Skip to content

Commit 46cac4b

Browse files
lindaxianglindaxiang
committed
add and update test jobs
1 parent 92af6ae commit 46cac4b

9 files changed

Lines changed: 201 additions & 11 deletions

‎payload-gen-rna-alignment/tests/expected/expected.test-job-1.out.json‎

Lines changed: 6 additions & 4 deletions
Original file line numberDiff line numberDiff line change
@@ -8,8 +8,8 @@
88
"workflow_version": "0.1.0",
99
"genome_build": "GRCh38_hla_decoy_ebv",
1010
"genome_annotation": "GENCODE v38",
11-
"run_id": "insane_hugle",
12-
"session_id": "67ccf9ba-915e-4dda-ac5c-975fd1ff0509",
11+
"run_id": "admiring_minsky",
12+
"session_id": "1b279d9a-2ed3-49e7-8bff-1ee0255a1245",
1313
"inputs": [
1414
{
1515
"analysis_type": "sequencing_experiment",
@@ -31,7 +31,8 @@
3131
"STAR"
3232
]
3333
},
34-
"fileName": "TEST-PRO.DO001.SA001.rna-seq.20211109.star.genome_aln.cram",
34+
"fileName": "TEST-PRO.DO001.SA001.rna-seq.20211207.star.genome_aln.cram",
35+
"fileType": "CRAM",
3536
"dataType": "Aligned Reads"
3637
},
3738
{
@@ -47,7 +48,8 @@
4748
"STAR"
4849
]
4950
},
50-
"fileName": "TEST-PRO.DO001.SA001.rna-seq.20211109.star.genome_aln.cram.crai",
51+
"fileName": "TEST-PRO.DO001.SA001.rna-seq.20211207.star.genome_aln.cram.crai",
52+
"fileType": "CRAI",
5153
"dataType": "Aligned Reads Index"
5254
}
5355
],

‎payload-gen-rna-alignment/tests/expected/expected.test-job-2.out.json‎

Lines changed: 6 additions & 4 deletions
Original file line numberDiff line numberDiff line change
@@ -8,8 +8,8 @@
88
"workflow_version": "0.1.0",
99
"genome_build": "GRCh38_hla_decoy_ebv",
1010
"genome_annotation": "GENCODE v38",
11-
"run_id": "deadly_ekeblad",
12-
"session_id": "e63af1d0-0eaa-42c2-b122-ec6f0bbaa49b",
11+
"run_id": "focused_shirley",
12+
"session_id": "09c96e0c-b63f-450a-b5aa-97ba0a4aa4a6",
1313
"inputs": [
1414
{
1515
"analysis_type": "sequencing_experiment",
@@ -64,7 +64,8 @@
6464
},
6565
"description": "RNA alignment metrics for a SAM or BAM file."
6666
},
67-
"fileName": "TEST-PRO.DO001.SA001.rna-seq.20211116.star.collectrnaseqmetrics.tgz",
67+
"fileName": "TEST-PRO.DO001.SA001.rna-seq.20211207.star.collectrnaseqmetrics.tgz",
68+
"fileType": "TGZ",
6869
"dataType": "Aligned Reads QC"
6970
},
7071
{
@@ -98,7 +99,8 @@
9899
]
99100
}
100101
},
101-
"fileName": "TEST-PRO.DO001.SA001.rna-seq.20211116.star.duplicates_metrics.tgz",
102+
"fileName": "TEST-PRO.DO001.SA001.rna-seq.20211207.star.duplicates_metrics.tgz",
103+
"fileType": "TGZ",
102104
"dataType": "Aligned Reads QC"
103105
}
104106
],

‎payload-gen-rna-alignment/tests/expected/expected.test-job-3.out.json‎

Lines changed: 4 additions & 3 deletions
Original file line numberDiff line numberDiff line change
@@ -8,8 +8,8 @@
88
"workflow_version": "0.1.0",
99
"genome_build": "GRCh38_hla_decoy_ebv",
1010
"genome_annotation": "GENCODE v38",
11-
"run_id": "jovial_ramanujan",
12-
"session_id": "26009d8f-0cdf-48d6-952d-69e1eb92d2bc",
11+
"run_id": "sick_hilbert",
12+
"session_id": "575a320a-f228-48d7-a311-b8a314d66e6b",
1313
"inputs": [
1414
{
1515
"analysis_type": "sequencing_experiment",
@@ -47,7 +47,8 @@
4747
},
4848
"description": "High level sequencing reads QC metrics generated by FastQC."
4949
},
50-
"fileName": "TEST-PRO.DO001.SA001.rna-seq.20211116.S01L1.fastqc.tgz",
50+
"fileName": "TEST-PRO.DO001.SA001.rna-seq.20211207.S01L1.fastqc.tgz",
51+
"fileType": "TGZ",
5152
"dataType": "Sequencing QC"
5253
}
5354
],

