diff --git a/.dockstore.yml b/.dockstore.yml index 59cd47f4..2652a1cd 100644 --- a/.dockstore.yml +++ b/.dockstore.yml @@ -26,3 +26,16 @@ workflows: tags: - dragen-alignment-pipeline/4.2.4 - dragen-alignment-pipeline/4.2.4__20240627051848 + - name: dragen-transcriptome-pipeline_4_2_4 + subclass: CWL + primaryDescriptorPath: + /.dockstore/dragen-transcriptome-pipeline/4.2.4/dragen-transcriptome-pipeline__4.2.4.packed.cwl.json + readMePath: + /.github/catalogue/docs/workflows/dragen-transcriptome-pipeline/4.2.4/dragen-transcriptome-pipeline__4.2.4.md + authors: + - name: Sehrish Kanwal + email: sehrish.kanwal@umccr.org + filters: + tags: + - dragen-transcriptome-pipeline/4.2.4 + - dragen-transcriptome-pipeline/4.2.4__20240627052945 diff --git a/.github/releases/dragen-transcriptome-pipeline__4.2.4__20240627052945/workflow.svg b/.github/releases/dragen-transcriptome-pipeline__4.2.4__20240627052945/workflow.svg new file mode 100644 index 00000000..85ca9c95 --- /dev/null +++ b/.github/releases/dragen-transcriptome-pipeline__4.2.4__20240627052945/workflow.svg @@ -0,0 +1,653 @@ + + + + + + +G + + +cluster_inputs + +Workflow Inputs + + +cluster_outputs + +Workflow Outputs + + + +run_dragen_transcriptome_step + +dragen-transcriptome v(4.2.4) + + + +arriba_drawing_step + +arriba-drawing v(2.4.0) + + + +run_dragen_transcriptome_step->arriba_drawing_step + + + + + +arriba_fusion_step + +arriba-fusion-calling v(2.4.0) + + + +run_dragen_transcriptome_step->arriba_fusion_step + + + + + +dragen_qc_step + +multiqc v(1.15.0) + + + +run_dragen_transcriptome_step->dragen_qc_step + + + + + +run_qualimap_step + +qualimap v(2.2.2) + + + +run_dragen_transcriptome_step->run_qualimap_step + + + + + +dragen_transcriptome_output_directory + +dragen_transcriptome_output_directory + + + +run_dragen_transcriptome_step->dragen_transcriptome_output_directory + + + + + +create_arriba_output_directory + +custom-create-directory v(1.0.0) + + + +arriba_drawing_step->create_arriba_output_directory + + + + + +arriba_fusion_step->arriba_drawing_step + + + + + +arriba_fusion_step->create_arriba_output_directory + + + + + +arriba_fusion_step->create_arriba_output_directory + + + + + +arriba_output_directory + +arriba_output_directory + + + +create_arriba_output_directory->arriba_output_directory + + + + + +create_dummy_file_step + +custom-create-dummy-file v(1.0.0) + + + +create_dummy_file_step->dragen_qc_step + + + + + +multiqc_output_directory + +multiqc_output_directory + + + +dragen_qc_step->multiqc_output_directory + + + + + +run_qualimap_step->dragen_qc_step + + + + + +qualimap_output_directory + +qualimap_output_directory + + + +run_qualimap_step->qualimap_output_directory + + + + + +annotation_file + +annotation_file + + + +annotation_file->run_dragen_transcriptome_step + + + + + +annotation_file->arriba_drawing_step + + + + + +annotation_file->arriba_fusion_step + + + + + +annotation_file->run_qualimap_step + + + + + +cytobands + +cytobands + + + +cytobands->arriba_drawing_step + + + + + +protein_domains + +protein_domains + + + +protein_domains->arriba_drawing_step + + + + + +blacklist + +blacklist + + + +blacklist->arriba_fusion_step + + + + + +contigs + +contigs + + + +contigs->arriba_fusion_step + + + + + +reference_fasta + +reference_fasta + + + +reference_fasta->arriba_fusion_step + + + + + +output_directory_name_arriba + +output_directory_name_arriba + + + +output_directory_name_arriba->create_arriba_output_directory + + + + + +cl_config + +cl_config + + + +cl_config->dragen_qc_step + + + + + +output_file_prefix + +output_file_prefix + + + +output_file_prefix->run_dragen_transcriptome_step + + + + + +output_file_prefix->dragen_qc_step + + + + + +output_file_prefix->dragen_qc_step + + + + + +output_file_prefix->dragen_qc_step + + + + + +output_file_prefix->dragen_qc_step + + + + + +output_file_prefix->run_qualimap_step + + + + + +qc_reference_samples + +qc_reference_samples + + + +qc_reference_samples->dragen_qc_step + + + + + +bam_input + +bam_input + + + +bam_input->run_dragen_transcriptome_step + + + + + +enable_duplicate_marking + +enable_duplicate_marking + + + +enable_duplicate_marking->run_dragen_transcriptome_step + + + + + +enable_map_align + +enable_map_align + + + +enable_map_align->run_dragen_transcriptome_step + + + + + +enable_map_align_output + +enable_map_align_output + + + +enable_map_align_output->run_dragen_transcriptome_step + + + + + +enable_rna_gene_fusion + +enable_rna_gene_fusion + + + +enable_rna_gene_fusion->run_dragen_transcriptome_step + + + + + +enable_rna_quantification + +enable_rna_quantification + + + +enable_rna_quantification->run_dragen_transcriptome_step + + + + + +enable_sort + +enable_sort + + + +enable_sort->run_dragen_transcriptome_step + + + + + +fastq_list + +fastq_list + + + +fastq_list->run_dragen_transcriptome_step + + + + + +fastq_list_rows + +fastq_list_rows + + + +fastq_list_rows->run_dragen_transcriptome_step + + + + + +lic_instance_id_location + +lic_instance_id_location + + + +lic_instance_id_location->run_dragen_transcriptome_step + + + + + +output_directory + +output_directory + + + +output_directory->run_dragen_transcriptome_step + + + + + +read_trimmers + +read_trimmers + + + +read_trimmers->run_dragen_transcriptome_step + + + + + +reference_tar + +reference_tar + + + +reference_tar->run_dragen_transcriptome_step + + + + + +soft_read_trimmers + +soft_read_trimmers + + + +soft_read_trimmers->run_dragen_transcriptome_step + + + + + +trim_adapter_r1_5prime + +trim_adapter_r1_5prime + + + +trim_adapter_r1_5prime->run_dragen_transcriptome_step + + + + + +trim_dapter_r2_5prime + +trim_dapter_r2_5prime + + + +trim_dapter_r2_5prime->run_dragen_transcriptome_step + + + + + +trim_adapter_read1 + +trim_adapter_read1 + + + +trim_adapter_read1->run_dragen_transcriptome_step + + + + + +trim_adapter_read2 + +trim_adapter_read2 + + + +trim_adapter_read2->run_dragen_transcriptome_step + + + + + +trim_adapter_stringency + +trim_adapter_stringency + + + +trim_adapter_stringency->run_dragen_transcriptome_step + + + + + +trim_r1_3prime + +trim_r1_3prime + + + +trim_r1_3prime->run_dragen_transcriptome_step + + + + + +trim_r1_5prime + +trim_r1_5prime + + + +trim_r1_5prime->run_dragen_transcriptome_step + + + + + +trim_r2_3prime + +trim_r2_3prime + + + +trim_r2_3prime->run_dragen_transcriptome_step + + + + + +trim_r2_5prime + +trim_r2_5prime + + + +trim_r2_5prime->run_dragen_transcriptome_step + + + + + +algorithm + +algorithm + + + +algorithm->run_qualimap_step + + + + + +java_mem + +java_mem + + + +java_mem->run_qualimap_step + + + + + +tmp_dir + +tmp_dir + + + +tmp_dir->run_qualimap_step + + + + + diff --git a/config/icav2.yaml b/config/icav2.yaml index 165c2ffb..59a2771c 100644 --- a/config/icav2.yaml +++ b/config/icav2.yaml @@ -1774,3 +1774,181 @@ bundles: - primary-analysis projects: - production + - bundle_name: dragen_transcriptome_pipeline_with_validation_data__4_2_4__20240627052945 + bundle_description: 'This bundle has been generated by the release of workflows/dragen-transcriptome-pipeline/4.2.4/dragen-transcriptome-pipeline__4.2.4.cwl. + The pipeline can be found at https://github.com/umccr/cwl-ica/releases/tag/dragen-transcriptome-pipeline/4.2.4__20240627052945. ' + bundle_version: v9_r3__20240627052945 + bundle_version_description: Bundle version description is currently redundant + while we cannot append versions to bundles. Regardless - the bunch version is + v9_r3 + bundle_region_id: 1efd315d-6309-4d7e-826b-d3824b0b5acb + bundle_region_city_name: Sydney + tenant_name: umccr-prod + pipeline_path: + workflows/dragen-transcriptome-pipeline/4.2.4/dragen-transcriptome-pipeline__4.2.4.cwl + pipeline_name: dragen-transcriptome-pipeline + pipeline_version: 4.2.4 + pipeline_release_url: + https://github.com/umccr/cwl-ica/releases/tag/dragen-transcriptome-pipeline/4.2.4__20240627052945 + pipeline_commit_id: dragen-transcriptome-pipeline/4.2.4__20240627052945 + pipeline_checksum: 7ae80f7cb086f5c300d86f82e07b8593 + pipeline_project_id: 5844391a-69db-4b52-86b5-6a0d55c2386f + bundle_creation_time: '2024-06-27T05:31:53Z' + bundle_release_status: draft + bunch_name: dragen_transcriptome_pipeline_with_validation_data__4_2_4 + bunch_version: v9_r3 + bunch_datasets: + - dataset_name: dragen_hash_table_v9_r3_alt_masked_cnv_hla_rna + dataset_creation_time: '2024-06-21T09:21:42Z' + dataset_id_hash: a5fe1d2e2fe35737bdbc0871d46878e1 + - dataset_name: hg38_fasta + dataset_creation_time: '2024-06-21T11:31:50Z' + dataset_id_hash: 5f129b14aca5b4a7fda902590b15abc2 + - dataset_name: arriba_2_4_0 + dataset_creation_time: '2024-06-21T11:31:26Z' + dataset_id_hash: 8695cf0a98c5cda5726f67d4922da67f + - dataset_name: wts_validation_fastq__SBJ00480 + dataset_creation_time: '2024-06-21T09:41:15Z' + dataset_id_hash: c8b8bdc7e384aaa470b12992ce196693 + - dataset_name: wts_validation_fastq__SBJ00028 + dataset_creation_time: '2024-06-21T09:42:31Z' + dataset_id_hash: fa76e6ca3a0fb0be2bf41840a7aeeb01 + - dataset_name: wts_validation_fastq__SBJ00061 + dataset_creation_time: '2024-06-21T09:42:54Z' + dataset_id_hash: 63ee438354c347b05218b9bddc53d936 + - dataset_name: wts_validation_fastq__SBJ00188 + dataset_creation_time: '2024-06-21T09:43:11Z' + dataset_id_hash: 