Explore Workflows

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

Graph Name Retrieved From View
workflow graph kmer_cache_retrieve

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

Path: task_types/tt_kmer_cache_retrieve.cwl

Branch/Commit ID: 2d851682ba1bf2aaaacb3677253b55ceb59c8568
workflow graph bacterial_kmer

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

Path: bacterial_kmer/wf_bacterial_kmer.cwl

Branch/Commit ID: 96dbb414d287f4382e2d477fb1851aeaa5f14f2b
workflow graph umi duplex alignment workflow

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

Path: definitions/subworkflows/duplex_alignment.cwl

Branch/Commit ID: 5fda2d9eb52a363bd51011b3851c2afb86318c0c
workflow graph umi per-lane alignment subworkflow

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

Path: definitions/subworkflows/umi_alignment.cwl

Branch/Commit ID: 5fda2d9eb52a363bd51011b3851c2afb86318c0c
workflow graph step-valuefrom-wf.cwl

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

Path: tests/step-valuefrom-wf.cwl

Branch/Commit ID: 3e90671b25f7840ef2926ad2bacbf447772dda94
workflow graph Deprecated. 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: d76110e0bfc40c874f82e37cef6451d74df4f908
workflow graph kmer_seq_entry_extract_wnode

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

Path: task_types/tt_kmer_seq_entry_extract_wnode.cwl

Branch/Commit ID: 96dbb414d287f4382e2d477fb1851aeaa5f14f2b
workflow graph tt_kmer_top_n.cwl

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

Path: task_types/tt_kmer_top_n.cwl

Branch/Commit ID: 96dbb414d287f4382e2d477fb1851aeaa5f14f2b
workflow graph gpas_gatk4.2.4.1_mutect2_tumor_only_workflow.cwl

https://github.com/NCI-GDC/gatk4_mutect2_cwl.git

Path: gatk4-mutect2-tumor-only-cwl/gpas_gatk4.2.4.1_mutect2_tumor_only_workflow.cwl

Branch/Commit ID: 138d484362084dfc97d9fb7d839855b4bc2c5599
workflow graph umi molecular alignment workflow

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

Path: definitions/subworkflows/molecular_alignment.cwl

Branch/Commit ID: 5fda2d9eb52a363bd51011b3851c2afb86318c0c