Explore Workflows

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

Graph Name Retrieved From View
workflow graph umi per-lane alignment subworkflow

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

Path: definitions/subworkflows/umi_alignment.cwl

Branch/Commit ID: 6f9f8a2057c6a9f221a44559f671e87a75c70075
workflow graph mutect parallel workflow

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

Path: definitions/subworkflows/mutect.cwl

Branch/Commit ID: a9133c999502acf94b433af8d39897e6c2cdf65f
workflow graph count-lines1-wf.cwl

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

Path: cwltool/schemas/v1.0/v1.0/count-lines1-wf.cwl

Branch/Commit ID: 46b7f9766d1bc8a4871474eee25ec730b4e173da
workflow graph cram_to_bam workflow

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

Path: definitions/subworkflows/cram_to_bam_and_index.cwl

Branch/Commit ID: f9600f9959acdc30259ba7e64de61104c9b01f0b
workflow graph Raw sequence data to BQSR

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

Path: definitions/subworkflows/sequence_to_bqsr.cwl

Branch/Commit ID: a9133c999502acf94b433af8d39897e6c2cdf65f
workflow graph Complete Mapping and Quality Control pipeline for Single-end data that also executes functions of the metaseqR2 package

A workflow which: i) Runs Hisat2 on each fastq while generating a fastq file containing unmapped reads ii) Runs Bowtie2 using the --very-sensitive-local option, on the unmapped reads iii) A subworkflow is employed to prepare BAM files, corresponding to the unmapped-remaped reads, to be merged with the mapped reads form Hisat2 iv) After the merged BAMs are created, they are sorted and assigned a user defined name (sample identifier) v) Corresponding index file for each sample is generated. vi) BAMs and index files are used to create bigWig files, to be used for exploring RNA signal in genome browsers vii) Above files are also used to calculate counts (counts.RData object) and generate the metaseqR2 html report viii) At the same time it performs quality control over the FASTQ using fastqc and assembles the MultiQC report

https://github.com/mr-c/elixir-gr-project.git

Path: CWL/workflows/mapping-se-qc-r.cwl

Branch/Commit ID: 6a1a6b9d5a152e783fe3f794ccce35387d02fd0d
workflow graph WGS QC workflow

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

Path: definitions/subworkflows/qc_wgs.cwl

Branch/Commit ID: a9133c999502acf94b433af8d39897e6c2cdf65f
workflow graph varscan somatic workflow

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

Path: definitions/subworkflows/varscan.cwl

Branch/Commit ID: ad65dc1dfff9afa5077f498b85e699716c47f6cb
workflow graph FastQC parallel and MultiQC

This CWL scatters FastQC quality control over multiple processors, one for each file and creates the MultiQC report version: 0.01

https://github.com/mr-c/elixir-gr-project.git

Path: CWL/workflows/qc-wf.cwl

Branch/Commit ID: 6a1a6b9d5a152e783fe3f794ccce35387d02fd0d
workflow graph bgzip and index VCF

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

Path: definitions/subworkflows/bgzip_and_index.cwl

Branch/Commit ID: ad65dc1dfff9afa5077f498b85e699716c47f6cb