From 4a7160333192b5cb4a86f5ccd985e266bde33109 Mon Sep 17 00:00:00 2001 From: Nico Trummer <52698566+nictru@users.noreply.github.com> Date: Fri, 18 Oct 2024 05:52:36 +0000 Subject: [PATCH] Remove problematic workflow snapshotting --- tests/main_pipeline_alevin.nf.test | 1 - tests/main_pipeline_alevin.nf.test.snap | 19 ----------------- tests/main_pipeline_cellranger.nf.test | 1 - tests/main_pipeline_cellranger.nf.test.snap | 21 +------------------ tests/main_pipeline_cellrangermulti.nf.test | 2 -- ...main_pipeline_cellrangermulti.nf.test.snap | 21 +------------------ tests/main_pipeline_kallisto.nf.test | 1 - tests/main_pipeline_kallisto.nf.test.snap | 21 +------------------ tests/main_pipeline_star.nf.test | 1 - tests/main_pipeline_star.nf.test.snap | 19 ----------------- 10 files changed, 3 insertions(+), 104 deletions(-) diff --git a/tests/main_pipeline_alevin.nf.test b/tests/main_pipeline_alevin.nf.test index 06d31f9e..be04fb76 100644 --- 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( "${outputDir}/results_alevin/alevin/Sample_X_alevin_results/af_quant/alevin/quants_mat_rows.txt" ), diff --git a/tests/main_pipeline_alevin.nf.test.snap b/tests/main_pipeline_alevin.nf.test.snap index e3d19f72..58976c6a 100644 --- a/tests/main_pipeline_alevin.nf.test.snap +++ b/tests/main_pipeline_alevin.nf.test.snap @@ -1,25 +1,6 @@ { "test-dataset_alevin_aligner": { "content": [ - { - "stderr": [ - - ], - "errorReport": "", - "exitStatus": 0, - "failed": false, - "stdout": [ - - ], - "errorMessage": "", - "trace": { - "tasksFailed": 0, - "tasksCount": 14, - "tasksSucceeded": 14 - }, - "name": "workflow", - "success": true - }, "quants_mat_cols.txt:md5,e9868982c17a330392e38c2a5933cf97", "quants_mat.mtx:md5,b8aa7b3c488fd8923de50a3621d4991f", "quants_mat_rows.txt:md5,6227df5a13127b71c71fb18cd8574857", diff --git a/tests/main_pipeline_cellranger.nf.test b/tests/main_pipeline_cellranger.nf.test index b62e615b..d1eb4191 100644 --- a/tests/main_pipeline_cellranger.nf.test +++ b/tests/main_pipeline_cellranger.nf.test @@ -47,7 +47,6 @@ nextflow_pipeline { // Check if files are the same // {assert snapshot( - workflow, path( "${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 index ef8874f8..6d276d82 100644 --- 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" } -} \ No newline at end of file +} diff --git a/tests/main_pipeline_cellrangermulti.nf.test b/tests/main_pipeline_cellrangermulti.nf.test index 9785ee75..9cf4b413 100644 --- 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 index d8cf3ae4..1594f01e 100644 --- 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" } -} \ No newline at end of file +} diff --git a/tests/main_pipeline_kallisto.nf.test b/tests/main_pipeline_kallisto.nf.test index 76c5e479..cb331986 100644 --- 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( "${outputDir}/results_kallisto/kallisto/Sample_X.count/counts_unfiltered/cells_x_genes.mtx" ), diff --git a/tests/main_pipeline_kallisto.nf.test.snap b/tests/main_pipeline_kallisto.nf.test.snap index f9b9c96a..82580178 100644 --- a/tests/main_pipeline_kallisto.nf.test.snap +++ b/tests/main_pipeline_kallisto.nf.test.snap @@ -1,25 +1,6 @@ { "test-dataset_kallisto_aligner": { "content": [ - { - "stderr": [ - - ], - "errorReport": "", - "exitStatus": 0, - "failed": false, - "stdout": [ - - ], - "errorMessage": "", - "trace": { - "tasksFailed": 0, - "tasksCount": 12, - "tasksSucceeded": 12 - }, - "name": "workflow", - "success": true - }, "cells_x_genes.barcodes.txt:md5,72d78bb1c1ee7cb174520b30f695aa48", "cells_x_genes.genes.txt:md5,acd9d00120f52031974b2add3e7521b6", "cells_x_genes.mtx:md5,894d60da192e3788de11fa8fc1fa711d", @@ -35,4 +16,4 @@ }, "timestamp": "2024-03-18T14:51:42.040931572" } -} \ No newline at end of file +} diff --git a/tests/main_pipeline_star.nf.test b/tests/main_pipeline_star.nf.test index 11b52efd..21eb1955 100644 --- a/tests/main_pipeline_star.nf.test +++ b/tests/main_pipeline_star.nf.test @@ -46,7 +46,6 @@ nextflow_pipeline { // Check if files are the same // {assert snapshot( - workflow, path( "${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 index 0aae74cf..88739a7b 100644 --- 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",