diff --git a/tests/pipeline/test_downstream.nf.test b/tests/pipeline/test_downstream.nf.test index 0b74606..7ec809a 100644 --- a/tests/pipeline/test_downstream.nf.test +++ b/tests/pipeline/test_downstream.nf.test @@ -19,9 +19,6 @@ nextflow_pipeline { // Data { assert file("$outputDir/CytAssist_11mm_FFPE_Human_Glioblastoma_2/data/st_adata_processed.h5ad").exists() }, - { assert file("$outputDir/CytAssist_11mm_FFPE_Human_Glioblastoma_2/data/st_adata_norm.h5ad").exists() }, - { assert file("$outputDir/CytAssist_11mm_FFPE_Human_Glioblastoma_2/data/st_adata_plain.h5ad").exists() }, - { assert file("$outputDir/CytAssist_11mm_FFPE_Human_Glioblastoma_2/data/st_adata_raw.h5ad").exists() }, // Reports { assert file("$outputDir/CytAssist_11mm_FFPE_Human_Glioblastoma_2/reports/st_qc_and_normalisation.html").text.contains("Distributions after filtering") }, diff --git a/tests/pipeline/test_spaceranger_ffpe_v1.nf.test b/tests/pipeline/test_spaceranger_ffpe_v1.nf.test index 8e4690e..928fa8a 100644 --- a/tests/pipeline/test_spaceranger_ffpe_v1.nf.test +++ b/tests/pipeline/test_spaceranger_ffpe_v1.nf.test @@ -24,9 +24,6 @@ nextflow_pipeline { // Data { assert file("$outputDir/Visium_FFPE_Human_Ovarian_Cancer/data/st_adata_processed.h5ad").exists() }, - { assert file("$outputDir/Visium_FFPE_Human_Ovarian_Cancer/data/st_adata_norm.h5ad").exists() }, - { assert file("$outputDir/Visium_FFPE_Human_Ovarian_Cancer/data/st_adata_plain.h5ad").exists() }, - { assert file("$outputDir/Visium_FFPE_Human_Ovarian_Cancer/data/st_adata_raw.h5ad").exists() }, // Reports { assert file("$outputDir/Visium_FFPE_Human_Ovarian_Cancer/reports/st_qc_and_normalisation.html").text.contains("Distributions after filtering") }, @@ -37,20 +34,17 @@ nextflow_pipeline { { assert file("$outputDir/Visium_FFPE_Human_Ovarian_Cancer/degs/st_spatial_de.csv").exists() }, // Space Ranger - { assert file("$outputDir/Visium_FFPE_Human_Ovarian_Cancer/outs/web_summary.html").exists() }, + { assert file("$outputDir/Visium_FFPE_Human_Ovarian_Cancer/spaceranger/outs/web_summary.html").exists() }, { assert snapshot( - path("$outputDir/Visium_FFPE_Human_Ovarian_Cancer/outs/raw_feature_bc_matrix.h5"), - path("$outputDir/Visium_FFPE_Human_Ovarian_Cancer/outs/filtered_feature_bc_matrix.h5"), + path("$outputDir/Visium_FFPE_Human_Ovarian_Cancer/spaceranger/outs/raw_feature_bc_matrix.h5"), + path("$outputDir/Visium_FFPE_Human_Ovarian_Cancer/spaceranger/outs/filtered_feature_bc_matrix.h5"), )}, - { assert file("$outputDir/Visium_FFPE_Human_Ovarian_Cancer/outs/raw_feature_bc_matrix.h5").exists() }, - { assert file("$outputDir/Visium_FFPE_Human_Ovarian_Cancer/outs/spatial/tissue_positions.csv").exists() }, + { assert file("$outputDir/Visium_FFPE_Human_Ovarian_Cancer/spaceranger/outs/raw_feature_bc_matrix.h5").exists() }, + { assert file("$outputDir/Visium_FFPE_Human_Ovarian_Cancer/spaceranger/outs/spatial/tissue_positions.csv").exists() }, // MultiQC { assert file("$outputDir/multiqc/multiqc_report.html").text.contains("Visium_FFPE_Human_Ovarian_Cancer")} ) } } - - - } diff --git a/tests/pipeline/test_spaceranger_ffpe_v1.nf.test.snap b/tests/pipeline/test_spaceranger_ffpe_v1.nf.test.snap index 1ea6423..9bdda01 100644 --- a/tests/pipeline/test_spaceranger_ffpe_v1.nf.test.snap +++ b/tests/pipeline/test_spaceranger_ffpe_v1.nf.test.snap @@ -1,15 +1,8 @@ { - "reports": { - "content": [ - "st_clustering.html:md5,905395042fa8b8a012718c1dbff39db4", - "st_qc_and_normalisation.html:md5,f89922b04edd7299e34ba1e43c257000" - ], - "timestamp": "2023-06-29T12:46:05+0000" - }, "software_versions": { "content": [ "{CUSTOM_DUMPSOFTWAREVERSIONS={python=3.12.0, yaml=6.0.1}, FASTQC={fastqc=0.12.1}, SPACERANGER_COUNT={spaceranger=2.1.0}, SPACERANGER_UNTAR_REFERENCE={untar=1.30}, ST_CLUSTERING={quarto=1.3.302, scanpy=1.9.3}, ST_QC_AND_NORMALISATION={quarto=1.3.302, scanpy=1.9.3}, ST_READ_DATA={scanpy=1.7.2}, ST_SPATIAL_DE={SpatialDE=1.1.3, leidenalg=0.9.1, quarto=1.3.302, scanpy=1.9.3}, Workflow={nf-core/spatialtranscriptomics=1.0dev}}" ], "timestamp": "2023-06-29T12:46:05+0000" } -} +} \ No newline at end of file diff --git a/tests/pipeline/test_spaceranger_ffpe_v2_cytassist.nf.test b/tests/pipeline/test_spaceranger_ffpe_v2_cytassist.nf.test index c67e138..94f54d3 100644 --- a/tests/pipeline/test_spaceranger_ffpe_v2_cytassist.nf.test +++ b/tests/pipeline/test_spaceranger_ffpe_v2_cytassist.nf.test @@ -24,9 +24,6 @@ nextflow_pipeline { // Data { assert file("$outputDir/CytAssist_11mm_FFPE_Human_Glioblastoma_2/data/st_adata_processed.h5ad").exists() }, - { assert file("$outputDir/CytAssist_11mm_FFPE_Human_Glioblastoma_2/data/st_adata_norm.h5ad").exists() }, - { assert file("$outputDir/CytAssist_11mm_FFPE_Human_Glioblastoma_2/data/st_adata_plain.h5ad").exists() }, - { assert file("$outputDir/CytAssist_11mm_FFPE_Human_Glioblastoma_2/data/st_adata_raw.h5ad").exists() }, // Reports { assert file("$outputDir/CytAssist_11mm_FFPE_Human_Glioblastoma_2/reports/st_qc_and_normalisation.html").text.contains("Distributions after filtering") }, @@ -37,13 +34,13 @@ nextflow_pipeline { { assert file("$outputDir/CytAssist_11mm_FFPE_Human_Glioblastoma_2/degs/st_spatial_de.csv").exists() }, // Space Ranger - { assert file("$outputDir/CytAssist_11mm_FFPE_Human_Glioblastoma_2/outs/web_summary.html").exists() }, + { assert file("$outputDir/CytAssist_11mm_FFPE_Human_Glioblastoma_2/spaceranger/outs/web_summary.html").exists() }, { assert snapshot( - path("$outputDir/CytAssist_11mm_FFPE_Human_Glioblastoma_2/outs/raw_feature_bc_matrix.h5"), - path("$outputDir/CytAssist_11mm_FFPE_Human_Glioblastoma_2/outs/filtered_feature_bc_matrix.h5"), + path("$outputDir/CytAssist_11mm_FFPE_Human_Glioblastoma_2/spaceranger/outs/raw_feature_bc_matrix.h5"), + path("$outputDir/CytAssist_11mm_FFPE_Human_Glioblastoma_2/spaceranger/outs/filtered_feature_bc_matrix.h5"), )}, - { assert file("$outputDir/CytAssist_11mm_FFPE_Human_Glioblastoma_2/outs/raw_feature_bc_matrix.h5").exists() }, - { assert file("$outputDir/CytAssist_11mm_FFPE_Human_Glioblastoma_2/outs/spatial/tissue_positions.csv").exists() }, + { assert file("$outputDir/CytAssist_11mm_FFPE_Human_Glioblastoma_2/spaceranger/outs/raw_feature_bc_matrix.h5").exists() }, + { assert file("$outputDir/CytAssist_11mm_FFPE_Human_Glioblastoma_2/spaceranger/outs/spatial/tissue_positions.csv").exists() }, // MultiQC { assert file("$outputDir/multiqc/multiqc_report.html").text.contains("CytAssist_11mm_FFPE_Human_Glioblastoma_2_4")} diff --git a/tests/pipeline/test_spaceranger_ffpe_v2_cytassist.nf.test.snap b/tests/pipeline/test_spaceranger_ffpe_v2_cytassist.nf.test.snap index 3acc223..94b2a26 100644 --- a/tests/pipeline/test_spaceranger_ffpe_v2_cytassist.nf.test.snap +++ b/tests/pipeline/test_spaceranger_ffpe_v2_cytassist.nf.test.snap @@ -1,15 +1,8 @@ { - "reports": { - "content": [ - "st_clustering.html:md5,b52e0fd3843c595634f1f2c6dbf76a3a", - "st_qc_and_normalisation.html:md5,82746189bdc1bef051724cd843fe8b20" - ], - "timestamp": "2023-06-29T12:48:09+0000" - }, "software_versions": { "content": [ "{CUSTOM_DUMPSOFTWAREVERSIONS={python=3.12.0, yaml=6.0.1}, FASTQC={fastqc=0.12.1}, SPACERANGER_COUNT={spaceranger=2.1.0}, SPACERANGER_UNTAR_REFERENCE={untar=1.30}, ST_CLUSTERING={quarto=1.3.302, scanpy=1.9.3}, ST_QC_AND_NORMALISATION={quarto=1.3.302, scanpy=1.9.3}, ST_READ_DATA={scanpy=1.7.2}, ST_SPATIAL_DE={SpatialDE=1.1.3, leidenalg=0.9.1, quarto=1.3.302, scanpy=1.9.3}, Workflow={nf-core/spatialtranscriptomics=1.0dev}}" ], "timestamp": "2023-06-29T12:48:09+0000" } -} +} \ No newline at end of file