icav2 projects listID NAME OWNER
a5690b16-a739-4bd7-a62a-dc4dc5c5de6c Project1 670fd8ea-2ddb-377d-bd8b-587e7781f2b5
ccb0667b-5949-489a-8902-692ef2f31827 Project2 f1aa8430-7058-4f6c-a726-b75ddf6252eb
No of items : 2icav2 projects enter a5690b16-a739-4bd7-a62a-dc4dc5c5de6cicav2 projectpipelines listID CODE DESCRIPTION
fbd6f3c3-cb70-4b35-8f57-372dce2aaf98 DRAGEN Somatic 3.9.5 The DRAGEN Somatic tool identifies somatic variants
b4dc6b91-5283-41f6-8095-62a5320ed092 DRAGEN Somatic Enrichment 3-10-4 The DRAGEN Somatic Enrichment pipeline identifies somatic variants which can exist at low allele frequencies in the tumor sample.
No of items : 2icav2 projectanalyses listID REFERENCE CODE STATUS
3539d676-ae99-4e5f-b7e4-0835f207e425 kyle-test-somatic-2-DRAGEN Somatic 3_9_5 DRAGEN Somatic 3.9.5 SUCCEEDED
f11e248e-9944-4cde-9061-c41e70172f20 kyle-test-somatic-1-DRAGEN Somatic 3_9_5 DRAGEN Somatic 3.9.5 FAILED
No of items : 2icav2 projectanalyses input 3539d676-ae99-4e5f-b7e4-0835f207e425CODE NAMES DATA ID
BED
CNV_B_Allele_VCF
CNV_Population_B_Allele_VCF
HLA_Allele_Frequency_File
HLA_BED
HLA_reference_file_(protein_FASTA)
Microsatellites_File
Normal_BAM_File
Normal_FASTQ_Files
Panel_of_Normals
Panel_of_Normals_TAR
Reference hg38_altaware_nohla-cnv-anchored.v8.tar fil.35e27101fdec404fb37d08d9adf63307
Systematic_Noise_BED
Tumor_BAM_File
Tumor_FASTQ_Files HCC1187C_S1_L001_R1_001.fastq.gz,HCC1187C_S1_L001_R2_001.fastq.gz fil.e1ec77f2647f45804fe508d9aecb19c4,fil.d89018f0c7784fc4b76708d9adf63307
curl -X 'POST' \
'https://ica.illumina.com/ica/rest/api/tokens' \
-H 'accept: application/vnd.illumina.v3+json' \
-H 'X-API-Key: <YOUR_APIKEY>' \
-d ''echo -ne '[email protected]:testpassword' | base64
<BASE64UN+PW>
curl -X 'POST' \
'https://ica.illumina.com/ica/rest/api/tokens' \
-H 'accept: application/vnd.illumina.v3+json' \
-H 'Authorization: Basic <BASE64UN+PW>' \
-d ''curl -X 'GET' \
'https://ica.illumina.com/ica/rest/api/projects/e501a0d5-f5e7-458c-a590-586c79bb87e0/analyses/3539d676-ae99-4e5f-b7e4-0835f207e425/configurations' \
-H 'accept: application/vnd.illumina.v3+json' \
-H 'Authorization: Bearer <Token>' \
-H 'X-API-Key: <APIKEY>'{
"items": [{
"name": "DRAGEN_Somatic__enable_variant_caller",
"multiValue": false,
"values": [
"true"
]
}]
}<pd:tool code="map_align"><pd:parameter code="enable_map_align" minValues="0" maxValues="1" classification="USER">
<pd:label>Enable Map/Align</pd:label>
<pd:description></pd:description>
<pd:optionsType>
<pd:option>true</pd:option>
<pd:option>false</pd:option>
</pd:optionsType>
<pd:value></pd:value>icav2 projectpipelines start cwl fbd6f3c3-cb70-4b35-8f57-372dce2aaf98 \
--user-reference kyle-test-somatic-9 \
--storage-size small \
--type-input STRUCTURED \
--input Reference:fil.35e27101fdec404fb37d08d9adf63307 \
--input Tumor_FASTQ_Files:fil.e1ec77f2647f45804fe508d9aecb19c4,fil.d89018f0c7784fc4b76708d9adf63307 \
--parameters DRAGEN_Somatic__enable_variant_caller:true \
--parameters DRAGEN_Somatic__enable_hrd:false \
--parameters DRAGEN_Somatic__enable_sv:true \
--parameters DRAGEN_Somatic__output_file_prefix:tumor \
--parameters DRAGEN_Somatic__enable_map_align:true \
--parameters DRAGEN_Somatic__cnv_use_somatic_vc_baf:false \
--parameters DRAGEN_Somatic__enable_cnv:false \
--parameters DRAGEN_Somatic__output_format:BAM \
--parameters DRAGEN_Somatic__vc_emit_ref_confidence:BP_RESOLUTION \
--parameters DRAGEN_Somatic__enable_hla:false \
--parameters DRAGEN_Somatic__enable_map_align_output:trueanalysisStorage.description 1.2 TB
analysisStorage.id 6e1b6c8f-f913-48b2-9bd0-7fc13eda0fd0
analysisStorage.name Small
analysisStorage.ownerId 8ec463f6-1acb-341b-b321-043c39d8716a
analysisStorage.tenantId f91bb1a0-c55f-4bce-8014-b2e60c0ec7d3
