Explore Workflows

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

Graph Name Retrieved From View
workflow graph kf-cram2gvcf-bam-input.cwl

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

Path: workflows/kf-cram2gvcf-bam-input.cwl

Branch/Commit ID: 55315b6abb488f1f25fe725407814e8d4c23ba81
workflow graph Build Bismark indices

Copy fasta_file file to the folder and run run bismark_genome_preparation script to prepare indices for Bismark Methylation Analysis. Bowtie2 aligner is used by default. The name of the output indices folder is equal to the genome input.

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

Path: workflows/bismark-index.cwl

Branch/Commit ID: f3e44d3b0f198cf5245c49011124dc3b6c2b06fd
workflow graph Unaligned BAM to BQSR and VCF

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

Path: definitions/subworkflows/bam_to_bqsr_no_dup_marking.cwl

Branch/Commit ID: ae57b60e9b01e3f0f02f4e828042748409dff5a3
workflow graph tt_kmer_compare_wnode

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

Path: task_types/tt_kmer_compare_wnode.cwl

Branch/Commit ID: 66b5bc323dcd23e1b2c14bf4783babf0f15ca43b
workflow graph Create Genomic Collection for Bacterial Pipeline

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

Path: genomic_source/wf_genomic_source.cwl

Branch/Commit ID: f2bd4687f06f85ea848b6f1ce04ec97f48525334
workflow graph Add snv and indel bam-readcount files to a vcf

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

Path: definitions/subworkflows/vcf_readcount_annotator.cwl

Branch/Commit ID: 60edaf6f57eaaf02cda1a3d8cb9a825aa64a43e2
workflow graph gcaccess_from_list

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

Path: task_types/tt_gcaccess_from_list.cwl

Branch/Commit ID: 3e7a3c1cc1ed5164ae0a51a96f20d7c480d1d70b
workflow graph js-expr-req-wf.cwl#wf

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

Path: testdata/js-expr-req-wf.cwl

Branch/Commit ID: 0ab1d42d10f7311bb4032956c4a6f3d2730d9507

Packed ID: wf
workflow graph SoupX Estimate

SoupX Estimate ==============

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

Path: workflows/soupx.cwl

Branch/Commit ID: f3e44d3b0f198cf5245c49011124dc3b6c2b06fd
workflow graph 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-read** 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-read RNA-Seq data. It performs the following steps: 1. Use STAR to align reads from input FASTQ file according to the predefined reference indices; generate unsorted BAM file and alignment statistics file 2. Use fastx_quality_stats to analyze input FASTQ file and generate quality statistics file 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) 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-se.cwl

Branch/Commit ID: 5e7385b8cfa4ddae822fff37b6bd22eb0370b389