‎payload-gen-rna-alignment/tests/expected/expected.test-job-4.out.json‎

Lines changed: 71 additions & 0 deletions
Original file line numberDiff line numberDiff line change
@@ -0,0 +1,71 @@
1+
{
2+
"analysisType": {
3+
"name": "supplement"
4+
},
5+
"studyId": "TEST-PRO",
6+
"workflow": {
7+
"workflow_name": "RNA Seq Alignment",
8+
"workflow_version": "0.1.0",
9+
"genome_build": "GRCh38_hla_decoy_ebv",
10+
"genome_annotation": "GENCODE v38",
11+
"run_id": "peaceful_lamarr",
12+
"session_id": "69bb68a1-8e00-4fca-8919-dd476f8deb53",
13+
"inputs": [
14+
{
15+
"analysis_type": "sequencing_experiment",
16+
"input_analysis_id": null
17+
}
18+
]
19+
},
20+
"files": [
21+
{
22+
"fileSize": 1985,
23+
"fileMd5sum": "ef7925492346751fe88557acbffef877",
24+
"fileAccess": "controlled",
25+
"info": {
26+
"data_category": "Supplement",
27+
"data_subtypes": [
28+
null
29+
],
30+
"analysis_tools": [
31+
"HiSAT2"
32+
],
33+
"files_in_tgz": [
34+
"SA001_RG_S01L1_metrics.txt",
35+
"SA001_RG_S01L2_metrics.txt",
36+
"SA001_RG_S01L1_summary.txt",
37+
"SA001_RG_S01L2_summary.txt",
38+
"align.log"
39+
]
40+
},
41+
"fileName": "TEST-PRO.DO001.SA001.rna-seq.20211207.hisat2.supplement.tgz",
42+
"fileType": "TGZ",
43+
"dataType": "Running Logs"
44+
}
45+
],
46+
"samples": [
47+
{
48+
"submitterSampleId": "donor1_sample1_id",
49+
"matchedNormalSubmitterSampleId": "sample1_normal",
50+
"sampleType": "RNA",
51+
"specimen": {
52+
"submitterSpecimenId": "donor1_sample1",
53+
"tumourNormalDesignation": "tumor",
54+
"specimenTissueSource": "simulated",
55+
"specimenType": "simulated"
56+
},
57+
"donor": {
58+
"submitterDonorId": "donor1",
59+
"gender": "male"
60+
}
61+
}
62+
],
63+
"experiment": {
64+
"submitter_sequencing_experiment_id": "TEST_EXP",
65+
"sequencing_center": "SIM",
66+
"platform": "ILLUMINA",
67+
"platform_model": "Polyester",
68+
"experimental_strategy": "RNA-Seq",
69+
"sequencing_date": "2021-04-21"
70+
}
71+
}

