Explore Workflows

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

Graph Name Retrieved From View
workflow graph count-lines4-wf.cwl

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

Path: cwltool/schemas/v1.0/v1.0/count-lines4-wf.cwl

Branch/Commit ID: 7ec307b01442936fad9b1149f4500496557505ff
workflow graph bam_readcount workflow

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

Path: definitions/subworkflows/bam_readcount.cwl

Branch/Commit ID: 3bebaf9b70331de9f4845e2223c55082f5a812fb
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: 282762f8bbaea57dd488115745ef798e128bade1
workflow graph umi duplex alignment fastq workflow

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

Path: definitions/pipelines/alignment_umi_duplex.cwl

Branch/Commit ID: 25eab0390f6866ce491b44c89d9e0435d228ab6f
workflow graph bams2gvcf.woBQSR_female.cwl

https://github.com/ddbj/human-reseq.git

Path: Workflows/bams2gvcf.woBQSR_female.cwl

Branch/Commit ID: 2862ec3c609561245267e5f32e7b94eb353e2d5b
workflow graph ani_top_n

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

Path: task_types/tt_ani_top_n.cwl

Branch/Commit ID: a7fced3ed8c839272c8f3a8db9da7bc8cd50271f
workflow graph Single-cell Differential Expression

Single-cell Differential Expression =================================== Runs differential expression analysis for a subset of cells between two selected conditions.

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

Path: workflows/sc_diff_expr.cwl

Branch/Commit ID: ebbf23764ede324cabc064bd50647c1f643726fa
workflow graph Whole genome alignment and somatic variant detection

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

Path: definitions/pipelines/somatic_wgs.cwl

Branch/Commit ID: 8dc462a7d9ba1479f764682af99c69d8574cb3dc
workflow graph Genomic regions intersection and visualization

Genomic regions intersection and visualization ============================================== 1. Merges intervals within each of the filtered peaks files from ChIP/ATAC experiments 2. Overlaps merged intervals and assigns the nearest genes to them

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

Path: workflows/intervene.cwl

Branch/Commit ID: c6bfa0de917efb536dd385624fc7702e6748e61d
workflow graph ani_top_n

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

Path: task_types/tt_ani_top_n.cwl

Branch/Commit ID: 733ab7198a66a0153d0f03c3022ab53c17325ff8