Explore Workflows

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

Graph Name Retrieved From View
workflow graph Trim Galore RNA-Seq pipeline single-read

The original [BioWardrobe's](https://biowardrobe.com) [PubMed ID:26248465](https://www.ncbi.nlm.nih.gov/pubmed/26248465) **RNA-Seq** basic analysis for a **single-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 single-end RNA-Seq data. It performs the following steps: 1. Trim adapters from input FASTQ file 2. Use STAR to align reads from input FASTQ file according to the predefined reference indices; generate unsorted BAM file and alignment statistics file 3. Use fastx_quality_stats to analyze input FASTQ file and generate quality statistics file 4. Use samtools sort to generate coordinate sorted BAM(+BAI) file pair from the unsorted BAM file obtained on the step 1 (after running STAR) 5. Generate BigWig file on the base of sorted BAM file 6. Map input FASTQ file to predefined rRNA reference indices using Bowtie to define the level of rRNA contamination; export resulted statistics to file 7. 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/trim-rnaseq-se.cwl

Branch/Commit ID: ce058d892d330125cd03d0a0d5fb3b321cda0be3
workflow graph count-lines2-wf.cwl

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

Path: tests/count-lines2-wf.cwl

Branch/Commit ID: ea9f8634e41824ac3f81c3dde698d5f0eef54f1b
workflow graph cond-wf-003.1.cwl

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

Path: testdata/cond-wf-003.1.cwl

Branch/Commit ID: 0ad6983898f0d9001fe0f416f97c4d8b940e384a
workflow graph umi molecular alignment workflow

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

Path: definitions/subworkflows/molecular_qc.cwl

Branch/Commit ID: 6f9f8a2057c6a9f221a44559f671e87a75c70075
workflow graph kfdrc_annoFuse_wf.cwl

https://github.com/kids-first/kf-rnaseq-workflow.git

Path: workflow/kfdrc_annoFuse_wf.cwl

Branch/Commit ID: 3fd55a819cda2a1fc48957b5daa2bebdaee843fb
workflow graph Nested workflow example

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

Path: tests/wf/nested.cwl

Branch/Commit ID: 0db44e3c9805a070564f954222efff71cd791b70
workflow graph Exome QC workflow

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

Path: definitions/subworkflows/qc_exome.cwl

Branch/Commit ID: 51724b44c96e5fd849ae55b752865b80bc47d66c
workflow graph etl.cwl

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

Path: workflows/bamfastq_align/etl.cwl

Branch/Commit ID: d5757ab1f3aad3c542950e1dbe8f9d2eec74bede
workflow graph step-valuefrom3-wf.cwl

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

Path: cwltool/schemas/v1.0/v1.0/step-valuefrom3-wf.cwl

Branch/Commit ID: 46b7f9766d1bc8a4871474eee25ec730b4e173da
workflow graph count-lines2-wf.cwl

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

Path: tests/count-lines2-wf.cwl

Branch/Commit ID: c7c97715b400ff2194aa29fc211d3401cea3a9bf