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: c5bae2ca862c764911b83d1f15ff6af4e2a0db28
workflow graph tt_blastn_wnode

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

Path: task_types/tt_blastn_wnode.cwl

Branch/Commit ID: 42df0c0f9a4e5697abadd9cb52440691fafc8f5d
workflow graph iwdr_with_nested_dirs.cwl

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

Path: tests/iwdr_with_nested_dirs.cwl

Branch/Commit ID: ea9f8634e41824ac3f81c3dde698d5f0eef54f1b
workflow graph umi molecular alignment workflow

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

Path: definitions/subworkflows/molecular_qc.cwl

Branch/Commit ID: c711498c04d6b8ddf92ddceb6219f074765f7993
workflow graph assm_assm_blastn_wnode

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

Path: task_types/tt_assm_assm_blastn_wnode.cwl

Branch/Commit ID: e3f18c61d1bbf65e40921dbd044369da4523ee3e
workflow graph count-lines7-wf_v1_1.cwl

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

Path: testdata/count-lines7-wf_v1_1.cwl

Branch/Commit ID: 0ab1d42d10f7311bb4032956c4a6f3d2730d9507
workflow graph foreign_screening.cwl

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

Path: vecscreen/foreign_screening.cwl

Branch/Commit ID: 5282690e0f634a5f83107ba878fe62cbbb347408
workflow graph spurious_annot

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

Path: spurious_annot/wf_spurious_annot_pass1.cwl

Branch/Commit ID: 8ea3637b0f11eac1ea5599c41d74e00d85fb778d
workflow graph Immunotherapy Workflow

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

Path: definitions/pipelines/immuno.cwl

Branch/Commit ID: 3f3b186da9bf82a5e2ae74ba27aef35a46174ebe
workflow graph mut3.cwl

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

Path: tests/wf/mut3.cwl

Branch/Commit ID: d6000d32f6c8fbd26421a2d30d79b28901d58fb0