Explore Workflows

View already parsed workflows here or click here to add your own

Graph Name Retrieved From View
workflow graph preprocess_vcf.cwl

This workflow will perform preprocessing steps on VCFs for the OxoG/Variantbam/Annotation workflow.

https://github.com/icgc-tcga-pancancer/pcawg-snv-indel-annotation.git

Path: preprocess_vcf.cwl

Branch/Commit ID: b4a02b7ba5733b3cc5b84b79ab0634ff9e4d1aeb
workflow graph annotator_sub_wf.cwl

This is a subworkflow of the main oxog_varbam_annotat_wf workflow - this is not meant to be run as a stand-alone workflow!

https://github.com/icgc-tcga-pancancer/pcawg-snv-indel-annotation.git

Path: annotator_sub_wf.cwl

Branch/Commit ID: b4a02b7ba5733b3cc5b84b79ab0634ff9e4d1aeb
workflow graph analysis-workflow.cwl

https://github.com/mskcc/pluto-cwl.git

Path: cwl/analysis-workflow.cwl

Branch/Commit ID: 59b69eed7ffefcffd81313ec8ffb84c0d716b933
workflow graph md_launch_mutate.cwl

https://github.com/douglowe/biobb_hpc_cwl_md_list.git

Path: md_launch_mutate.cwl

Branch/Commit ID: 97122f21048a5ac4a12b21059b751d1d07050cbd
workflow graph qa_check_subwf.cwl

This subworkflow will perform a QA check on the OxoG outputs. It will perform the QA check on a single tumour and it associated VCFs

https://github.com/svonworl/OxoG-Dockstore-Tools.git

Path: qa_check_subwf.cwl

Branch/Commit ID: b38a8a4785746b8267913ea5389e21ae6dc921a3
workflow graph workflow_input_sf_expr.cwl

https://github.com/common-workflow-language/cwl-utils.git

Path: testdata/workflow_input_sf_expr.cwl

Branch/Commit ID: 139c64b55f7693d22e6646b8afe585f90da11dcb
workflow graph Conversion and compression of RDF files

Workflow to convert a RDF file to the HDT format and GZIP compress it for long term storage

 https://git.wageningenur.nl/unlock/cwl.git

Path: cwl/workflows/workflow_toHDT_compression.cwl

Branch/Commit ID: b9097b82e6ab6f2c9496013ce4dd6877092956a0
workflow graph taxcheck.cwl

Perform taxonomic identification tasks on an input genome

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

Path: taxcheck.cwl

Branch/Commit ID: 91181df8d9ef8eed9d8f40db707b9a4376fecaf5
workflow graph gatk4.2.4.1_mutect2_workflow.cwl

GATK4.2.4.1 Mutect2 workflow

https://github.com/nci-gdc/gatk4_mutect2_cwl.git

Path: subworkflows/gatk4.2.4.1_mutect2_workflow.cwl

Branch/Commit ID: 58b62b1bf329b3fbffbd5d9080709999bebc1763
workflow graph Deprecated. RNA-Seq pipeline single-read strand specific

Note: should be updated The original [BioWardrobe's](https://biowardrobe.com) [PubMed ID:26248465](https://www.ncbi.nlm.nih.gov/pubmed/26248465) **RNA-Seq** basic analysis for **strand specific single-read** experiment. A corresponded input [FASTQ](http://maq.sourceforge.net/fastq.shtml) file has to be provided. Current workflow should be used only with the single-read RNA-Seq data. It performs the following steps: 1. Use STAR to align reads from input FASTQ file according to the predefined reference indices; generate unsorted BAM file and alignment statistics file 2. Use fastx_quality_stats to analyze input FASTQ file and generate quality statistics file 3. Use samtools sort to generate coordinate sorted BAM(+BAI) file pair from the unsorted BAM file obtained on the step 1 (after running STAR) 5. Generate BigWig file on the base of sorted BAM file 6. Map input FASTQ file to predefined rRNA reference indices using Bowtie to define the level of rRNA contamination; export resulted statistics to file 7. Calculate isoform expression level for the sorted BAM file and GTF/TAB annotation file using GEEP reads-counting utility; export results to file

 https://github.com/datirium/workflows.git

Path: workflows/rnaseq-se-dutp.cwl

Branch/Commit ID: 472d453995dcda1b66884c31db562f4fb6094e5a