diff --git a/config/icav2.yaml b/config/icav2.yaml index b333a4b4..b717c0f5 100644 --- a/config/icav2.yaml +++ b/config/icav2.yaml @@ -1567,6 +1567,31 @@ bunches: - dataset_name: rnasum_1_0_0 dataset_creation_time: '2024-06-23T10:39:55Z' dataset_id_hash: b8e45195afdbb7384012421978363b08 + - bunch_name: rnasum_prod__1_1_0 + bunch_description: Contains the UMCCR rnasum pipeline for RNA-seq data analysis + with reference data + tenant_name: umccr-prod + pipeline_path: workflows/rnasum-pipeline/1.1.0/rnasum-pipeline__1.1.0.cwl + pipeline_project_name: pipelines + bunch_region_id: 1efd315d-6309-4d7e-826b-d3824b0b5acb + bunch_region_city_name: Sydney + projects: + - development + - staging + - production + categories: + - wts + - tertiary-analysis + - production + bunch_versions: + - version: 1.1.0 + version_description: This version of the bunch contains the rnasum 1.0.0 reference + data + version_creation_date: 2024-09-01T05:28:42+00:00Z + datasets: + - dataset_name: rnasum_1_0_0 + dataset_creation_time: '2024-06-23T10:39:55Z' + dataset_id_hash: b8e45195afdbb7384012421978363b08 # UMCCRise - bunch_name: umccrise_prod__2_3_1 diff --git a/config/workflow.yaml b/config/workflow.yaml index 6f3444c8..1e050d83 100644 --- a/config/workflow.yaml +++ b/config/workflow.yaml @@ -282,6 +282,9 @@ workflows: - name: 1.0.0 path: 1.0.0/rnasum-pipeline__1.0.0.cwl md5sum: 4f9161e89c88ccc5da02935d1d1d0df9 + - name: 1.1.0 + path: 1.1.0/rnasum-pipeline__1.1.0.cwl + md5sum: 28bb78f3359e7f977c4be97880886a02 categories: [] - name: bclconvert-interop-qc path: bclconvert-interop-qc diff --git a/workflows/rnasum-pipeline/1.1.0/rnasum-pipeline__1.1.0.cwl b/workflows/rnasum-pipeline/1.1.0/rnasum-pipeline__1.1.0.cwl new file mode 100644 index 00000000..5f0bedaa --- /dev/null +++ b/workflows/rnasum-pipeline/1.1.0/rnasum-pipeline__1.1.0.cwl @@ -0,0 +1,294 @@ +cwlVersion: v1.1 +class: Workflow + +# Extensions +$namespaces: + s: https://schema.org/ +$schemas: + - https://schema.org/version/latest/schemaorg-current-http.rdf + +# Metadata +s:author: + class: s:Person + s:name: Alexis Lucattini + s:email: Alexis.Lucattini@umccr.org + s:identifier: https://orcid.org/0000-0001-9754-647X + +# ID/Docs +id: rnasum-pipeline--1.1.0 +label: rnasum-pipeline v(1.1.0) +doc: | + Documentation for rnasum-pipeline v1.1.0 + +requirements: + InlineJavascriptRequirement: {} + ScatterFeatureRequirement: {} + MultipleInputFeatureRequirement: {} + StepInputExpressionRequirement: {} + +inputs: + # Input folders + dragen_wts_dir: + label: dragen transcriptome directory + doc: | + Location of the results from Dragen RNA-seq pipeline + type: Directory? + dragen_mapping_metrics: + label: dragen mapping metrics + doc: | + Location of the mapping metrics from Dragen RNA-seq pipeline + type: File? + dragen_fusions: + label: dragen fusions + doc: | + Location of the fusion output from Dragen RNA-seq pipeline + type: File? + salmon: + label: salmom + doc: | + Location of the quantification output from salmon + type: File? + arriba_dir: + label: arriba directory + doc: | + Location of the arriba outputs directory + type: Directory? + arriba_pdf: + label: arriba pdf + doc: | + Location of the pdf output from arriba + type: File? + arriba_tsv: + label: arriba tsv + doc: | + Location of the tsv output from arriba + type: File? + umccrise: + label: umccrise directory + doc: | + The umccrise output directory + type: Directory? + manta_tsv: + label: manta tsv + doc: | + Location of the tsv output from manta + type: File? + report_dir: + label: report dir + doc: | + Desired location for the outputs + type: string + # Additional inputs + sample_name: + label: sample name + doc: | + Desired sample name to be presented in the report + type: string + transform: + label: transform + default: "CPM" + doc: | + Transformation method to be used when converting read counts + type: string? + norm: + label: norm + default: "TMM" + doc: | + Normalisation method + type: string? + scaling: + label: scaling + default: "gene-wise" + doc: | + Apply "gene-wise" (default) or "group-wise" data scaling + type: string? + drugs: + label: drugs + doc: | + Include drug matching section in the report. + type: boolean? + immunogram: + label: immunogram + doc: | + Include drug matching section in the report. + type: boolean? + pcgr_tiers_tsv: + label: pcgr tiers tsv + doc: | + Location of the tsv output from pcgr + type: File? + purple_gene_tsv: + label: purple gene tsv + doc: | + Location of the tsv output from purple + type: File? + pcgr_tier: + label: pcgr tier + default: 4 + doc: | + Tier threshold for reporting variants reported in PCGR. + type: int? + cn_loss: + label: cn loss + default: 5 + doc: | + CN threshold value to classify genes within lost regions. + type: int? + cn_gain: + label: cn gain + default: 95 + doc: | + CN threshold value to classify genes within gained regions. + type: int? + subject_id: + label: subject id + doc: | + Subject ID. If umccrise output is specified (flag --umccrise) then Subject ID + is extracted from there and used to overwrite this argument. + type: string? + sample_source: + label: sample source + doc: | + Source of investigated sample (e.g. fresh frozen tissue, organoid). + This information is for annotation purposes only + type: string? + dataset_name_incl: + label: dataset name incl + doc: | + Include dataset in the report and sample name. + type: boolean? + project: + label: project + doc: | + Project name. This information is for annotation purposes only + type: string? + top_genes: + label: top genes + default: 5 + doc: | + The number of top ranked genes to be presented. + type: int? + dataset: + label: dataset + default: "PANCAN" + doc: | + Reference dataset selection from https://github.com/umccr/RNAsum/blob/master/TCGA_projects_summary.md + type: string + batch_rm: + label: batch rm + default: TRUE + doc: | + Remove batch-associated effects between datasets. Available options are: "TRUE" (default) and "FALSE" + type: boolean? + filter: + label: filter + default: TRUE + doc: | + Filtering out low expressed genes. Available options are: "TRUE" (default) and "FALSE" + type: boolean? + log: + label: log + default: TRUE + doc: | + Log (base 2) transform data before normalisation. Available options are: "TRUE" (default) and "FALSE" + type: boolean? + save_tables: + label: save tables + default: TRUE + doc: | + Save interactive summary tables as HTML. Available options are: "TRUE" (default) and "FALSE" + type: boolean? + pcgr_splice_vars: + label: PCGR splice vars + default: TRUE + doc: | + Include non-coding splice region variants reported in PCGR. Available options are: "TRUE" (default) and "FALSE" + type: boolean? + +steps: + run_rnasum_step: + label: run rnasum step + doc: | + Run the rnasum pipeline + in: + dragen_wts_dir: + source: dragen_wts_dir + dragen_mapping_metrics: + source: dragen_mapping_metrics + dragen_fusions: + source: dragen_fusions + salmon: + source: salmon + arriba_dir: + source: arriba_dir + arriba_pdf: + source: arriba_pdf + arriba_tsv: + source: arriba_tsv + umccrise: + source: umccrise + manta_tsv: + source: manta_tsv + report_dir: + source: report_dir + sample_name: + source: sample_name + transform: + source: transform + norm: + source: norm + scaling: + source: scaling + drugs: + source: drugs + immunogram: + source: immunogram + pcgr_tiers_tsv: + source: pcgr_tiers_tsv + purple_gene_tsv: + source: purple_gene_tsv + pcgr_tier: + source: pcgr_tier + cn_loss: + source: cn_loss + cn_gain: + source: cn_gain + subject_id: + source: subject_id + sample_source: + source: sample_source + dataset_name_incl: + source: dataset_name_incl + project: + source: project + top_genes: + source: top_genes + dataset: + source: dataset + batch_rm: + source: batch_rm + filter: + source: filter + log: + source: log + save_tables: + source: save_tables + pcgr_splice_vars: + source: pcgr_splice_vars + out: + - id: rnasum_output_directory + - id: rnasum_html + run: ../../../tools/rnasum/1.1.0/rnasum__1.1.0.cwl + +outputs: + rnasum_output_directory: + label: RNAsum output directory + doc: Output directory containing all outputs of the RNAsum run + type: Directory + outputSource: run_rnasum_step/rnasum_output_directory + rnasum_html: + label: rnasum html + doc: | + The HTML report output of RNAsum + type: File + outputSource: run_rnasum_step/rnasum_html