18656: Add missing test files

Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <peter.amstutz@curii.com>

diff --git a/sdk/cwl/tests/chipseq/DATEST/ChIP-Seq/Raw/fastq/Input_R1.fastq.gz b/sdk/cwl/tests/chipseq/DATEST/ChIP-Seq/Raw/fastq/Input_R1.fastq.gz
new file mode 100644 (file)
index 0000000..e69de29

diff --git a/sdk/cwl/tests/chipseq/DATEST/ChIP-Seq/Raw/fastq/Input_R2.fastq.gz b/sdk/cwl/tests/chipseq/DATEST/ChIP-Seq/Raw/fastq/Input_R2.fastq.gz
new file mode 100644 (file)
index 0000000..e69de29

diff --git a/sdk/cwl/tests/chipseq/DATEST/ChIP-Seq/Raw/fastq/Input_R3.fastq.gz b/sdk/cwl/tests/chipseq/DATEST/ChIP-Seq/Raw/fastq/Input_R3.fastq.gz
new file mode 100644 (file)
index 0000000..e69de29

diff --git a/sdk/cwl/tests/chipseq/chip-seq-single.json b/sdk/cwl/tests/chipseq/chip-seq-single.json
new file mode 100644 (file)
index 0000000..758390e
--- /dev/null
+++ b/sdk/cwl/tests/chipseq/chip-seq-single.json
@@ -0,0 +1,99 @@
+{
+    "referenceGenomeSequence": {
+        "class": "File",
+        "location": "data/Genomes/Homo_sapiens/GRCh38.p2/WholeGenome/genome.fa",
+        "metadata": {
+            "reference_genome": {
+                "organism": "Homo sapiens",
+                "version": "hg38"
+            },
+            "annotation": {
+                "source": "gencode",
+                "version": "v24"
+            }
+        }
+    },
+    "referenceGenomeSequenceDrosophila": {
+        "class": "File",
+        "location": "data/Genomes/Drosophila_melanogaster/dmel_r6.16/WholeGenome/genome.fa",
+        "metadata": {
+            "reference_genome": {
+                "organism": "Drosophila melanogaster",
+                "version": "rmel_r6.16"
+            }
+        }
+    },
+    "blacklistBed": {
+        "class": "File",
+        "location": "data/Genomes/Blacklist/lists2/hg38-blacklist.v2.bed",
+        "metadata": {
+            "reference_genome": {
+                "organism": "Homo sapiens",
+                "version": "hg38"
+            },
+            "annotation": {
+                "source": "gencode",
+                "version": "v24"
+            }
+        }
+    },
+    "BowtieHumanReference": {
+        "class": "Directory",
+        "location": "data/Genomes/Homo_sapiens/GRCh38.p2/Bowtie2Index/",
+        "metadata": {
+            "reference_genome": {
+                "organism": "Homo sapiens",
+                "version": "hg38"
+            },
+            "annotation": {
+                "source": "gencode",
+                "version": "v24"
+            }
+        }
+    },
+    "BowtieDrosophilaReference": {
+        "class": "Directory",
+        "location": "data/Genomes/Drosophila_melanogaster/dmel_r6.16/Bowtie2Index/",
+        "metadata": {
+            "reference_genome": {
+                "organism": "Drosophila melanogaster",
+                "version": "rmel_r6.16"
+            }
+        }
+    },
+    "sampleName": "LED054_0p03nMR1.0",
+    "inputFastq1": {
+        "class": "File",
+        "metadata": {
+            "user": "kmavrommatis",
+            "sample_id": [
+               2
+            ]
+        },
+        "location": "DATEST/ChIP-Seq/Raw/fastq/Input_R1.fastq.gz",
+        "secondaryFiles": []
+    },
+    "inputFastq2": {
+        "class": "File",
+        "metadata": {
+            "user": "kmavrommatis",
+            "sample_id": [
+                2
+            ]
+        },
+        "location": "DATEST/ChIP-Seq/Raw/fastq/Input_R3.fastq.gz",
+        "secondaryFiles": []
+    },
+    "inputFastqUMI": {
+        "class": "File",
+        "metadata": {
+            "user": "kmavrommatis",
+            "sample_id": [
+               2
+            ]
+        },
+        "location": "DATEST/ChIP-Seq/Raw/fastq/Input_R2.fastq.gz",
+        "secondaryFiles": []
+    }
+}
+

