Explore Workflows
View already parsed workflows here or click here to add your own
Graph | Name | Retrieved From | View |
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Apply filters to VCF file
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https://github.com/genome/analysis-workflows.git
Path: definitions/subworkflows/filter_vcf_mouse.cwl Branch/Commit ID: 869b331cfeb9dbd5907498e3eccdebc7c28283e5 |
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exome alignment with qc
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https://github.com/genome/analysis-workflows.git
Path: definitions/pipelines/exome_alignment.cwl Branch/Commit ID: ddd748516b25256a461ea9277303406fa2759b00 |
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umi per-lane alignment subworkflow
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https://github.com/genome/analysis-workflows.git
Path: definitions/subworkflows/umi_alignment.cwl Branch/Commit ID: 6f9f8a2057c6a9f221a44559f671e87a75c70075 |
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mutect parallel workflow
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https://github.com/genome/analysis-workflows.git
Path: definitions/subworkflows/mutect.cwl Branch/Commit ID: a9133c999502acf94b433af8d39897e6c2cdf65f |
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count-lines1-wf.cwl
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https://github.com/common-workflow-language/cwltool.git
Path: cwltool/schemas/v1.0/v1.0/count-lines1-wf.cwl Branch/Commit ID: 46b7f9766d1bc8a4871474eee25ec730b4e173da |
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cram_to_bam workflow
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https://github.com/genome/analysis-workflows.git
Path: definitions/subworkflows/cram_to_bam_and_index.cwl Branch/Commit ID: f9600f9959acdc30259ba7e64de61104c9b01f0b |
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Raw sequence data to BQSR
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https://github.com/genome/analysis-workflows.git
Path: definitions/subworkflows/sequence_to_bqsr.cwl Branch/Commit ID: a9133c999502acf94b433af8d39897e6c2cdf65f |
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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 |
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WGS QC workflow
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https://github.com/genome/analysis-workflows.git
Path: definitions/subworkflows/qc_wgs.cwl Branch/Commit ID: a9133c999502acf94b433af8d39897e6c2cdf65f |
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varscan somatic workflow
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https://github.com/genome/analysis-workflows.git
Path: definitions/subworkflows/varscan.cwl Branch/Commit ID: ad65dc1dfff9afa5077f498b85e699716c47f6cb |