analysisStorage.tenantName ica-cp-admin
analysisStorage.timeCreated 2021-11-05T10:28:20Z
analysisStorage.timeModified 2021-11-05T10:28:20Z
id 51abe34a-2506-4ab5-adef-22df621d95d5
ownerId 47793c21-75a6-3aa8-8147-81b354d0af4d
pipeline.analysisStorage.description 1.2 TB
pipeline.analysisStorage.id 6e1b6c8f-f913-48b2-9bd0-7fc13eda0fd0
pipeline.analysisStorage.name Small
pipeline.analysisStorage.ownerId 8ec463f6-1acb-341b-b321-043c39d8716a
pipeline.analysisStorage.tenantId f91bb1a0-c55f-4bce-8014-b2e60c0ec7d3
pipeline.analysisStorage.tenantName ica-cp-admin
pipeline.analysisStorage.timeCreated 2021-11-05T10:28:20Z
pipeline.analysisStorage.timeModified 2021-11-05T10:28:20Z
pipeline.code DRAGEN Somatic 3.9.5
pipeline.description The DRAGEN Somatic tool identifies somatic variants which can exist at low allele frequencies in the tumor sample. The pipeline can analyze tumor/normal pairs and tumor-only sequencing data. The normal sample, if present, is used to avoid calls at sites with germline variants or systematic sequencing artifacts. Unlike germline analysis, the somatic platform makes no ploidy assumptions about the tumor sample, allowing sensitive detection of low-frequency alleles.
pipeline.id fbd6f3c3-cb70-4b35-8f57-372dce2aaf98
pipeline.language CWL
pipeline.ownerId e9dd2ff5-c9ba-3293-857e-6546c5503d76
pipeline.tenantId 55cb0a54-efab-4584-85da-dc6a0197d4c4
pipeline.tenantName ilmn-dragen
pipeline.timeCreated 2021-11-23T22:55:49Z
pipeline.timeModified 2021-12-09T16:42:14Z
reference kyle-test-somatic-9-DRAGEN Somatic 3_9_5-bc56d4b1-f90e-4039-b3a4-b11d29263e4e
status REQUESTED
summary
tenantId b5b750a6-49d4-49de-9f18-75f4f6a81112
tenantName ilmn-cci
timeCreated 2022-03-16T22:48:31Z
timeModified 2022-03-16T22:48:31Z
userReference kyle-test-somatic-9400 Bad Request : ICA_API_004 : com.fasterxml.jackson.databind.exc.InvalidFormatException: Cannot deserialize value of type `java.util.UUID` from String "8f57-372dce2aaf98": UUID has to be represented by standard 36-char representation
at [Source: (io.undertow.servlet.spec.ServletInputStreamImpl); line: 1, column: 983] (through reference chain: com.bluebee.rest.v3.publicapi.dto.analysis.SearchMatchingActivationCodesForCwlAnalysisDto["pipelineId"]) (ref. c9cd9090-4ddb-482a-91b5-8471bff0be58)404 Not Found : ICA_GNRC_001 : Could not find data with ID [fil.35dec404fb37d08d9adf63307] (ref. 91b70c3c-378c-4de2-acc9-794bf18258ec)400 Bad Request : ICA_EXEC_007 : The specified variableName [DRAGEN] does not exist. Make sure to use an existing variableName (ref. ab296d4e-9060-412c-a4c9-562c63450022)icav2 projectpipelines start nextflow b4dc6b91-5283-41f6-8095-62a5320ed092 \
--user-reference "somatic-3-10-test5" \
--project-id e501a0d5-f5e7-458c-a590-586c79bb87e0 \
--storage-size Small \
--input ref_tar:fil.35e27101fdec404fb37d08d9adf63307 \
--input tumor_fastqs:fil.e1ec77f2647f45804fe508d9aecb19c4,fil.d89018f0c7784fc4b76708d9adf63307 \
--parameters enable_map_align:true \
--parameters enable_map_align_output:true \
--parameters output_format:BAM \
--parameters enable_variant_caller:true \
--parameters vc_emit_ref_confidence:BP_RESOLUTION \
--parameters enable_cnv:false \
--parameters enable_sv:true \
--parameters repeat_genotype_enable:true \
--parameters enable_hla:false \
--parameters enable_variant_annotation:false \
--parameters output_file_prefix:Tumor% icav2 projects list
ID NAME OWNER
422d5119-708b-4062-b91b-b398a3371eab demo b23f3ea6-9a84-3609-bf1d-19f1ea931fa3% icav2 projectdata mount mnt --project-id 422d5119-708b-4062-b91b-b398a3371eab
% ls mnt
sampleX.final.count.tsv% icav2 projectdata unmount
Project with identifier 422d5119-708b-4062-b91b-b398a3371eab was unmounted from mnt.