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Graph Name Retrieved From View
workflow graph bambino_rna_indel.cwl

Somatic indel detector for tumor RNA-Seq data

https://github.com/stjude/RNAIndel.git

Path: bambino_rna_indel.cwl

Branch/Commit ID: 3f42fde37f333c69ad5f95dd4be60672fb4a0842
workflow graph schemadef-wf.cwl

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

Path: v1.0/v1.0/schemadef-wf.cwl

Branch/Commit ID: 26c8b9ca0ffd37c5f76a46a36315f6fd944833fe
workflow graph sec-wf.cwl

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

Path: tests/wf/sec-wf.cwl

Branch/Commit ID: d64178072bc4fc9700ab80cdf90146890b96587e
workflow graph exome alignment with qc

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

Path: definitions/pipelines/exome_alignment.cwl

Branch/Commit ID: c711498c04d6b8ddf92ddceb6219f074765f7993
workflow graph readgroup_fastq_se.cwl

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

Path: workflows/bamfastq_align/readgroup_fastq_se.cwl

Branch/Commit ID: 017c7572ea309c7d5b34bcc9bc1bdafbe47cb515
workflow graph count-lines5-wf.cwl

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

Path: cwltool/schemas/v1.0/v1.0/count-lines5-wf.cwl

Branch/Commit ID: d64178072bc4fc9700ab80cdf90146890b96587e
workflow graph blastp_wnode_naming

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

Path: task_types/tt_blastp_wnode_naming.cwl

Branch/Commit ID: f5c11df465aaadf712c38ba4933679fe1cbe03ca
workflow graph wf_amr_dna.cwl

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

Path: amr_finder/wf_amr_dna.cwl

Branch/Commit ID: 7a5fae087e42ec7d2bfdf3f88ba2ea1e8fdc9ddf
workflow graph extract_readgroup_fastq_se.cwl

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

Path: workflows/bamfastq_align/extract_readgroup_fastq_se.cwl

Branch/Commit ID: 10c05314890db2b5bd85c3d338d7f5657fe0c646
workflow graph Xenbase ChIP-Seq pipeline single-read

1. Convert input SRA file into FASTQ file (run fastq-dump) 2. Analyze quality of FASTQ file (run fastqc) 3. If any of the following fields in fastqc generated report is marked as failed: \"Per base sequence quality\", \"Per sequence quality scores\", \"Overrepresented sequences\", \"Adapter Content\", - trim adapters (run trimmomatic) 4. Align original or trimmed FASTQ file 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-se.cwl

Branch/Commit ID: bfa3843bcf36125ff258d6314f64b41336f06e6b