Sign Parabricks skill

library-skills/parabricks/evals/files/rna-batch.json

@@ -0,0 +1,173 @@
+{
+  "parabricks_version": "4.7.1",
+  "reference_assets": "The FASTA and STAR library use the same reference sequences and annotation; the library was built by STAR 2.7.2a. Input data paths are deployment paths, not local files to probe.",
+  "jobs": [
+    {
+      "id": "treated",
+      "cpu_star_argv": [
+        "STAR",
+        "--genomeDir",
+        "/ref/GRCh38_STAR_2.7.2a",
+        "--readFilesIn",
+        "/reads/Batch 7/T_L001_R1.fastq.gz,/reads/Batch 7/T_L002_R1.fastq.gz,/reads/Batch 7/T_L003_R1.fastq.gz",
+        "/reads/Batch 7/T_L001_R2.fastq.gz,/reads/Batch 7/T_L002_R2.fastq.gz,/reads/Batch 7/T_L003_R2.fastq.gz",
+        "--outSAMattrRGline",
+        "ID:T.L1",
+        "SM:treated",
+        "LB:lib7",
+        "PL:ILLUMINA",
+        "PU:FC7.1",
+        "DS:treated day 7",
+        ",",
+        "ID:T.L2",
+        "SM:treated",
+        "LB:lib7",
+        "PL:ILLUMINA",
+        "PU:FC7.2",
+        "DS:treated day 7",
+        ",",
+        "ID:T.L3",
+        "SM:treated",
+        "LB:lib7",
+        "PL:ILLUMINA",
+        "PU:FC7.3",
+        "DS:treated day 7",
+        "--outSAMtype",
+        "BAM",
+        "SortedByCoordinate",
+        "--readFilesCommand",
+        "zcat",
+        "--outFileNamePrefix",
+        "/legacy/treated.",
+        "--outSAMattributes",
+        "NH",
+        "HI",
+        "AS",
+        "nM",
+        "NM",
+        "MD",
+        "XS",
+        "--alignSJstitchMismatchNmax",
+        "0",
+        "-1",
+        "0",
+        "0",
+        "--twopassMode",
+        "Basic",
+        "--chimSegmentMin",
+        "15",
+        "--chimOutType",
+        "WithinBAM",
+        "SoftClip",
+        "--runThreadN",
+        "24",
+        "--outSAMunmapped",
+        "Within"
+      ],
+      "target": {
+        "reference": "/ref/GRCh38.fa",
+        "output_directory": "/results/treated/star",
+        "bam": "/results/treated/treated.bam",
+        "mark_duplicates": false
+      },
+      "required_behavior": "Coordinate-sorted BAM, no duplicate marking. Preserve supplied alignment settings and read groups."
+    },
+    {
+      "id": "control",
+      "cpu_star_argv": [
+        "STAR",
+        "--genomeDir",
+        "/ref/GRCh38_STAR_2.7.2a",
+        "--readFilesIn",
+        "/reads/C_L001.fastq.gz,/reads/C_L002.fastq.gz",
+        "--outSAMattrRGline",
+        "ID:C.L1",
+        "SM:control",
+        "PL:ILLUMINA",
+        "PU:FC8.1",
+        ",",
+        "ID:C.L2",
+        "SM:control",
+        "PL:ILLUMINA",
+        "PU:FC8.2",
+        "--outSAMtype",
+        "BAM",
+        "SortedByCoordinate",
+        "--readFilesCommand",
+        "zcat",
+        "--outFileNamePrefix",
+        "/legacy/control.",
+        "--outSAMattributes",
+        "Standard",
+        "--twopassMode",
+        "None",
+        "--outFilterMismatchNmax",
+        "3",
+        "--outFilterMultimapNmax",
+        "8",
+        "--genomeSAindexNbases",
+        "14",
+        "--outSAMmapqUnique",
+        "60",
+        "--runThreadN",
+        "4"
+      ],
+      "target": {
+        "reference": "/ref/GRCh38.fa",
+        "output_directory": "/results/control/star",
+        "bam": "/results/control/control.bam",
+        "mark_duplicates": false
+      },
+      "required_behavior": "Coordinate-sorted BAM, no duplicate marking. Preserve supplied alignment settings and read groups."
+    },
+    {
+      "id": "rescue",
+      "cpu_star_argv": [
+        "STAR",
+        "--genomeDir",
+        "/ref/GRCh38_STAR_2.7.2a",
+        "--readFilesIn",
+        "/reads/rescue_R1.fastq.gz",
+        "/reads/rescue_R2.fastq.gz",
+        "--outSAMattrRGline",
+        "ID:R.L1",
+        "SM:rescue",
+        "PL:ILLUMINA",
+        "PU:FC9.1",
+        "--outSAMtype",
+        "BAM",
+        "SortedByCoordinate",
+        "--readFilesCommand",
+        "gzip -dc",
+        "--outFileNamePrefix",
+        "/legacy/rescue.",
+        "--alignEndsType",
+        "EndToEnd",
+        "--scoreGap",
+        "-4",
+        "--outFilterMatchNminOverLread",
+        "0.75",
+        "--outReadsUnmapped",
+        "Fastx",
+        "--outSAMunmapped",
+        "Within",
+        "--chimSegmentMin",
+        "12",
+        "--chimOutType",
+        "Junctions",
+        "--outSAMattributes",
+        "NH",
+        "HI",
+        "AS",
+        "nM"
+      ],
+      "target": {
+        "reference": "/ref/GRCh38.fa",
+        "output_directory": "/results/rescue/star",
+        "bam": "/results/rescue/rescue.bam",
+        "mark_duplicates": false
+      },
+      "required_behavior": "Coordinate-sorted BAM, no duplicate marking. Preserve supplied alignment settings and read groups."
+    }
+  ]
+}

