Merge branch 'master' of github.com:mskcc/beagle into hotfix/v2_nucle…

…o_agg
mskcc · Feb 11, 2025 · 52ecbee · 52ecbee
2 parents 73713a0 + 608a1eb
commit 52ecbee
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Showing 18 changed files with 2,585 additions and 3 deletions.
diff --git a/fixtures/tests/08944_B.argos.input.json b/fixtures/tests/08944_B.argos.input.json
@@ -23,6 +23,7 @@
         }
       ],
       "bam": [],
+      "zBam": [],
       "RG_ID": [
         "s_C_MP76JR_X001_d_H3MV7BBXY"
       ],
@@ -55,6 +56,7 @@
         }
       ],
       "bam": [],
+      "zBam": [],
       "RG_ID": [
         "s_C_MP76JR_N001_d_H3MV7BBXY"
       ],
@@ -392,6 +394,7 @@
         }
       ],
       "bam": [],
+      "zBam": [],
       "RG_ID": [
         "s_C_4LM16H_X001_d_H3MV7BBXY"
       ],
@@ -424,6 +427,7 @@
         }
       ],
       "bam": [],
+      "zBam": [],
       "RG_ID": [
         "s_C_4LM16H_N001_d_H3MV7BBXY"
       ],

diff --git a/fixtures/tests/08944_B.argos_bam.input.json b/fixtures/tests/08944_B.argos_bam.input.json
@@ -23,6 +23,7 @@
         }
       ],
       "bam": [],
+      "zBam": [],
       "RG_ID": [
         "s_C_MP76JR_X001_d_H3MV7BBXY"
       ],
@@ -55,6 +56,7 @@
       "zR1": [],
       "zR2": [],
       "bam": [],
+      "zBam": [],
       "RG_ID": [
         "s_C_MP76JR_N001_d_H3MV7BBXY"
       ],
@@ -167,6 +169,7 @@
         }
       ],
       "bam": [],
+      "zBam": [],
       "RG_ID": [
         "s_C_4LM16H_X001_d_H3MV7BBXY"
       ],
@@ -199,6 +202,7 @@
       "zR1": [],
       "zR2": [],
       "bam": [],
+      "zBam": [],
       "RG_ID": [
         "s_C_4LM16H_N001_d_H3MV7BBXY"
       ],

diff --git a/fixtures/tests/10075_D_single_TN_pair.argos_1_7_0.input.json b/fixtures/tests/10075_D_single_TN_pair.argos_1_7_0.input.json
@@ -23,6 +23,7 @@
       "zR1": [],
       "zR2": [],
       "bam": [],
+      "zBam": [],
       "RG_ID": [
         "s_C_8VK0V7_R001_d_HFTCNBBXY_GTATTGGC-TTGTCGGT"
       ],
@@ -55,6 +56,7 @@
       "zR1": [],
       "zR2": [],
       "bam": [],
+      "zBam": [],
       "RG_ID": [
         "s_C_8VK0V7_N001_d_HCYYWBBXY"
       ],

diff --git a/fixtures/tests/10075_D_single_TN_pair.argos_bam.input.json b/fixtures/tests/10075_D_single_TN_pair.argos_bam.input.json
@@ -101,6 +101,7 @@
             "zR1": [],
             "zR2": [],
             "bam": [],
+            "zBam": [],
             "RG_ID": [
                 "s_C_8VK0V7_R001_d_HFTCNBBXY_GTATTGGC-TTGTCGGT"
             ],
@@ -133,6 +134,7 @@
             "zR1": [],
             "zR2": [],
             "bam": [],
+            "zBam": [],
             "RG_ID": [
                 "s_C_8VK0V7_N001_d_HCYYWBBXY"
             ],

