Merge pull request #80 from icgc-argo/[email protected]

[release]

.github/workflows/build-test-release.yml

@@ -258,4 +258,4 @@ jobs:
         upload_url: ${{ steps.create_release.outputs.upload_url }}
         asset_path: ./pkg-release.json
         asset_name: pkg-release.json
-        asset_content_type: application/json
+        asset_content_type: application/json

payload-json-to-tsvs/main.nf

@@ -24,7 +24,7 @@
 /* this block is auto-generated based on info from pkg.json where   */
 /* changes can be made if needed, do NOT modify this block manually */
 nextflow.enable.dsl = 2
-version = '0.1.1'
+version = '0.1.2'
 
 container = [
     'ghcr.io': 'ghcr.io/icgc-argo/argo-data-submission.payload-json-to-tsvs'

payload-json-to-tsvs/main.py

@@ -84,9 +84,9 @@ def make_experiment_tsv(metadata):
         for field in [
             'submitter_sequencing_experiment_id','sequencing_center',
             'platform', 'platform_model','experimental_strategy', 'sequencing_date',
-            "library_isolation_protocol","library_preparation_kit",
-            "library_strandedness","rin","dv200","spike_ins_included","spike_ins_fasta",
-            "spike_ins_concentration","target_capture_kit"]:
+            "library_preparation_kit","library_strandedness","rin","dv200",
+            "primary_target_regions","capture_target_regions","number_of_genes",
+            "gene_padding","coverage","target_capture_kit"]:
                 return_metadata[field]=metadata['experiment'].get(field) if metadata['experiment'].get(field) else None  
 
         return_metadata['program_id']=metadata.get("studyId")

payload-json-to-tsvs/pkg.json

@@ -1,6 +1,6 @@
 {
     "name": "payload-json-to-tsvs",
-    "version": "0.1.1",
+    "version": "0.1.2",
     "description": "Converts JSON payload to 3 TSVs : Experiment,Files,Read groups",
     "main": "main.nf",
     "deprecated": false,

payload-json-to-tsvs/tests/checker.nf

@@ -29,7 +29,7 @@
 /* this block is auto-generated based on info from pkg.json where   */
 /* changes can be made if needed, do NOT modify this block manually */
 nextflow.enable.dsl = 2
-version = '0.1.1'
+version = '0.1.2'
 
 container = [
     'ghcr.io': 'ghcr.io/icgc-argo/argo-data-submission.payload-json-to-tsvs'

payload-json-to-tsvs/tests/expected/expected_experiment.tsv

@@ -1,2 +1,2 @@
-type	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	submitter_sequencing_experiment_id	sequencing_center	platform	platform_model	experimental_strategy	sequencing_date	library_isolation_protocol	library_preparation_kit	library_strandedness	rin	dv200	spike_ins_included	spike_ins_fasta	spike_ins_concentration	target_capture_kit	program_id	read_group_count
-sequencing_experiment	TEST_SUBMITTER_DONOR_ID_jpupbblgfa	Male	TEST_SUBMITTER_SPECIMEN_ID_jpupbblgfa	Tumour	Primary tumour - adjacent to normal	Buccal cell	TEST_SUBMITTER_SAMPLE_ID_jpupbblgfaRNA	Total RNA		EXP-9	QCMG	ILLUMINA	Illumina HiSeq 2000	RNA-Seq				FIRST_READ_ANTISENSE_STRAND							TEST-QA	4
+type	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	submitter_sequencing_experiment_id	sequencing_center	platform	platform_model	experimental_strategy	sequencing_date	library_preparation_kit	library_strandedness	rin	dv200	primary_target_regions	capture_target_regions	number_of_genes	gene_padding	coverage	target_capture_kit	program_id	read_group_count
+sequencing_experiment	TEST_SUBMITTER_DONOR_ID_jpupbblgfa	Male	TEST_SUBMITTER_SPECIMEN_ID_jpupbblgfa	Tumour	Primary tumour - adjacent to normal	Buccal cell	TEST_SUBMITTER_SAMPLE_ID_jpupbblgfaRNA	Total RNA		EXP-9	QCMG	ILLUMINA	Illumina HiSeq 2000	RNA-Seq			FIRST_READ_ANTISENSE_STRAND									TEST-QA	4

