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 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 **pair-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 files 2. Use STAR to align reads from input FASTQ files according to the predefined reference indices; generate unsorted BAM file and alignment statistics file 3. Use fastx_quality_stats to analyze input FASTQ files and generate quality statistics files 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 files 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-pe.cwl

Branch/Commit ID: 730b40bc403263b724399a952c0f3e2d28f13519
workflow graph ani_top_n

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

Path: task_types/tt_ani_top_n.cwl

Branch/Commit ID: 0bc1c33a2293e054ad00974971edc79c13252cc7
workflow graph qc-assembled.workflow.cwl

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

Path: CWL/Workflows/qc-assembled.workflow.cwl

Branch/Commit ID: 1844de830f6935901849ccd9966685fbf13e8042
workflow graph scatter-wf1_v1_2.cwl

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

Path: testdata/scatter-wf1_v1_2.cwl

Branch/Commit ID: 0ab1d42d10f7311bb4032956c4a6f3d2730d9507
workflow graph Exome QC workflow

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

Path: definitions/subworkflows/qc_exome.cwl

Branch/Commit ID: e59c77629936fad069007ba642cad49fef7ad29f
workflow graph analysis for assembled sequences

rna / protein - qc, annotation, index, abundance

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

Path: CWL/Workflows/assembled.workflow.cwl

Branch/Commit ID: 1844de830f6935901849ccd9966685fbf13e8042
workflow graph chipseq-gen-bigwig.cwl

https://github.com/datirium/workflows.git

Path: subworkflows/chipseq-gen-bigwig.cwl

Branch/Commit ID: 942f453603bc1df04cee28d6ac6b3b8b649fda55
workflow graph exome alignment with qc, no bqsr, no verify_bam_id

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

Path: definitions/pipelines/alignment_exome_mouse.cwl

Branch/Commit ID: 8438316338e66823e1c9aca9f675b2bf33f2aa59
workflow graph umi duplex alignment workflow

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

Path: definitions/subworkflows/duplex_alignment.cwl

Branch/Commit ID: 9c0b1497c467393e1a54735575043dced73e95c4
workflow graph revsort.cwl

Reverse the lines in a document, then sort those lines.

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

Path: tests/wf/revsort.cwl

Branch/Commit ID: d6000d32f6c8fbd26421a2d30d79b28901d58fb0