Explore Workflows

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

Graph Name Retrieved From View
workflow graph mixed_library_metrics.cwl

https://github.com/nci-gdc/gdc-dnaseq-cwl.git

Path: workflows/mirnaseq/mixed_library_metrics.cwl

Branch/Commit ID: b2f7a697e08220234062a9cf558ba169d255b4a4
workflow graph kallisto-demo.cwl

https://github.com/alexbarrera/GGR-cwl.git

Path: workflows/workflows/kallisto-demo.cwl

Branch/Commit ID: e019c548a0bc2f17b13365abd213259887069978
workflow graph readgroups_bam_to_readgroups_fastq_lists.cwl

https://github.com/NCI-GDC/gdc-dnaseq-cwl.git

Path: workflows/bamfastq_align/readgroups_bam_to_readgroups_fastq_lists.cwl

Branch/Commit ID: 0d3fdddeae5a398e476d91aa98766965866d8eae
workflow graph extract_readgroups_bam_http.cwl

https://github.com/nci-gdc/gdc-dnaseq-cwl.git

Path: workflows/bamfastq_align/extract_readgroups_bam_http.cwl

Branch/Commit ID: 0d3fdddeae5a398e476d91aa98766965866d8eae
workflow graph revcomp.cwl

https://github.com/alexbarrera/GGR-cwl.git

Path: workflows/workflows/sanbi_cwltutorial/revcomp/revcomp.cwl

Branch/Commit ID: e019c548a0bc2f17b13365abd213259887069978
workflow graph 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: 6bf56698c6fe6e781723dea32bc922b91ef49cf3
workflow graph 01-qc-se.cwl

ATAC-seq 01 QC - reads: SE

 https://github.com/Duke-GCB/GGR-cwl.git

Path: v1.0/ATAC-seq_pipeline/01-qc-se.cwl

Branch/Commit ID: ffdc6d7b155fe301cd49b6e499097cce966159ef
workflow graph PGAP Pipeline, simple user input, PGAPX-134

PGAP pipeline for external usage, powered via containers, simple user input: (FASTA + yaml only, no template)

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

Path: pgap.cwl

Branch/Commit ID: be5ae41801b19ebc69a2889d8fdb39e8e2359611
workflow graph Per-chromosome pindel

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

Path: definitions/subworkflows/pindel_cat.cwl

Branch/Commit ID: f45b52a24c7b54a75368dcbab24b4eb2c5a9c75a
workflow graph transform.cwl

https://github.com/nci-gdc/gdc-dnaseq-cwl.git

Path: workflows/fastq_readgroup_stats/transform.cwl

Branch/Commit ID: dd7f86b3cc10eb1cda07dc2fc279ba2529c8ad61