Explore Workflows

https://git.astron.nl/RD/LINC.git

Path: workflows/linc_target/dp3_prep_targ.cwl

Branch/Commit ID: 0c5bd78e3f2d08564f5c9a563bcc8bb7704e6202

https://github.com/common-workflow-language/cwltool.git

Path: cwltool/schemas/v1.0/v1.0/count-lines2-wf.cwl

Branch/Commit ID: 19f2cb6e21db8624155c7e253b89c57df536fcc1

https://github.com/common-workflow-language/cwltool.git

Path: cwltool/schemas/v1.0/v1.0/step-valuefrom-wf.cwl

Branch/Commit ID: 4c2667ef937c341af26e4f72b01056a06dce84fb

The pipeline implemented in this workflow allows for the analysis of paired normal tumor NGS WES BAM files. It runs a comprehensive characterization of the data. In order to ensure the validity of the analysis some QC metrics are included in the pipeline as the normal/tumor genotype distance (to ensure that samples are properly paired) and quality metrics (Picard HsMetrics). Ethnicity is automatically inferred by using EthSEQ. The pipeline then calls SNVs, indels and copy number profiles and next infers purity and ploidy of the tumor sample by using CLONETv2. Upon ploidy and admixture correction, CLONETv2 generates corrected copy number and allele specific copy numbers (the number of copies of each parental allele) calls together with segment clonality (the fraction of the tumor that have a certain aberration). A second purity inference method based on SNVs (TPES) is also run on the data. As a final result the pipeline produces two folders: one with the analysis results (data) and the second that includes the logs of each tool (logs).

https://github.com/demichelislab/SPICE-pipeline-CWL.git

Path: cwl/workflows/pipeline.cwl

Branch/Commit ID: 06e4a6f868651c8e26a88db518af1974159ecba9

https://github.com/ncbi/pgap.git

Path: task_types/tt_kmer_cache_retrieve.cwl

Branch/Commit ID: d40ef1462a4c210be3184609dbb3467ff61fc017

https://github.com/common-workflow-language/cwltool.git

Path: tests/wf/mut3.cwl

Branch/Commit ID: 17268d1493d9e558113b2c35c0be6b3fb961b2a3

https://git.astron.nl/RD/LINC.git

Path: workflows/linc_calibrator.cwl

Branch/Commit ID: 058606391dc5f129b6f25112f016fe2f0a164528

https://github.com/E3SM-Project/e3sm_to_cmip.git

Path: scripts/cwl_workflows/atm-unified/atm-unified.cwl

Branch/Commit ID: 330559dfb86d112fd2d3b0ef05a630622766f5ec

https://github.com/genome/analysis-workflows.git

Path: definitions/pipelines/cle_aml_trio.cwl

Branch/Commit ID: 60edaf6f57eaaf02cda1a3d8cb9a825aa64a43e2

https://github.com/genome/analysis-workflows.git

Path: definitions/subworkflows/bam_to_trimmed_fastq_and_hisat_alignments.cwl

Branch/Commit ID: f7ac3eff79128831c9f7a565d5b187882f39aa58