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added schema check
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‎payload-gen-seq-experiment/main.py‎

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‎payload-gen-seq-experiment/tests/input/208c5ea6-c17a-4a63-981e-4bb91d3119f2.sequencing_experiment.payload.json‎

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{
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"analysisType": {
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"name": "sequencing_experiment"
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},
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"studyId": "TEST-PRO",
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"experiment": {
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"submitter_sequencing_experiment_id": "TEST_EXP",
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"sequencing_center": "EXT",
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"platform": "ILLUMINA",
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"platform_model": "HiSeq 2000",
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"experimental_strategy": "RNA-Seq",
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"sequencing_date": "2014-12-12",
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"library_strandedness": "FIRST_READ_ANTISENSE_STRAND"
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},
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"read_group_count": 3,
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"read_groups": [
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{
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"submitter_read_group_id": "C0HVY.2",
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"read_group_id_in_bam": null,
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"platform_unit": "74_8a",
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"is_paired_end": true,
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"file_r1": "test_rg_3.bam",
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"file_r2": "test_rg_3.bam",
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"read_length_r1": 150,
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"read_length_r2": 150,
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"insert_size": 298,
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"sample_barcode": null,
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"library_name": "Pond-147580"
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},
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{
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"submitter_read_group_id": "D0RE2.1",
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"read_group_id_in_bam": null,
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"platform_unit": "74_8b",
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"is_paired_end": true,
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"file_r1": "test_rg_3.bam",
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"file_r2": "test_rg_3.bam",
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"read_length_r1": 150,
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"read_length_r2": 150,
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"insert_size": 298,
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"sample_barcode": null,
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"library_name": "Pond-147580"
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},
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{
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"submitter_read_group_id": "D0RH0.2",
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"read_group_id_in_bam": null,
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"platform_unit": "74_8c",
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"is_paired_end": true,
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"file_r1": "test_rg_3.bam",
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"file_r2": "test_rg_3.bam",
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"read_length_r1": 150,
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"read_length_r2": 150,
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"insert_size": 298,
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"sample_barcode": null,
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"library_name": "Pond-147580"
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}
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],
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"samples": [
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{
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"submitterSampleId": "HCC1143_BAM_INPUT",
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"matchedNormalSubmitterSampleId": null,
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"sampleType": "RNA",
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"specimen": {
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"submitterSpecimenId": "HCC1143_BAM_INPUT",
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"tumourNormalDesignation": "Normal",
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"specimenTissueSource": "Blood derived",
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"specimenType": "Cell line - derived from normal"
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},
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"donor": {
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"submitterDonorId": "HCC1143",
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"gender": "Female"
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}
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}
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],
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"files": [
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{
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"fileName": "test_rg_3.bam",
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"fileSize": 14911,
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"fileMd5sum": "178f97f7b1ca8bfc28fd5586bdd56799",
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"fileType": "BAM",
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"fileAccess": "controlled",
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"dataType": "Submitted Reads",
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"info": {
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"data_category": "Sequencing Reads"
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},
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"EGAF": "EGAF000001"
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}
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]
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}

‎payload-gen-seq-experiment/tests/input/d9c99af9-b97d-4481-9be8-f65e57d86673.sequencing_experiment.payload.json‎

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{
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"analysisType": {
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"name": "sequencing_experiment"
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},
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"studyId": "TEST-PRO",
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"experiment": {
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"submitter_sequencing_experiment_id": "TEST_EXP",
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"sequencing_center": "EXT",
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"platform": "ILLUMINA",
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"platform_model": "HiSeq 2000",
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"experimental_strategy": "WGS",
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"sequencing_date": "2014-12-12"
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},
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"read_group_count": 3,
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"read_groups": [
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{
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"submitter_read_group_id": "C0HVY.2",
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"read_group_id_in_bam": null,
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"platform_unit": "74_8a",
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"is_paired_end": true,
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"file_r1": "test_rg_3.bam",
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"file_r2": "test_rg_3.bam",
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"read_length_r1": 150,
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"read_length_r2": 150,
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"insert_size": 298,
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"sample_barcode": null,
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"library_name": "Pond-147580"
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},
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{
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"submitter_read_group_id": "D0RE2.1",
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"read_group_id_in_bam": null,
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"platform_unit": "74_8b",
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"is_paired_end": true,
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"file_r1": "test_rg_3.bam",
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"file_r2": "test_rg_3.bam",
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"read_length_r1": 150,
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"read_length_r2": 150,
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"insert_size": 298,
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"sample_barcode": null,
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"library_name": "Pond-147580"
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},
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{
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"submitter_read_group_id": "D0RH0.2",
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"read_group_id_in_bam": null,
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"platform_unit": "74_8c",
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"is_paired_end": true,
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"file_r1": "test_rg_3.bam",
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"file_r2": "test_rg_3.bam",
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"read_length_r1": 150,
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"read_length_r2": 150,
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"insert_size": 298,
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"sample_barcode": null,
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"library_name": "Pond-147580"
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}
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],
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"samples": [
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{
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"submitterSampleId": "HCC1143_BAM_INPUT",
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"matchedNormalSubmitterSampleId": null,
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"sampleType": "DNA",
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"specimen": {
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"submitterSpecimenId": "HCC1143_BAM_INPUT",
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"tumourNormalDesignation": "Normal",
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"specimenTissueSource": "Blood derived",
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"specimenType": "Cell line - derived from normal"
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},
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"donor": {
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"submitterDonorId": "HCC1143",
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"gender": "Female"
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}
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}
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],
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"files": [
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{
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"fileName": "test_rg_3.bam",
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"fileSize": 14911,
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"fileMd5sum": "178f97f7b1ca8bfc28fd5586bdd56799",
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"fileType": "BAM",
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"fileAccess": "controlled",
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"dataType": "Submitted Reads",
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"info": {
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"data_category": "Sequencing Reads"
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}
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}
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]
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}

