Explore Workflows

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Graph Name Retrieved From View
workflow graph Cell Ranger Count (ATAC)

Cell Ranger Count (ATAC) Quantifies single-cell chromatin accessibility of the sequencing data from a single 10x Genomics library. The results of this workflow are used in either the “Single-Cell ATAC-Seq Filtering Analysis” or “Cell Ranger Aggregate (ATAC)” pipeline.

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

Path: workflows/cellranger-atac-count.cwl

Branch/Commit ID: 93b844a80f4008cc973ea9b5efedaff32a343895
workflow graph Exome QC workflow

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

Path: definitions/subworkflows/qc_exome.cwl

Branch/Commit ID: 0a9a4ce83b49ed4e7eee5bcc09d83725136a36b0
workflow graph heatmap-prepare.cwl

Workflow runs homer-make-tag-directory.cwl tool using scatter for the following inputs - bam_file - fragment_size - total_reads `dotproduct` is used as a `scatterMethod`, so one element will be taken from each array to construct each job: 1) bam_file[0] fragment_size[0] total_reads[0] 2) bam_file[1] fragment_size[1] total_reads[1] ... N) bam_file[N] fragment_size[N] total_reads[N] `bam_file`, `fragment_size` and `total_reads` arrays should have the identical order.

https://github.com/Barski-lab/workflows.git

Path: tools/heatmap-prepare.cwl

Branch/Commit ID: a8909e86f5bcb048d136f9a7d70b4b6f8f4e485f
workflow graph Unaligned BAM to BQSR and VCF

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

Path: definitions/subworkflows/bam_to_bqsr.cwl

Branch/Commit ID: 0a9a4ce83b49ed4e7eee5bcc09d83725136a36b0
workflow graph RNA-Seq pipeline paired-end strand specific

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

Branch/Commit ID: a68821bf3a9ceadc3b2ffbb535d601d9a645b377
workflow graph scatter-wf1.cwl

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

Path: v1.0/v1.0/scatter-wf1.cwl

Branch/Commit ID: 4fd45edb9531a03223c18a586e32d0baf0d5acb2
workflow graph assemble.cwl

Assemble a set of reads using SKESA

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

Path: assemble.cwl

Branch/Commit ID: 77a9fa25b89ce73582a1ce6ba75fa6d2537fb8e8
workflow graph Xenbase ChIP-Seq pipeline paired-end

1. Convert input SRA file into pair of upsrtream and downstream FASTQ files (run fastq-dump) 2. Analyze quality of FASTQ files (run fastqc with each of the FASTQ files) 3. If any of the following fields in fastqc generated report is marked as failed for at least one of input FASTQ files: \"Per base sequence quality\", \"Per sequence quality scores\", \"Overrepresented sequences\", \"Adapter Content\", - trim adapters (run trimmomatic) 4. Align original or trimmed FASTQ files to reference genome (run Bowtie2) 5. Sort and index generated by Bowtie2 BAM file (run samtools sort, samtools index) 6. Remove duplicates in sorted BAM file (run picard) 7. Sort and index BAM file after duplicates removing (run samtools sort, samtools index) 8. Count mapped reads number in sorted BAM file (run bamtools stats) 9. Generate genome coverage BED file (run bedtools genomecov) 10. Sort genearted BED file (run sort) 11. Generate genome coverage bigWig file from BED file (run bedGraphToBigWig)

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

Path: workflows/xenbase-chipseq-pe.cwl

Branch/Commit ID: 9ee330737f4603e4e959ffe786fbb2046db70a00
workflow graph no-inputs-wf.cwl

Workflow without inputs.

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

Path: tests/no-inputs-wf.cwl

Branch/Commit ID: 57baec040c99d7edef8242ef51b5470b1c82d733
workflow graph count-lines13-wf.cwl

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

Path: tests/count-lines13-wf.cwl

Branch/Commit ID: 57baec040c99d7edef8242ef51b5470b1c82d733