update test reflecting new cellranger version

mskcc · Apr 1, 2024 · 8c4d027 · 8c4d027
1 parent 8fbc4b7
commit 8c4d027
Showing 1 changed file with 3 additions and 16 deletions.
diff --git a/test_scripts.py b/test_scripts.py
@@ -21,26 +21,13 @@ def testCellranger_generate_cellranger_cmd():
         if genome_dict[sample] != "Human" and genome_dict[sample] != "Mouse":
             genome_dict[sample] = "Mouse"
         cmd.append(cellranger.generate_cellranger_cmd(sample, "count", genome_dict[sample], fastq_file_list_dict[sample], "DIANA_0453_AHFKJ5DRXY"))
-    test_result = ["bsub -J DIANA_0453_AHFKJ5DRXY_Project_06265_AG_06265_8869_1_IGO_06265_AG_3_count_cellranger -o DIANA_0453_AHFKJ5DRXY_Project_06265_AG_06265_8869_1_IGO_06265_AG_3_count_cellranger.out /igo/work/nabors/tools/cellranger-7.0.0/cellranger count --id=Sample_06265_8869_1_IGO_06265_AG_3__count --transcriptome=/igo/work/nabors/genomes/10X_Genomics/GEX/refdata-gex-GRCh38-2020-A --fastqs=/igo/staging/FASTQ/DIANA_0453_AHFKJ5DRXY/Project_06265_AG/Sample_06265_8869_1_IGO_06265_AG_3 --nopreflight --jobmode=lsf --mempercore=64 --disable-ui --maxjobs=200",   
-    "bsub -J DIANA_0453_AHFKJ5DRXY_Project_11969_E_Third-Transcriptome_IGO_11969_E_3_count_cellranger -o DIANA_0453_AHFKJ5DRXY_Project_11969_E_Third-Transcriptome_IGO_11969_E_3_count_cellranger.out /igo/work/nabors/tools/cellranger-7.0.0/cellranger count --id=Sample_Third-Transcriptome_IGO_11969_E_3__count --transcriptome=/igo/work/nabors/genomes/10X_Genomics/GEX/refdata-gex-mm10-2020-A --fastqs=/igo/staging/FASTQ/DIANA_0450_AH3JL3DSX3/Project_11969_E/Sample_Third-Transcriptome_IGO_11969_E_3,/igo/staging/FASTQ/DIANA_0454_BH555MDMXY/Project_11969_E/Sample_Third-Transcriptome_IGO_11969_E_3 --nopreflight --jobmode=lsf --mempercore=64 --disable-ui --maxjobs=200",
-    "bsub -J DIANA_0453_AHFKJ5DRXY_Project_11969_E_Second_IGO_11969_E_2_count_cellranger -o DIANA_0453_AHFKJ5DRXY_Project_11969_E_Second_IGO_11969_E_2_count_cellranger.out /igo/work/nabors/tools/cellranger-7.0.0/cellranger count --id=Sample_Second_IGO_11969_E_2__count --transcriptome=/igo/work/nabors/genomes/10X_Genomics/GEX/refdata-gex-mm10-2020-A --fastqs=/igo/staging/FASTQ/DIANA_0453_AHFKJ5DRXY/Project_11969_E/Sample_Second_IGO_11969_E_2,/igo/staging/FASTQ/DIANA_0450_AH3JL3DSX3/Project_11969_E/Sample_Second_IGO_11969_E_2 --nopreflight --jobmode=lsf --mempercore=64 --disable-ui --maxjobs=200"]
+    test_result = ["bsub -J DIANA_0453_AHFKJ5DRXY_Project_06265_AG_06265_8869_1_IGO_06265_AG_3_count_cellranger -o DIANA_0453_AHFKJ5DRXY_Project_06265_AG_06265_8869_1_IGO_06265_AG_3_count_cellranger.out /igo/work/nabors/tools/cellranger-8.0.0/cellranger count --id=Sample_06265_8869_1_IGO_06265_AG_3__count --transcriptome=/igo/work/nabors/genomes/10X_Genomics/GEX/refdata-gex-GRCh38-2020-A --fastqs=/igo/staging/FASTQ/DIANA_0453_AHFKJ5DRXY/Project_06265_AG/Sample_06265_8869_1_IGO_06265_AG_3 --nopreflight --jobmode=lsf --mempercore=64 --disable-ui --maxjobs=200",   
+    "bsub -J DIANA_0453_AHFKJ5DRXY_Project_11969_E_Third-Transcriptome_IGO_11969_E_3_count_cellranger -o DIANA_0453_AHFKJ5DRXY_Project_11969_E_Third-Transcriptome_IGO_11969_E_3_count_cellranger.out /igo/work/nabors/tools/cellranger-8.0.0/cellranger count --id=Sample_Third-Transcriptome_IGO_11969_E_3__count --transcriptome=/igo/work/nabors/genomes/10X_Genomics/GEX/refdata-gex-mm10-2020-A --fastqs=/igo/staging/FASTQ/DIANA_0450_AH3JL3DSX3/Project_11969_E/Sample_Third-Transcriptome_IGO_11969_E_3,/igo/staging/FASTQ/DIANA_0454_BH555MDMXY/Project_11969_E/Sample_Third-Transcriptome_IGO_11969_E_3 --nopreflight --jobmode=lsf --mempercore=64 --disable-ui --maxjobs=200",
+    "bsub -J DIANA_0453_AHFKJ5DRXY_Project_11969_E_Second_IGO_11969_E_2_count_cellranger -o DIANA_0453_AHFKJ5DRXY_Project_11969_E_Second_IGO_11969_E_2_count_cellranger.out /igo/work/nabors/tools/cellranger-8.0.0/cellranger count --id=Sample_Second_IGO_11969_E_2__count --transcriptome=/igo/work/nabors/genomes/10X_Genomics/GEX/refdata-gex-mm10-2020-A --fastqs=/igo/staging/FASTQ/DIANA_0453_AHFKJ5DRXY/Project_11969_E/Sample_Second_IGO_11969_E_2,/igo/staging/FASTQ/DIANA_0450_AH3JL3DSX3/Project_11969_E/Sample_Second_IGO_11969_E_2 --nopreflight --jobmode=lsf --mempercore=64 --disable-ui --maxjobs=200"]
 
     for i in range (3): 
         assert(cmd[i] == test_result[i])
 
-def testCellranger_get_SCRI_tag():
-    sample1 = "SD-1680_Patient_D_nucseq_H_VDJ_IGO_12437_AN_5"
-    sample2 = "SDtest_IGO_12437_AN_4"
-    sample3 = "SDtest_GE_IGO_12437_AN_4"
-
-    tag_genome1 = cellranger.get_SCRI_tag(sample1)
-    tag_genome2 = cellranger.get_SCRI_tag(sample2)
-    tag_genome3 = cellranger.get_SCRI_tag(sample3)
-
-    assert(tag_genome1 == ("vdj", "Human"))
-    assert(tag_genome2 == ("Skip", "na"))
-    assert(tag_genome3 == ("Skip", "na"))
-
 def testCellranger_get_tag():
     assert(cellranger.get_tag("10X_genomic") == "Skip")
     assert(cellranger.get_tag("10X_Genomics_GeneExpression-3") == "count")