401d12d90e00db19918e5c9ce13a3da0 + - dataset_name: wts_validation_fastq__SBJ00199 + dataset_creation_time: '2024-06-21T09:49:27Z' + dataset_id_hash: b95ac04c7e3c03a8b1868a4571d23d5f + - dataset_name: wts_validation_fastq__SBJ00236 + dataset_creation_time: '2024-06-21T09:49:54Z' + dataset_id_hash: f084081c52ddda14328294d7bb7f13f4 + - dataset_name: wts_validation_fastq__SBJ00238 + dataset_creation_time: '2024-06-21T09:50:29Z' + dataset_id_hash: ba04ff08acbfbd1c17f1aadc0e8b3cf5 + - dataset_name: wts_multiqc__2023_07_21__4_2_4__Ref_1_Good__SBJ01563 + dataset_creation_time: '2024-06-21T11:33:06Z' + dataset_id_hash: 8de637be95f6ded72f61103bc842da45 + - dataset_name: wts_multiqc__2023_07_21__4_2_4__Ref_2_Good__SBJ01147 + dataset_creation_time: '2024-06-21T11:34:05Z' + dataset_id_hash: e11d32cd8efced32065a52eea33b06d1 + - dataset_name: wts_multiqc__2023_07_21__4_2_4__Ref_3_Good__SBJ01620 + dataset_creation_time: '2024-06-21T11:34:29Z' + dataset_id_hash: 0f0fee1a6b1f7b46978643839ffc0e88 + - dataset_name: wts_multiqc__2023_07_21__4_2_4__Ref_4_Bad__SBJ01286 + dataset_creation_time: '2024-06-21T11:34:51Z' + dataset_id_hash: 3d9dae1be84d29848f24df81d1ab4219 + - dataset_name: wts_multiqc__2023_07_21__4_2_4__Ref_5_Bad__SBJ01673 + dataset_creation_time: '2024-06-21T11:35:25Z' + dataset_id_hash: 42a9396b3f5d7e919e30a0f59f2401b7 + bundle_id: 8c2c600f-d3ff-4e42-8e44-8ee7ce914d71 + bundle_data_ids: + - fil.2082d35d90fb4b9e126a08dc7a0472f4 + - fil.33b0c303aa2a44efda7008dc8578d1bb + - fil.8ab696eccee945064fe608dc9159afed + - fil.8950646b2bcf4137dac908dc8578d1bb + - fil.361af4dcff7840b5dab808dc8578d1bb + - fil.e956bc1d6e124433503f08dc9159afed + - fil.00db7f575e3c4741766608dc8682e79a + - fil.848678f252004cae726508dc8578d1b7 + - fil.e47895b2674b40cf727508dc8578d1b7 + - fil.f7b97fcf876b4409727608dc8578d1b7 + - fil.ad6640db600e44e1727a08dc8578d1b7 + - fil.6e3e68b7fc8b48ef76a908dc8682e79a + - fil.25ae81b4f33146b2769708dc8682e79a + - fil.dc806da29f02402076aa08dc8682e79a + - fil.8ed5724bce234ff276ad08dc8682e79a + - fil.2c3073bee29c47ea76ae08dc8682e79a + - fil.a191c268b58b414972ae08dc8578d1b7 + - fil.f4d61a69d418416a76af08dc8682e79a + - fil.554ab8b39c49488a76b208dc8682e79a + - fil.728b7d6332dd4d2e72af08dc8578d1b7 + - fol.4bfb05e08c2c46e7927908dc8578d1b7 + - fol.a3f65803908c4f29969508dc8682e79a + - fol.841783fe78e64b7e96cd08dc8682e79a + - fol.0dcfcd90b98d4b58925408dc8578d1b7 + - fol.7ff6b53c0f0148b7970c08dc8682e79a + bundle_pipeline_id: fb8ba85b-244f-47c1-82cb-baea6db9d90d + bundle_url: + https://ica.illumina.com/ica/bundles/8c2c600f-d3ff-4e42-8e44-8ee7ce914d71/bundleDetails + bundle_categories: + - wts + - somatic + - validation + - secondary-analysis + projects: + - development + - staging + - bundle_name: dragen_transcriptome_pipeline_prod__4_2_4__20240627052945 + bundle_description: 'This bundle has been generated by the release of workflows/dragen-transcriptome-pipeline/4.2.4/dragen-transcriptome-pipeline__4.2.4.cwl. + The pipeline can be found at https://github.com/umccr/cwl-ica/releases/tag/dragen-transcriptome-pipeline/4.2.4__20240627052945. ' + bundle_version: