Explore Workflows

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

Graph Name Retrieved From View
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: 9b4dc225c537685b9c9a32d931d3892d20953dd7
workflow graph count-lines8-wf.cwl

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

Path: cwltool/schemas/v1.0/v1.0/count-lines8-wf.cwl

Branch/Commit ID: 4a5fe26e32d244d95f9483c3edfc3df04f3e5f7b
workflow graph HS Metrics workflow

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

Path: definitions/subworkflows/hs_metrics.cwl

Branch/Commit ID: 8cee1920920ed73384fb3ab74272da9c92a20cf2
workflow graph kfdrc_bwamem_subwf.cwl

https://github.com/kids-first/kf-alignment-workflow.git

Path: workflows/kfdrc_bwamem_subwf.cwl

Branch/Commit ID: dbaad281888ab5346892917c11ea3dd61ce2fbbd
workflow graph xenbase-sra-to-fastq-pe.cwl

https://github.com/datirium/workflows.git

Path: subworkflows/xenbase-sra-to-fastq-pe.cwl

Branch/Commit ID: 02ffbbd7eb8e06bfb759edea440f78bdc8bb2631
workflow graph BLAST against rRNA db

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

Path: bacterial_noncoding/wf_blastn.cwl

Branch/Commit ID: 66b5bc323dcd23e1b2c14bf4783babf0f15ca43b
workflow graph Create Genomic Collection for Bacterial Pipeline, ASN.1 input

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

Path: genomic_source/wf_genomic_source_asn.cwl

Branch/Commit ID: 7edbf07405191db65a913e311a7f2260b076d36c
workflow graph Create Genomic Collection for Bacterial Pipeline, ASN.1 input

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

Path: genomic_source/wf_genomic_source_asn.cwl

Branch/Commit ID: f6950321e5c9ee733ad68a273d2ad8e802a6b982
workflow graph bam-bedgraph-bigwig.cwl

Workflow converts input BAM file into bigWig and bedGraph files

https://github.com/datirium/workflows.git

Path: subworkflows/bam-bedgraph-bigwig.cwl

Branch/Commit ID: 3b2e0de49d9ee6fd9a8c9580b6a02d0f7e4c8f7c
workflow graph trnascan_wnode and gpx_qdump combined

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

Path: bacterial_trna/wf_scan_and_dump.cwl

Branch/Commit ID: be5ae41801b19ebc69a2889d8fdb39e8e2359611