Explore Workflows

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

Graph Name Retrieved From View
workflow graph find_hotspots_in_normals.cwl

Workflow to find hotspot VAFs from duplex (for Tumor sample) and unfiltered (for Normal sample) pileups. These inputs are all required to be sorted in the same order: sample_ids patient_ids sample_classes unfiltered_pileups duplex_pileups

https://github.com/andurill/ACCESS-Pipeline.git

Path: workflows/subworkflows/find_hotspots_in_normals.cwl

Branch/Commit ID: 3441040dfaecba58150c13a95a6a93657b00778a
workflow graph module-2.cwl

https://github.com/andurill/ACCESS-Pipeline.git

Path: workflows/module-2.cwl

Branch/Commit ID: 3441040dfaecba58150c13a95a6a93657b00778a
workflow graph module-1.cwl

https://github.com/andurill/ACCESS-Pipeline.git

Path: workflows/module-1.cwl

Branch/Commit ID: 3441040dfaecba58150c13a95a6a93657b00778a
workflow graph standard_pipeline.cwl

This is a workflow to go from UMI-tagged fastqs to standard bams. It does not include collapsing, or QC It does include modules 1 and 2

https://github.com/andurill/ACCESS-Pipeline.git

Path: workflows/standard_pipeline.cwl

Branch/Commit ID: 3441040dfaecba58150c13a95a6a93657b00778a
workflow graph star-cufflinks_wf_pe.cwl

https://github.com/pitagora-network/pitagora-cwl.git

Path: workflows/star-cufflinks/paired_end/star-cufflinks_wf_pe.cwl

Branch/Commit ID: 4e84905f265e1db212c406d34ae4db2bf565e856
workflow graph Exome QC workflow

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

Path: definitions/subworkflows/qc_exome.cwl

Branch/Commit ID: 051074fce4afd9732ef34db9dd43d3a1d8e979d6
workflow graph bam to trimmed fastqs and HISAT alignments

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

Path: definitions/subworkflows/bam_to_trimmed_fastq_and_hisat_alignments.cwl

Branch/Commit ID: 051074fce4afd9732ef34db9dd43d3a1d8e979d6
workflow graph umi per-lane alignment subworkflow

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

Path: definitions/subworkflows/umi_alignment.cwl

Branch/Commit ID: 22fce2dbdada0c4135b6f0677f78535cf980cb07
workflow graph preprocess_vcf.cwl

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

https://github.com/david4096/OxoG-Dockstore-Tools.git

Path: preprocess_vcf.cwl

Branch/Commit ID: 6366ed398da10019b6d81a789291af6d909f28f4
workflow graph Trim Galore RNA-Seq pipeline paired-end

The original [BioWardrobe's](https://biowardrobe.com) [PubMed ID:26248465](https://www.ncbi.nlm.nih.gov/pubmed/26248465) **RNA-Seq** basic analysis for a **pair-end** 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-end RNA-Seq data. It performs the following steps: 1. Trim adapters from input FASTQ files 2. Use STAR to align reads from input FASTQ files according to the predefined reference indices; generate unsorted BAM file and alignment statistics file 3. Use fastx_quality_stats to analyze input FASTQ files and generate quality statistics files 4. 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 files 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/trim-rnaseq-pe.cwl

Branch/Commit ID: a1f6ca50fcb0881781b3ba0306dd61ebf555eaba