payload-json-to-tsvs/tests/expected/expected_experiment2.tsv

@@ -1,2 +1,2 @@
-type	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	submitter_sequencing_experiment_id	sequencing_center	platform	platform_model	experimental_strategy	sequencing_date	library_isolation_protocol	library_preparation_kit	library_strandedness	rin	dv200	spike_ins_included	spike_ins_fasta	spike_ins_concentration	target_capture_kit	program_id	read_group_count
-sequencing_experiment	TEST_SUBMITTER_DONOR_ID_jpupbblgfa	Male	TEST_SUBMITTER_SPECIMEN_ID_jpupbblgfa	Tumour	Primary tumour	Other	TEST_SUBMITTER_SAMPLE_ID_jpupbblgfa	Total RNA		EXP-9	QCMG	ILLUMINA	Illumina HiSeq 2000	RNA-Seq				FIRST_READ_ANTISENSE_STRAND							TEST-PR	5
+type	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	submitter_sequencing_experiment_id	sequencing_center	platform	platform_model	experimental_strategy	sequencing_date	library_preparation_kit	library_strandedness	rin	dv200	primary_target_regions	capture_target_regions	number_of_genes	gene_padding	coverage	target_capture_kit	program_id	read_group_count
+sequencing_experiment	TEST_SUBMITTER_DONOR_ID_jpupbblgfa	Male	TEST_SUBMITTER_SPECIMEN_ID_jpupbblgfa	Tumour	Primary tumour	Other	TEST_SUBMITTER_SAMPLE_ID_jpupbblgfa	Total RNA		EXP-9	QCMG	ILLUMINA	Illumina HiSeq 2000	RNA-Seq			FIRST_READ_ANTISENSE_STRAND									TEST-PR	5

payload-json-to-tsvs/tests/expected/expected_experiment3.tsv

@@ -0,0 +1,2 @@
+type	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	submitter_sequencing_experiment_id	sequencing_center	platform	platform_model	experimental_strategy	sequencing_date	library_preparation_kit	library_strandedness	rin	dv200	primary_target_regions	capture_target_regions	number_of_genes	gene_padding	coverage	target_capture_kit	program_id	read_group_count
+sequencing_experiment	HCC1143	Female	HCC1143_BAM_INPUT	Normal	Cell line - derived from normal	Blood derived	HCC1143_BAM_INPUT	Total DNA		TEST_EXP	EXT	ILLUMINA	HiSeq 2000	WXS	2014-12-12					DUMMY_VAL	DUMMY_VAL				DUMMY_VAL	TEST-PRO	3

payload-json-to-tsvs/tests/expected/expected_files3.tsv

@@ -0,0 +1,2 @@
+name	size	md5sum	ega_file_id	ega_dataset_id	ega_experiment_id	ega_sample_id	ega_study_id	ega_run_id	ega_policy_id	ega_analysis_id	ega_submission_id	ega_dac_id	path	type	format
+test_rg_3.bam	14911	178f97f7b1ca8bfc28fd5586bdd56799											input/test_rg_3.bam	file	BAM

payload-json-to-tsvs/tests/expected/expected_read_groups3.tsv

@@ -0,0 +1,4 @@
+submitter_read_group_id	read_group_id_in_bam	submitter_sequencing_experiment_id	platform_unit	is_paired_end	file_r1	file_r2	read_length_r1	read_length_r2	insert_size	sample_barcode	library_name	type
+C0HVY.2			74_8a	True	test_rg_3.bam	test_rg_3.bam			298		Pond-147580	read_group
+D0RE2.1			74_8b	True	test_rg_3.bam	test_rg_3.bam			298		Pond-147580	read_group
+D0RH0.2			74_8c	True	test_rg_3.bam	test_rg_3.bam			298		Pond-147580	read_group

payload-json-to-tsvs/tests/input/b9167a75-83ea-4c43-be30-e87faf3557dd.sequencing_experiment.payload.json