diff --git a/fixtures/tests/10075_D_single_TN_pair.argos_bam_1_0_0.input.json b/fixtures/tests/10075_D_single_TN_pair.argos_bam_1_0_0.input.json
@@ -0,0 +1,146 @@
+[
+    {
+        "assay": "IMPACT468_BAITS",
+        "pi": "John Smith",
+        "pi_email": "[email protected]",
+        "patient_id": "C-8VK0V7",
+        "genome": "GRCh37",
+        "intervals": [
+            "1",
+            "2",
+            "3",
+            "4",
+            "5",
+            "6",
+            "7",
+            "8",
+            "9",
+            "10",
+            "11",
+            "12",
+            "13",
+            "14",
+            "15",
+            "16",
+            "17",
+            "18",
+            "19",
+            "20",
+            "21",
+            "22",
+            "X",
+            "Y",
+            "MT"
+        ],
+        "opt_dup_pix_dist": "2500",
+        "hapmap": {
+            "class": "File",
+            "location": "juno:///rtsess01/compute/juno/bic/juno/work/ci/resources/request_files/hapmap/hapmap_3.3.b37.vcf"
+        },
+        "dbsnp": {
+            "class": "File",
+            "location": "juno:///rtsess01/compute/juno/bic/juno/work/ci/resources/request_files/dbsnp/dbsnp_138.b37.excluding_sites_after_129.vcf"
+        },
+        "indels_1000g": {
+            "class": "File",
+            "location": "juno:///rtsess01/compute/juno/bic/juno/work/ci/resources/request_files/indels_1000g/Mills_and_1000G_gold_standard.indels.b37.vcf"
+        },
+        "snps_1000g": {
+            "class": "File",
+            "location": "juno:///rtsess01/compute/juno/bic/juno/work/ci/resources/request_files/snps_1000g/1000G_phase1.snps.high_confidence.b37.vcf"
+        },
+        "covariates": [
+            "CycleCovariate",
+            "ContextCovariate",
+            "ReadGroupCovariate",
+            "QualityScoreCovariate"
+        ],
+        "abra_ram_min": 84000,
+        "gatk_jar_path": "/usr/bin/gatk.jar",
+        "bait_intervals": {
+            "class": "File",
+            "location": "juno:///rtsess01/compute/juno/bic/juno/work/ci/resources/genomic_resources/targets/IMPACT468/b37/picard_baits.interval_list"
+        },
+        "target_intervals": {
+            "class": "File",
+            "location": "juno:///rtsess01/compute/juno/bic/juno/work/ci/resources/genomic_resources/targets/IMPACT468/b37/picard_targets.interval_list"
+        },
+        "fp_intervals": {
+            "class": "File",
+            "location": "juno:///rtsess01/compute/juno/bic/juno/work/ci/resources/genomic_resources/targets/IMPACT468/b37/FP_tiling_intervals.list"
+        },
+        "ref_fasta": {
+            "class": "File",
+            "location": "juno:///rtsess01/compute/juno/bic/juno/work/ci/resources/genomes/GRCh37/fasta/b37.fasta"
+        },
+        "mouse_fasta": {
+            "class": "File",
+            "location": "juno:///rtsess01/compute/juno/bic/juno/work/ci/resources/genomes/GRCm38/GRCm38.fasta"
+        },
+        "conpair_markers_bed": "/usr/bin/conpair/data/markers/GRCh37.autosomes.phase3_shapeit2_mvncall_integrated.20130502.SNV.genotype.sselect_v4_MAF_0.4_LD_0.8.bed",
+        "tumor": {
+            "ID": "s_C_8VK0V7_R001_d",
+            "CN": "MSKCC",
+            "LB": "10075_D_5_1_1_1",
+            "PL": "Illumina",
+            "PU": [
+                "HFTCNBBXY_GTATTGGC-TTGTCGGT"
+            ],
+            "R1": [
+                {
+                    "class": "File",
+                    "location": "juno:///ifs/archive/GCL/hiseq/FASTQ/PITT_0439_BHFTCNBBXY/Project_10075_D/Sample_SK_MEL_1091A_T_IGO_10075_D_5/SK_MEL_1091A_T_IGO_10075_D_5_S80_R1_001.fastq.gz"
+                }
+            ],
+            "R2": [
+                {
+                    "class": "File",
+                    "location": "juno:///ifs/archive/GCL/hiseq/FASTQ/PITT_0439_BHFTCNBBXY/Project_10075_D/Sample_SK_MEL_1091A_T_IGO_10075_D_5/SK_MEL_1091A_T_IGO_10075_D_5_S80_R2_001.fastq.gz"
+                }
+            ],
+            "zR1": [],
+            "zR2": [],
+            "bam": [],
+            "RG_ID": [
+                "s_C_8VK0V7_R001_d_HFTCNBBXY_GTATTGGC-TTGTCGGT"
+            ],
+            "adapter": "AGATCGGAAGAGCACACGTCTGAACTCCAGTCACATGAGCATCTCGTATGCCGTCTTCTGCTTG",
+            "adapter2": "AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT",
+            "bwa_output": "s_C_8VK0V7_R001_d.bam",
+            "request_id": "10075_D",
+            "specimen_type": "Resection"
+        },
+        "normal": {
+            "ID": "s_C_8VK0V7_N001_d",
+            "CN": "MSKCC",
+            "LB": "10075_D_3",
+            "PL": "Illumina",
+            "PU": [
+                "HCYYWBBXY"
+            ],
+            "R1": [
+                {
+                    "class": "File",
+                    "location": "juno:///ifs/archive/GCL/hiseq/FASTQ/JAX_0397_BHCYYWBBXY/Project_10075_D/Sample_JW_MEL_007_NORM_IGO_10075_D_3/JW_MEL_007_NORM_IGO_10075_D_3_S15_R1_001.fastq.gz"
+                }
+            ],
+            "R2": [
+                {
+                    "class": "File",
+                    "location": "juno:///ifs/archive/GCL/hiseq/FASTQ/JAX_0397_BHCYYWBBXY/Project_10075_D/Sample_JW_MEL_007_NORM_IGO_10075_D_3/JW_MEL_007_NORM_IGO_10075_D_3_S15_R2_001.fastq.gz"
+                }
+            ],
+            "zR1": [],
+            "zR2": [],
+            "bam": [],
+            "RG_ID": [
+                "s_C_8VK0V7_N001_d_HCYYWBBXY"
+            ],
+            "adapter": "AGATCGGAAGAGCACACGTCTGAACTCCAGTCACATGAGCATCTCGTATGCCGTCTTCTGCTTG",
+            "adapter2": "AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT",
+            "bwa_output": "s_C_8VK0V7_N001_d.bam",
+            "request_id": "10075_D",
+            "specimen_type": "Normal"
+        }
+    }
+]