‎payload-gen-rna-alignment/tests/expected/expected.test-job-5.out.json‎

Lines changed: 64 additions & 0 deletions
Original file line numberDiff line numberDiff line change
@@ -0,0 +1,64 @@
1+
{
2+
"analysisType": {
3+
"name": "splice_junctions"
4+
},
5+
"studyId": "TEST-PRO",
6+
"workflow": {
7+
"workflow_name": "RNA Seq Alignment",
8+
"workflow_version": "0.1.0",
9+
"genome_build": "GRCh38_hla_decoy_ebv",
10+
"genome_annotation": "GENCODE v38",
11+
"run_id": "hopeful_noyce",
12+
"session_id": "2702543c-1cb1-47e5-b2c6-5f362f2ee269",
13+
"inputs": [
14+
{
15+
"analysis_type": "sequencing_experiment",
16+
"input_analysis_id": null
17+
}
18+
]
19+
},
20+
"files": [
21+
{
22+
"fileSize": 371,
23+
"fileMd5sum": "14bc8619e7463a4c01f957729dae174e",
24+
"fileAccess": "controlled",
25+
"info": {
26+
"data_category": "Transcriptome Profiling",
27+
"data_subtypes": [
28+
null
29+
],
30+
"analysis_tools": [
31+
"HiSAT2"
32+
]
33+
},
34+
"fileName": "TEST-PRO.DO001.SA001.rna-seq.20211207.hisat2.splice_junctions.txt",
35+
"fileType": "TXT",
36+
"dataType": "Splice Junctions"
37+
}
38+
],
39+
"samples": [
40+
{
41+
"submitterSampleId": "donor1_sample1_id",
42+
"matchedNormalSubmitterSampleId": "sample1_normal",
43+
"sampleType": "RNA",
44+
"specimen": {
45+
"submitterSpecimenId": "donor1_sample1",
46+
"tumourNormalDesignation": "tumor",
47+
"specimenTissueSource": "simulated",
48+
"specimenType": "simulated"
49+
},
50+
"donor": {
51+
"submitterDonorId": "donor1",
52+
"gender": "male"
53+
}
54+
}
55+
],
56+
"experiment": {
57+
"submitter_sequencing_experiment_id": "TEST_EXP",
58+
"sequencing_center": "SIM",
59+
"platform": "ILLUMINA",
60+
"platform_model": "Polyester",
61+
"experimental_strategy": "RNA-Seq",
62+
"sequencing_date": "2021-04-21"
63+
}
64+
}

‎payload-gen-rna-alignment/tests/test-job-4.json‎

Lines changed: 16 additions & 0 deletions
Original file line numberDiff line numberDiff line change
@@ -0,0 +1,16 @@
1+
{
2+
"seq_experiment_analysis": "input/s3.881fe6cf-8c80-4c7b-9f4d-b8dac9601d01.sequencing_experiment.payload.json",
3+
"files_to_upload": [
4+
"input/SA001.hisat2.all_logs.supplement.tar.gz"
5+
],
6+
"expected_output": "expected/expected.test-job-4.out.json",
7+
"aligner": "hisat2",
8+
"analysis_type": "supplement",
9+
"genome_annotation": "GENCODE v38",
10+
"genome_build": "GRCh38_hla_decoy_ebv",
11+
"wf_name": "rna-seq-alignment",
12+
"wf_version": "0.1.0",
13+
"publish_dir": "outdir",
14+
"cpus": 1,
15+
"mem": 0.5
16+
}

‎payload-gen-rna-alignment/tests/test-job-5.json‎

Lines changed: 16 additions & 0 deletions
Original file line numberDiff line numberDiff line change
@@ -0,0 +1,16 @@
1+
{
2+
"seq_experiment_analysis": "input/s3.881fe6cf-8c80-4c7b-9f4d-b8dac9601d01.sequencing_experiment.payload.json",
3+
"files_to_upload": [
4+
"input/SA001.hisat2.novel_splicesites.txt"
5+
],
6+
"expected_output": "expected/expected.test-job-5.out.json",
7+
"aligner": "hisat2",
8+
"analysis_type": "splice_junctions",
9+
"genome_annotation": "GENCODE v38",
10+
"genome_build": "GRCh38_hla_decoy_ebv",
11+
"wf_name": "rna-seq-alignment",
12+
"wf_version": "0.1.0",
13+
"publish_dir": "outdir",
14+
"cpus": 1,
15+
"mem": 0.5
16+
}

‎tests/data/SA001.hisat2.all_logs.supplement.tar.gz‎

1.94 KB
Binary file not shown.

‎tests/data/SA001.hisat2.novel_splicesites.txt‎

Lines changed: 18 additions & 0 deletions
Original file line numberDiff line numberDiff line change
@@ -0,0 +1,18 @@
1+
chr1 1161 6612 +
2+
chr1 6724 7004 +
3+
chr1 7102 7188 +
4+
chr1 7408 9247 +
5+
chr1 9329 9825 +
6+
chr1 9962 10781 +
7+
chr1 10936 11221 +
8+
chr1 11432 11653 +
9+
chr1 1613327 1613883 -
10+
chr1 1614008 1615068 -
11+
chr1 1615173 1616667 -
12+
chr1 1616744 1616830 -
13+
chr1 1616964 1617614 -
14+
chr1 1617700 1618665 -
15+
chr1 1618768 1620420 -
16+
chr1 1620492 1628336 -
17+
chr1 1628452 1629078 -
18+
chr1 1629230 1631601 -

0 commit comments

Comments
 (0)