@@ -0,0 +1,95 @@
+{
+  "analysisType": {
+    "name": "sequencing_experiment"
+  },
+  "studyId": "TEST-PRO",
+  "experiment": {
+    "submitter_sequencing_experiment_id": "TEST_EXP",
+    "sequencing_center": "EXT",
+    "platform": "ILLUMINA",
+    "platform_model": "HiSeq 2000",
+    "experimental_strategy": "WXS",
+    "sequencing_date": "2014-12-12",
+    "library_preparation_kit": null,
+    "library_strandedness": null,
+    "dv200": null,
+    "target_capture_kit": "DUMMY_VAL",
+    "number_of_genes": null,
+    "gene_padding": null,
+    "coverage": null,
+    "primary_target_regions": "DUMMY_VAL",
+    "capture_target_regions": "DUMMY_VAL"
+  },
+  "read_group_count": 3,
+  "read_groups": [
+    {
+      "submitter_read_group_id": "C0HVY.2",
+      "read_group_id_in_bam": null,
+      "platform_unit": "74_8a",
+      "is_paired_end": true,
+      "file_r1": "test_rg_3.bam",
+      "file_r2": "test_rg_3.bam",
+      "read_length_r1": null,
+      "read_length_r2": null,
+      "insert_size": 298,
+      "sample_barcode": null,
+      "library_name": "Pond-147580"
+    },
+    {
+      "submitter_read_group_id": "D0RE2.1",
+      "read_group_id_in_bam": null,
+      "platform_unit": "74_8b",
+      "is_paired_end": true,
+      "file_r1": "test_rg_3.bam",
+      "file_r2": "test_rg_3.bam",
+      "read_length_r1": null,
+      "read_length_r2": null,
+      "insert_size": 298,
+      "sample_barcode": null,
+      "library_name": "Pond-147580"
+    },
+    {
+      "submitter_read_group_id": "D0RH0.2",
+      "read_group_id_in_bam": null,
+      "platform_unit": "74_8c",
+      "is_paired_end": true,
+      "file_r1": "test_rg_3.bam",
+      "file_r2": "test_rg_3.bam",
+      "read_length_r1": null,
+      "read_length_r2": null,
+      "insert_size": 298,
+      "sample_barcode": null,
+      "library_name": "Pond-147580"
+    }
+  ],
+  "samples": [
+    {
+      "submitterSampleId": "HCC1143_BAM_INPUT",
+      "matchedNormalSubmitterSampleId": null,
+      "sampleType": "Total DNA",
+      "specimen": {
+        "submitterSpecimenId": "HCC1143_BAM_INPUT",
+        "tumourNormalDesignation": "Normal",
+        "specimenTissueSource": "Blood derived",
+        "specimenType": "Cell line - derived from normal"
+      },
+      "donor": {
+        "submitterDonorId": "HCC1143",
+        "gender": "Female"
+      }
+    }
+  ],
+  "files": [
+    {
+      "fileName": "test_rg_3.bam",
+      "fileSize": 14911,
+      "fileMd5sum": "178f97f7b1ca8bfc28fd5586bdd56799",
+      "fileType": "BAM",
+      "fileAccess": "controlled",
+      "dataType": "Submitted Reads",
+      "info": {
+        "data_category": "Sequencing Reads"
+      }
+    }
+  ]
+}

payload-json-to-tsvs/tests/test-job3.json

@@ -0,0 +1,7 @@
+{
+    "json_file":"input/b9167a75-83ea-4c43-be30-e87faf3557dd.sequencing_experiment.payload.json",
+    "data_directory":"input",
+    "expected_experiment_tsv":"expected/expected_experiment3.tsv",
+    "expected_file_tsv":"expected/expected_files3.tsv",
+    "expected_read_group_tsv":"expected/expected_read_groups3.tsv"
+}