Explore Workflows

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Graph Name Retrieved From View
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: 664de58d95728edbf7d369d894f9037ebe2475fa
workflow graph exome alignment with qc

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

Path: definitions/pipelines/exome_alignment.cwl

Branch/Commit ID: 641083e9ed933d388f36fa04c00c20a810599e94
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 bact_get_kmer_reference

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

Path: task_types/tt_bact_get_kmer_reference.cwl

Branch/Commit ID: c009eeba7379efbbd37b8d5013a83f161f06939b
workflow graph stage_workflow.cwl

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

Path: utils-cwl/subworkflow/stage_workflow.cwl

Branch/Commit ID: 138d484362084dfc97d9fb7d839855b4bc2c5599
workflow graph dynresreq-workflow-stepdefault.cwl

https://github.com/common-workflow-language/cwl-v1.2.git

Path: tests/dynresreq-workflow-stepdefault.cwl

Branch/Commit ID: 57baec040c99d7edef8242ef51b5470b1c82d733
workflow graph count-lines15-wf.cwl

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

Path: tests/count-lines15-wf.cwl

Branch/Commit ID: b1d4a69df86350059bd49aa127c02be0c349f7de
workflow graph rna-seq-pipeline.cwl

https://github.com/sbg/sbg_dockstore_tools.git

Path: gtex-rnaseq-pipeline/rna-seq-pipeline.cwl

Branch/Commit ID: 01f35f8040b45199c6cf58bbd838f398d0ec8dc3
workflow graph phase VCF

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

Path: definitions/subworkflows/phase_vcf.cwl

Branch/Commit ID: 6a55118f915e24d2ad008c93a02d9de5643f5511
workflow graph input_fastq_processing_workflow.cwl

https://github.com/NCI-GDC/gdc-rnaseq-cwl.git

Path: rnaseq-star-align/subworkflows/preprocessing/input_fastq_processing_workflow.cwl

Branch/Commit ID: 88fb720c62a3c2b00ca475d412fba088c4a08f92