Explore Workflows
View already parsed workflows here or click here to add your own
Graph | Name | Retrieved From | View |
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bam-bedgraph-bigwig.cwl
Workflow converts input BAM file into bigWig and bedGraph files |
https://github.com/Barski-lab/workflows.git
Path: subworkflows/bam-bedgraph-bigwig.cwl Branch/Commit ID: 6dca77dfd89996079bff84d07849a1583455b54f |
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kfdrc_bwamem_subwf.cwl
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https://github.com/kids-first/kf-alignment-workflow.git
Path: workflows/kfdrc_bwamem_subwf.cwl Branch/Commit ID: 9e983f1d09892dfc8c17bcb6ff59c075c86b46a6 |
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Run genomic CMsearch (5S rRNA)
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https://github.com/ncbi/pgap.git
Path: bacterial_noncoding/wf_gcmsearch.cwl Branch/Commit ID: 4ea5956bb97ea2eb6de124bc9b6a6a81a14fd2e7 |
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Xenbase RNA-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, calculate genes and isoforms expression (run RSEM) 5. Count mapped reads number in sorted BAM file (run bamtools stats) 6. Generate genome coverage BED file (run bedtools genomecov) 7. Sort genearted BED file (run sort) 8. Generate genome coverage bigWig file from BED file (run bedGraphToBigWig) |
https://github.com/datirium/workflows.git
Path: workflows/xenbase-rnaseq-pe.cwl Branch/Commit ID: dda9e6e06a656b7b3fa7504156474b962fe3953c |
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scatter-valuefrom-wf3.cwl#main
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https://github.com/common-workflow-language/cwltool.git
Path: cwltool/schemas/v1.0/v1.0/scatter-valuefrom-wf3.cwl Branch/Commit ID: 4a5fe26e32d244d95f9483c3edfc3df04f3e5f7b Packed ID: main |
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scatter-wf2.cwl
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https://github.com/common-workflow-language/cwltool.git
Path: cwltool/schemas/v1.0/v1.0/scatter-wf2.cwl Branch/Commit ID: 665141f319e6b23bd9924b14844f2e979f141944 |
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Subworkflow that runs cnvkit in single sample mode and returns a vcf file
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https://github.com/genome/analysis-workflows.git
Path: definitions/subworkflows/cnvkit_single_sample.cwl Branch/Commit ID: a670f323e77e02d9b77be9a13d73d5276dd3676c |
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02-trim-se.cwl
ChIP-seq 02 trimming - reads: SE |
https://github.com/alexbarrera/GGR-cwl.git
Path: v1.0/ChIP-seq_pipeline/02-trim-se.cwl Branch/Commit ID: 7696e7eb27a9251fba53ef4ccacc84cc8f8b0685 |
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Workflow to create a FASTA file for the tagset
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https://github.com/curoverse/l7g.git
Path: cwl-version/tagset/l7g-tagset.cwl Branch/Commit ID: 604f393a8e1883bf7c275303f2777b368eb7fef8 |
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workflow.cwl
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https://github.com/aniewielska/RD_pipeline.git
Path: workflow.cwl Branch/Commit ID: 644d3bec99f6467614ea3a0e9b83da66cd1300c5 |