v9_r3__20240627052945 + bundle_version_description: Bundle version description is currently redundant + while we cannot append versions to bundles. Regardless - the bunch version is + v9_r3 + bundle_region_id: 1efd315d-6309-4d7e-826b-d3824b0b5acb + bundle_region_city_name: Sydney + tenant_name: umccr-prod + pipeline_path: + workflows/dragen-transcriptome-pipeline/4.2.4/dragen-transcriptome-pipeline__4.2.4.cwl + pipeline_name: dragen-transcriptome-pipeline + pipeline_version: 4.2.4 + pipeline_release_url: + https://github.com/umccr/cwl-ica/releases/tag/dragen-transcriptome-pipeline/4.2.4__20240627052945 + pipeline_commit_id: dragen-transcriptome-pipeline/4.2.4__20240627052945 + pipeline_checksum: 7ae80f7cb086f5c300d86f82e07b8593 + pipeline_project_id: 5844391a-69db-4b52-86b5-6a0d55c2386f + bundle_creation_time: '2024-06-27T05:35:40Z' + bundle_release_status: draft + bunch_name: dragen_transcriptome_pipeline_prod__4_2_4 + bunch_version: v9_r3 + bunch_datasets: + - dataset_name: dragen_hash_table_v9_r3_alt_masked_cnv_hla_rna + dataset_creation_time: '2024-06-21T09:21:42Z' + dataset_id_hash: a5fe1d2e2fe35737bdbc0871d46878e1 + - dataset_name: hg38_fasta + dataset_creation_time: '2024-06-21T11:31:50Z' + dataset_id_hash: 5f129b14aca5b4a7fda902590b15abc2 + - dataset_name: arriba_2_4_0 + dataset_creation_time: '2024-06-21T11:31:26Z' + dataset_id_hash: 8695cf0a98c5cda5726f67d4922da67f + - dataset_name: wts_multiqc__2023_07_21__4_2_4__Ref_1_Good__SBJ01563 + dataset_creation_time: '2024-06-21T11:33:06Z' + dataset_id_hash: 8de637be95f6ded72f61103bc842da45 + - dataset_name: wts_multiqc__2023_07_21__4_2_4__Ref_2_Good__SBJ01147 + dataset_creation_time: '2024-06-21T11:34:05Z' + dataset_id_hash: e11d32cd8efced32065a52eea33b06d1 + - dataset_name: wts_multiqc__2023_07_21__4_2_4__Ref_3_Good__SBJ01620 + dataset_creation_time: '2024-06-21T11:34:29Z' + dataset_id_hash: 0f0fee1a6b1f7b46978643839ffc0e88 + - dataset_name: wts_multiqc__2023_07_21__4_2_4__Ref_4_Bad__SBJ01286 + dataset_creation_time: '2024-06-21T11:34:51Z' + dataset_id_hash: 3d9dae1be84d29848f24df81d1ab4219 + - dataset_name: wts_multiqc__2023_07_21__4_2_4__Ref_5_Bad__SBJ01673 + dataset_creation_time: '2024-06-21T11:35:25Z' + dataset_id_hash: 42a9396b3f5d7e919e30a0f59f2401b7 + bundle_id: 6d1a08b6-d0d4-429d-bd22-1471add8ea9b + bundle_data_ids: + - fil.2082d35d90fb4b9e126a08dc7a0472f4 + - fil.33b0c303aa2a44efda7008dc8578d1bb + - fil.8ab696eccee945064fe608dc9159afed + - fil.8950646b2bcf4137dac908dc8578d1bb + - fil.361af4dcff7840b5dab808dc8578d1bb + - fil.e956bc1d6e124433503f08dc9159afed + - fol.4bfb05e08c2c46e7927908dc8578d1b7 + - fol.a3f65803908c4f29969508dc8682e79a + - fol.841783fe78e64b7e96cd08dc8682e79a + - fol.0dcfcd90b98d4b58925408dc8578d1b7 + - fol.7ff6b53c0f0148b7970c08dc8682e79a + bundle_pipeline_id: fb8ba85b-244f-47c1-82cb-baea6db9d90d + bundle_url: + https://ica.illumina.com/ica/bundles/6d1a08b6-d0d4-429d-bd22-1471add8ea9b/bundleDetails + bundle_categories: + - wts + - somatic + - production + - secondary-analysis + projects: + - production