diff --git a/sdk/cwl/tests/chipseq/cwl-packed.json b/sdk/cwl/tests/chipseq/cwl-packed.json
new file mode 100644 (file)
index 0000000..8921bcb
--- /dev/null
+++ b/sdk/cwl/tests/chipseq/cwl-packed.json
@@ -0,0 +1,94 @@
+{
+    "$graph": [
+        {
+            "class": "Workflow",
+            "id": "#main",
+            "doc": "Pipeline that is applied on single ChIP-seq samples.\n\nStarts with QC on the reads and trimming (for adapters and based on quality)\n\nAligns to human genome and adds UMI\n\nAligns to Drosophila genome and counts the number of reads.\n\nAfter the alignment to human genome the files are filtered for duplicates, multimappers and alignments in black listed regions",
+            "label": "ChIP-Seq (single sample)",
+            "inputs": [
+                {
+                    "id": "#inputFastq1",
+                    "type": "File",
+                    "https://www.sevenbridges.com/fileTypes": "fastq",
+                    "https://www.sevenbridges.com/x": 0,
+                    "https://www.sevenbridges.com/y": 1726.25
+                },
+                {
+                    "id": "#blacklistBed",
+                    "type": "File",
+                    "https://www.sevenbridges.com/x": 746.4744873046875,
+                    "https://www.sevenbridges.com/y": 1903.265625
+                },
+                {
+                    "id": "#referenceGenomeSequence",
+                    "type": "File",
+                    "secondaryFiles": [
+                        ".fai",
+                        "^.dict"
+                    ],
+                    "https://www.sevenbridges.com/fileTypes": "fasta, fa",
+                    "https://www.sevenbridges.com/x": 0,
+                    "https://www.sevenbridges.com/y": 1405.203125
+                },
+                {
+                    "id": "#sampleName",
+                    "type": "string",
+                    "https://www.sevenbridges.com/x": 0,
+                    "https://www.sevenbridges.com/y": 1191.171875
+                },
+                {
+                    "id": "#inputFastq2",
+                    "type": [
+                        "null",
+                        "File"
+                    ],
+                    "https://www.sevenbridges.com/fileTypes": "fastq",
+                    "https://www.sevenbridges.com/x": 0,
+                    "https://www.sevenbridges.com/y": 1619.234375
+                },
+                {
+                    "id": "#inputFastqUMI",
+                    "type": "File",
+                    "https://www.sevenbridges.com/x": 0,
+                    "https://www.sevenbridges.com/y": 1512.21875
+                },
+                {
+                    "id": "#BowtieHumanReference",
+                    "type": "Directory",
+                    "https://www.sevenbridges.com/x": 363.875,
+                    "https://www.sevenbridges.com/y": 1519.21875
+                },
+                {
+                    "id": "#BowtieDrosophilaReference",
+                    "type": "Directory",
+                    "https://www.sevenbridges.com/x": 363.875,
+                    "https://www.sevenbridges.com/y": 1626.234375
+                },
+                {
+                    "id": "#referenceGenomeSequenceDrosophila",
+                    "type": "File",
+                    "secondaryFiles": [
+                        ".fai"
+                    ],
+                    "https://www.sevenbridges.com/x": 0,
+                    "https://www.sevenbridges.com/y": 1298.1875
+                }
+            ],
+            "outputs": [
+            ],
+            "steps": [
+                {
+                    "id": "#step1",
+                    "in": {
+                        "inp": "#inputFastq1"
+                    },
+                    "out": [],
+                    "run": "../cat.cwl"
+                }
+            ],
+            "requirements": [
+            ]
+        },
+   ],
+    "cwlVersion": "v1.0"
+}

diff --git a/sdk/cwl/tests/chipseq/data/Genomes/Blacklist/lists2/hg38-blacklist.v2.bed b/sdk/cwl/tests/chipseq/data/Genomes/Blacklist/lists2/hg38-blacklist.v2.bed
new file mode 100644 (file)
index 0000000..e69de29

diff --git a/sdk/cwl/tests/chipseq/data/Genomes/Drosophila_melanogaster/dmel_r6.16/Bowtie2Index/genome.fa b/sdk/cwl/tests/chipseq/data/Genomes/Drosophila_melanogaster/dmel_r6.16/Bowtie2Index/genome.fa
new file mode 100644 (file)
index 0000000..e69de29

diff --git a/sdk/cwl/tests/chipseq/data/Genomes/Drosophila_melanogaster/dmel_r6.16/WholeGenome/genome.fa b/sdk/cwl/tests/chipseq/data/Genomes/Drosophila_melanogaster/dmel_r6.16/WholeGenome/genome.fa
new file mode 100644 (file)
index 0000000..e69de29

diff --git a/sdk/cwl/tests/chipseq/data/Genomes/Homo_sapiens/GRCh38.p2/Bowtie2Index/genome.fa b/sdk/cwl/tests/chipseq/data/Genomes/Homo_sapiens/GRCh38.p2/Bowtie2Index/genome.fa
new file mode 100644 (file)
index 0000000..e69de29

diff --git a/sdk/cwl/tests/chipseq/data/Genomes/Homo_sapiens/GRCh38.p2/WholeGenome/genome.fa b/sdk/cwl/tests/chipseq/data/Genomes/Homo_sapiens/GRCh38.p2/WholeGenome/genome.fa
new file mode 100644 (file)
index 0000000..e69de29