Explore Workflows

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

Graph Name Retrieved From View
workflow graph realign-distr.cwl

https://github.com/sentieon/sentieon-cwl.git

Path: stage/realign-distr.cwl

Branch/Commit ID: d20382adfe7285cb517a25d95d2bcb7586546e23
workflow graph wgs alignment and germline variant detection

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

Path: definitions/pipelines/germline_wgs.cwl

Branch/Commit ID: e2a34d2b8c406db9aed8e49e8bdcf36f51444379
workflow graph align_sort_sa

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

Path: task_types/tt_align_sort_sa.cwl

Branch/Commit ID: 3a89a217ca75ec042ce3a11ebb6d1664a3ec6e7e
workflow graph Subworkflow that runs cnvkit in single sample mode and returns a vcf file

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

Path: definitions/subworkflows/cnvkit_single_sample.cwl

Branch/Commit ID: 0c4f4e59c265eb22aed3d2d37b173cb5430773d2
workflow graph readgroup_fastq_se.cwl

https://github.com/nci-gdc/gdc-dnaseq-cwl.git

Path: workflows/bamfastq_align/readgroup_fastq_se.cwl

Branch/Commit ID: 8edf6a5e4e7790434ad0742e50d0c97a5d0bb846
workflow graph count-lines7-wf.cwl

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

Path: cwltool/schemas/v1.0/v1.0/count-lines7-wf.cwl

Branch/Commit ID: 1eb6bfe3c77aebaf69453a669d21ae7a5a78056f
workflow graph pindel parallel workflow

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

Path: definitions/subworkflows/pindel.cwl

Branch/Commit ID: a9133c999502acf94b433af8d39897e6c2cdf65f
workflow graph 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 **paired-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 paired-end RNA-Seq data. It performs the following steps: 1. Use STAR to align reads from input FASTQ files according to the predefined reference indices; generate unsorted BAM file and alignment statistics file 2. Use fastx_quality_stats to analyze input FASTQ files and generate quality statistics files 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) 4. Generate BigWig file on the base of sorted BAM file 5. Map input FASTQ files to predefined rRNA reference indices using Bowtie to define the level of rRNA contamination; export resulted statistics to file 6. 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-pe.cwl

Branch/Commit ID: a0b22644ca178b640fb74849d23b7c631022f0b5
workflow graph extract_gencoll_ids

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

Path: task_types/tt_extract_gencoll_ids.cwl

Branch/Commit ID: d218e081d8f6a4fdab56a38ce0fc2fae6216cecc
workflow graph Nested workflow example

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

Path: tests/wf/nested.cwl

Branch/Commit ID: bffea7fd5e864c5221c13a815d00d0a2fad178cc