library-skills/parabricks/evals/files/rna-contracts.json

@@ -0,0 +1,122 @@
+{
+  "parabricks_version": "4.7.1",
+  "reference_assets": "The FASTA and STAR library use the same reference sequences and annotation; the library was built by STAR 2.7.2a. Input data paths are deployment paths, not local files to probe.",
+  "jobs": [
+    {
+      "id": "per_alignment",
+      "cpu_star_argv": [
+        "STAR",
+        "--genomeDir",
+        "/ref/GRCh38_STAR_2.7.2a",
+        "--readFilesIn",
+        "/reads/P_R1.fastq.gz",
+        "/reads/P_R2.fastq.gz",
+        "--outSAMattrRGline",
+        "ID:P",
+        "SM:P",
+        "PU:P.1",
+        "--outSAMtype",
+        "BAM",
+        "Unsorted",
+        "--outSAMunmapped",
+        "Within",
+        "KeepPairs",
+        "--outFilterMultimapNmax",
+        "10"
+      ],
+      "target": {
+        "reference": "/ref/GRCh38.fa",
+        "output_directory": "/results/per_alignment/star",
+        "bam": "/results/per_alignment/per_alignment.bam",
+        "mark_duplicates": false
+      },
+      "required_behavior": "The CPU STAR unsorted BAM is sorted later. A consumer requires one unmapped-mate record for every reported alignment of the mapped mate, including multi-mappers. Keep that record multiplicity in the final sorted BAM; ordinary unmapped-read inclusion is insufficient."
+    },
+    {
+      "id": "ordinary",
+      "cpu_star_argv": [
+        "STAR",
+        "--genomeDir",
+        "/ref/GRCh38_STAR_2.7.2a",
+        "--readFilesIn",
+        "/reads/O_R1.fastq.gz",
+        "/reads/O_R2.fastq.gz",
+        "--outSAMattrRGline",
+        "ID:O",
+        "SM:O",
+        "PU:O.1",
+        "--outSAMtype",
+        "BAM",
+        "SortedByCoordinate",
+        "--outSAMunmapped",
+        "Within",
+        "KeepPairs",
+        "--runThreadN",
+        "16"
+      ],
+      "target": {
+        "reference": "/ref/GRCh38.fa",
+        "output_directory": "/results/ordinary/star",
+        "bam": "/results/ordinary/ordinary.bam",
+        "mark_duplicates": false
+      },
+      "required_behavior": "Coordinate-sorted BAM with ordinary unmapped-read inclusion. No adjacency or extra unmapped-mate copies for multi-mapping alignments are required. No duplicate marking."
+    },
+    {
+      "id": "primary_ties",
+      "cpu_star_argv": [
+        "STAR",
+        "--genomeDir",
+        "/ref/GRCh38_STAR_2.7.2a",
+        "--readFilesIn",
+        "/reads/T_R1.fastq.gz",
+        "/reads/T_R2.fastq.gz",
+        "--outSAMattrRGline",
+        "ID:T",
+        "SM:T",
+        "PU:T.1",
+        "--outSAMtype",
+        "BAM",
+        "SortedByCoordinate",
+        "--outSAMprimaryFlag",
+        "AllBestScore"
+      ],
+      "target": {
+        "reference": "/ref/GRCh38.fa",
+        "output_directory": "/results/primary_ties/star",
+        "bam": "/results/primary_ties/primary_ties.bam",
+        "mark_duplicates": false
+      },
+      "required_behavior": "Preserve the AllBestScore policy: all alignments tied for best score must retain primary status. Do not substitute a single-primary policy."
+    },
+    {
+      "id": "unmatched_lanes",
+      "cpu_star_argv": [
+        "STAR",
+        "--genomeDir",
+        "/ref/GRCh38_STAR_2.7.2a",
+        "--readFilesIn",
+        "/reads/U_L1_R1.fastq.gz,/reads/U_L2_R1.fastq.gz",
+        "/reads/U_L1_R2.fastq.gz",
+        "--outSAMattrRGline",
+        "ID:U1",
+        "SM:U",
+        "PU:U.1",
+        ",",
+        "ID:U2",
+        "SM:U",
+        "PU:U.2",
+        "--outSAMtype",
+        "BAM",
+        "SortedByCoordinate"
+      ],
+      "target": {
+        "reference": "/ref/GRCh38.fa",
+        "output_directory": "/results/unmatched_lanes/star",
+        "bam": "/results/unmatched_lanes/unmatched_lanes.bam",
+        "mark_duplicates": false
+      },
+      "required_behavior": "Keep both paired-end lanes. A mate file may be missing; do not guess names, concatenate lanes, or change pairing."
+    }
+  ]
+}