Explore Workflows

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

Graph Name Retrieved From View
workflow graph Apply filters to VCF file

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

Path: definitions/subworkflows/filter_vcf.cwl

Branch/Commit ID: a670f323e77e02d9b77be9a13d73d5276dd3676c
workflow graph checkm_wnode

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

Path: task_types/tt_checkm_wnode.cwl

Branch/Commit ID: 8ea3637b0f11eac1ea5599c41d74e00d85fb778d
workflow graph step-valuefrom-wf.cwl

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

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

Branch/Commit ID: e9c83739a93fa0b18f8dea2f98b632a9e32725c9
workflow graph count-lines7-wf.cwl

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

Path: cwltool/schemas/v1.0/v1.0/count-lines7-wf.cwl

Branch/Commit ID: 4635090ef98247b1902b3c7a25c007d9db1cb883
workflow graph bam_readcount workflow

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

Path: definitions/subworkflows/bam_readcount.cwl

Branch/Commit ID: e59c77629936fad069007ba642cad49fef7ad29f
workflow graph RNA-Seq pipeline paired-end stranded mitochondrial

Slightly changed original [BioWardrobe's](https://biowardrobe.com) [PubMed ID:26248465](https://www.ncbi.nlm.nih.gov/pubmed/26248465) **RNA-Seq** basic analysis for **strand specific pair-end** experiment. An additional steps were added to map data to mitochondrial chromosome only and then merge the output. Experiment files in [FASTQ](http://maq.sourceforge.net/fastq.shtml) format either compressed or not can be used. Current workflow should be used only with the pair-end strand specific RNA-Seq data. It performs the following steps: 1. `STAR` to align reads from input FASTQ file according to the predefined reference indices; generate unsorted BAM file and alignment statistics file 2. `fastx_quality_stats` to analyze input FASTQ file and generate quality statistics file 3. `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/rnaseq-pe-dutp-mitochondrial.cwl

Branch/Commit ID: ce058d892d330125cd03d0a0d5fb3b321cda0be3
workflow graph scatter-valuefrom-wf6.cwl

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

Path: cwltool/schemas/v1.0/v1.0/scatter-valuefrom-wf6.cwl

Branch/Commit ID: 4635090ef98247b1902b3c7a25c007d9db1cb883
workflow graph Exome QC workflow

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

Path: definitions/subworkflows/qc_exome.cwl

Branch/Commit ID: ec45fad68ca10fb64d5c58e704991b146dc31d28
workflow graph Compute average of average per cross-mapped famil(y)ies

Compute average structure for all averaged structures corresponding to UniProt domain instances cross-mapped from Pfam/CATH to a CATH/Pfam family. First computes average per UniProt domain instance and then average all averaged structures per Pfam family.

https://github.com/HrishiDhondge/CroMaSt.git

Path: Tools/other_avg_subwf.cwl

Branch/Commit ID: a030726eafe217f8fea39bbdd05321d10b61a229
workflow graph kmer_cache_store

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

Path: task_types/tt_kmer_cache_store.cwl

Branch/Commit ID: 1e7aa9f0c34987ddafa35f9b1d2c77d99fafbdab