 18,
-                    "tasksSucceeded": 18
-                },
-                "name": "workflow",
-                "success": true
-            },
             "barcodes.tsv.gz:md5,fe6e51564b4405b37ca8604a844b1f2e",
             "features.tsv.gz:md5,99e453cb1443a3e43e99405184e51a5e",
             "matrix.mtx.gz:md5,1528b9b0fccc78dec95695928e42e710",
@@ -43,4 +24,4 @@
         },
         "timestamp": "2024-04-16T09:43:45.32298954"
     }
-}
+}
diff --git a/tests/main_pipeline_cellrangermulti.nf.test b/tests/main_pipeline_cellrangermulti.nf.test
@@ -69,8 +69,6 @@ nextflow_pipeline {
                 // Check if files are the same
                 //
                 {assert snapshot(
-                    workflow,
-
                     // barcodes.tsv.gz files
                     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" ),

diff --git a/tests/main_pipeline_cellrangermulti.nf.test.snap b/tests/main_pipeline_cellrangermulti.nf.test.snap
@@ -1,25 +1,6 @@
 {
     "test-dataset_cellrangermulti_aligner": {
         "content": [
-            {
-                "stderr": [
-
-                ],
-                "errorReport": "",
-                "exitStatus": 0,
-                "failed": false,
-                "stdout": [
-
-                ],
-                "errorMessage": "",
-                "trace": {
-                    "tasksFailed": 0,
-                    "tasksCount": 55,
-                    "tasksSucceeded": 55
-                },
-                "name": "workflow",
-                "success": true
-            },
             "barcodes.tsv.gz:md5,a3937e73aa76a2acff554ca2f81a108d",
             "barcodes.tsv.gz:md5,60c25e3ecc0d185048bad6ee78b03ec5",
             "barcodes.tsv.gz:md5,74ccf55411109ed9c3f2b6f73ae91ddc",
@@ -99,4 +80,4 @@
         },
         "timestamp": "2024-05-06T11:40:54.060867657"
     }
-}
+}
diff --git a/tests/main_pipeline_kallisto.nf.test b/tests/main_pipeline_kallisto.nf.test
@@ -46,7 +46,6 @@ nextflow_pipeline {
                 // Check if files are the same
                 //
                 {assert snapshot(
-                    workflow,
                     path( "${outputDir}/results_kallisto/kallisto/Sample_X.count/counts_unfiltered/cells_x_genes.barcodes.txt" ),
                     path( "${outputDir}/results_kallisto/kallisto/Sample_X.count/counts_unfiltered/cells_x_genes.genes.txt" ),
                     path( "${outputDir}/results_kallisto/kallisto/Sample_X.count/counts_unfiltered/cells_x_genes.mtx" ),

diff --git a/tests/main_pipeline_kallisto.nf.test.snap b/tests/main_pipeline_kallisto.nf.test.snap
@@ -1,25 +1,6 @@
 {
     "test-dataset_kallisto_aligner": {
         "content": [
-            {
-                "stderr": [
-
-                ],
-                "errorReport": "",
-                "exitStatus": 0,
-                "failed": false,
-                "stdout": [
-
-                ],
-                "errorMessage": "",
-                "trace": {
-                    "tasksFailed": 0,
-                    "tasksCount": 12,
-                    "tasksSucceeded": 12
-                },
-                "name": "workflow",
-                "success": true
-            },
             "cells_x_genes.barcodes.txt:md5,72d78bb1c1ee7cb174520b30f695aa48",
             "cells_x_genes.genes.txt:md5,acd9d00120f52031974b2add3e7521b6",
             "cells_x_genes.mtx:md5,894d60da192e3788de11fa8fc1fa711d",
@@ -35,4 +16,4 @@
         },
         "timestamp": "2024-03-18T14:51:42.040931572"
     }
-}
+}
diff --git a/tests/main_pipeline_star.nf.test b/tests/main_pipeline_star.nf.test
@@ -46,7 +46,6 @@ nextflow_pipeline {
                 // Check if files are the same
                 //
                 {assert snapshot(
-                    workflow,
                     path( "${outputDir}/results_star/star/Sample_X/Sample_X.SJ.out.tab"                             ),
                     path( "${outputDir}/results_star/star/Sample_X/Sample_X.Solo.out/Barcodes.stats"                ),
                     path( "${outputDir}/results_star/star/Sample_X/Sample_X.Solo.out/Gene/filtered/matrix.mtx.gz"   ),

diff --git a/tests/main_pipeline_star.nf.test.snap b/tests/main_pipeline_star.nf.test.snap
@@ -1,25 +1,6 @@
 {
     "test-dataset_star_aligner": {
         "content": [
-            {
-                "stderr": [
-
-                ],
-                "errorReport": "",
-                "exitStatus": 0,
-                "failed": false,
-                "stdout": [
-
-                ],
-                "errorMessage": "",
-                "trace": {
-                    "tasksFailed": 0,
-                    "tasksCount": 17,
-                    "tasksSucceeded": 17
-                },
-                "name": "workflow",
-                "success": true
-            },
             "Sample_X.SJ.out.tab:md5,d2d7f0abe38029012571bdf6622fc6eb",
             "Barcodes.stats:md5,7f99dc8aa5e074fbe5779ea7712c0886",
             "matrix.mtx.gz:md5,6a923393343aa1a69b0cf1bd998c9285",