Explore Workflows

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Graph Name Retrieved From View
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
workflow graph 1st-workflow.cwl

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

Path: cwltool/schemas/v1.0/examples/1st-workflow.cwl

Branch/Commit ID: d64178072bc4fc9700ab80cdf90146890b96587e
workflow graph cluster_blastp_wnode and gpx_qdump combined

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

Path: task_types/tt_cluster_and_qdump.cwl

Branch/Commit ID: 5461e63dc4714bb81e1c9f58e436c8465107a199
workflow graph qc-merge.cwl

https://github.com/mskcc/roslin-variant.git

Path: setup/cwl/tools/roslin-qc/qc-merge.cwl

Branch/Commit ID: bf7303dd44d7f0ec3d3cd2e0829e28a78bd941e2
workflow graph exome alignment with qc

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

Path: definitions/pipelines/exome_alignment.cwl

Branch/Commit ID: 0c4855bf23622828413ecb09dd30754691c28014
workflow graph hmmsearch_wnode and gpx_qdump combined workflow to apply scatter/gather

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

Path: task_types/tt_hmmsearch_wnode_plus_qdump.cwl

Branch/Commit ID: 5461e63dc4714bb81e1c9f58e436c8465107a199
workflow graph Filter Protein Seeds I; Find ProSplign Alignments I

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

Path: protein_alignment/wf_compart_filter_prosplign.cwl

Branch/Commit ID: 5461e63dc4714bb81e1c9f58e436c8465107a199
workflow graph Seed Protein Alignments I

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

Path: protein_alignment/wf_seed_1.cwl

Branch/Commit ID: 5461e63dc4714bb81e1c9f58e436c8465107a199