Explore Workflows

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

Graph Name Retrieved From View
workflow graph scatter-valuefrom-inputs-wf1.cwl

https://github.com/common-workflow-language/cwl-v1.1.git

Path: tests/scatter-valuefrom-inputs-wf1.cwl

Branch/Commit ID: 664835e83eb5e57eee18a04ce7b05fb9d70d77b7
workflow graph umi molecular alignment workflow

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

Path: definitions/subworkflows/molecular_qc.cwl

Branch/Commit ID: 3bebaf9b70331de9f4845e2223c55082f5a812fb
workflow graph Subworkflow to allow calling cnvkit with cram instead of bam files

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

Path: definitions/subworkflows/cram_to_cnvkit.cwl

Branch/Commit ID: 3bebaf9b70331de9f4845e2223c55082f5a812fb
workflow graph RNA-Seq pipeline paired-end strand specific

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-dutp.cwl

Branch/Commit ID: ebbf23764ede324cabc064bd50647c1f643726fa
workflow graph downsample unaligned BAM and align

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

Path: definitions/subworkflows/downsampled_alignment.cwl

Branch/Commit ID: 3bebaf9b70331de9f4845e2223c55082f5a812fb
workflow graph Detect DoCM variants

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

Path: definitions/subworkflows/docm_germline.cwl

Branch/Commit ID: a3e26136043c03192c38c335316d2d36e3e67478
workflow graph extract_gencoll_ids

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

Path: task_types/tt_extract_gencoll_ids.cwl

Branch/Commit ID: f10de890d1d2271299931349fa8aea660acef4ee
workflow graph metabarcode (gene amplicon) analysis for fastq files

protein - qc, preprocess, annotation, index, abundance

 https://github.com/MG-RAST/pipeline.git

Path: CWL/Workflows/metabarcode-fasta.workflow.cwl

Branch/Commit ID: 6c5d0068bdb4f19a36a653c39964aefb9e5a7b1b
workflow graph LBA_calibrator.cwl

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

Path: workflows/LBA_calibrator.cwl

Branch/Commit ID: 8a697be0fa85795f7822146015edf963a5681ca7
workflow graph pindel parallel workflow

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

Path: definitions/subworkflows/pindel.cwl

Branch/Commit ID: a3e26136043c03192c38c335316d2d36e3e67478