‎payload-gen-seq-experiment/tests/input/experiment.correct.rnaseq.tsv‎

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type study_id submitter_sequencing_experiment_id submitter_donor_id gender submitter_specimen_id tumour_normal_designation specimen_type specimen_tissue_source submitter_sample_id sample_type submitter_matched_normal_sample_id sequencing_center platform platform_model experimental_strategy sequencing_date read_group_count library_strandedness
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sequencing_experiment TEST-PRO TEST_EXP HCC1143 Female HCC1143_BAM_INPUT Normal Cell line - derived from normal Blood derived HCC1143_BAM_INPUT RNA EXT ILLUMINA HiSeq 2000 RNA-Seq 2014-12-12 3 FIRST_READ_ANTISENSE_STRAND

‎payload-gen-seq-experiment/tests/input/experiment.incorrect.rnaseq.tsv‎

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type study_id submitter_sequencing_experiment_id submitter_donor_id gender submitter_specimen_id tumour_normal_designation specimen_type specimen_tissue_source submitter_sample_id sample_type submitter_matched_normal_sample_id sequencing_center platform platform_model experimental_strategy sequencing_date read_group_count
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sequencing_experiment TEST-PRO TEST_EXP HCC1143 Female HCC1143_BAM_INPUT Normal Cell line - derived from normal Blood derived HCC1143_BAM_INPUT RNA EXT ILLUMINA HiSeq 2000 RNA-Seq 2014-12-12 3

‎payload-gen-seq-experiment/tests/input/file.v3.tsv‎

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type name format size md5sum path EGAF
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file test_rg_3.bam BAM 14911 178f97f7b1ca8bfc28fd5586bdd56799 test_rg_3.bam EGAF000001

‎payload-gen-seq-experiment/tests/test-job-bam.tsv.nf.json‎

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"experiment_info_tsv": "input/experiment.v2.tsv",
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"read_group_info_tsv": "input/read_group.v2.tsv",
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"file_info_tsv": "input/file.v2.tsv",
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"extra_info_tsv": "input/extra_info.v2.tsv",
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"expected_output": "input/98690064-627e-4a2b-a0c2-60fc9ca8433c.sequencing_experiment.payload.json",
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"expected_output": "input/d9c99af9-b97d-4481-9be8-f65e57d86673.sequencing_experiment.payload.json",
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"publish_dir": "outdir"
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}

‎payload-gen-seq-experiment/tests/test-job-rnaseqbam.nf.json‎

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{
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"experiment_info_tsv": "input/experiment.correct.rnaseq.tsv",
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"read_group_info_tsv": "input/read_group.v2.tsv",
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"file_info_tsv": "input/file.v3.tsv",
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"expected_output": "input/208c5ea6-c17a-4a63-981e-4bb91d3119f2.sequencing_experiment.payload.json",
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"publish_dir": "outdir"
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}

‎tests/data/experiment-fq.v2.tsv‎

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type program_id submitter_sequencing_experiment_id submitter_donor_id gender submitter_specimen_id tumour_normal_designation specimen_type specimen_tissue_source submitter_sample_id sample_type submitter_matched_normal_sample_id sequencing_center platform platform_model experimental_strategy sequencing_date read_group_count
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type study_id submitter_sequencing_experiment_id submitter_donor_id gender submitter_specimen_id tumour_normal_designation specimen_type specimen_tissue_source submitter_sample_id sample_type submitter_matched_normal_sample_id sequencing_center platform platform_model experimental_strategy sequencing_date read_group_count
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sequencing_experiment TEST-PRO TEST_EXP HCC1143 Female HCC1143_FASTQ_INPUT Tumour Cell line - derived from tumour Blood derived HCC1143_FASTQ_INPUT DNA HCC1143_BAM_INPUT EXT ILLUMINA HiSeq 2000 WGS 2014-12-12 3

‎tests/data/experiment.v2.tsv‎

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type program_id submitter_sequencing_experiment_id submitter_donor_id gender submitter_specimen_id tumour_normal_designation specimen_type specimen_tissue_source submitter_sample_id sample_type submitter_matched_normal_sample_id sequencing_center platform platform_model experimental_strategy sequencing_date read_group_count
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type study_id submitter_sequencing_experiment_id submitter_donor_id gender submitter_specimen_id tumour_normal_designation specimen_type specimen_tissue_source submitter_sample_id sample_type submitter_matched_normal_sample_id sequencing_center platform platform_model experimental_strategy sequencing_date read_group_count
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sequencing_experiment TEST-PRO TEST_EXP HCC1143 Female HCC1143_BAM_INPUT Normal Cell line - derived from normal Blood derived HCC1143_BAM_INPUT DNA EXT ILLUMINA HiSeq 2000 WGS 2014-12-12 3

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