Explore Workflows

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

Graph Name Retrieved From View
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: 91181df8d9ef8eed9d8f40db707b9a4376fecaf5
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: 2768d117212e50859edebea74b0641dfaf4feba4
workflow graph merge_filter.cwl

https://github.com/CompEpigen/ChIPseq_workflows.git

Path: CWL/workflow_modules/merge_filter.cwl

Branch/Commit ID: b7709bff6bd6e93a28dfc2fee0655f6aceef0901
workflow graph blastp_wnode_naming

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

Path: task_types/tt_blastp_wnode_naming.cwl

Branch/Commit ID: 7b5130d2408bce82ee15c666b37d931ef6f452e3
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: e238d1756f1db35571e84d72e1699e5d1540f10c
workflow graph output-arrays-int-wf.cwl

https://github.com/common-workflow-language/cwl-v1.1.git

Path: tests/output-arrays-int-wf.cwl

Branch/Commit ID: 0e37d46e793e72b7c16b5ec03e22cb3ce1f55ba3
workflow graph kmer_seq_entry_extract_wnode

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

Path: task_types/tt_kmer_seq_entry_extract_wnode.cwl

Branch/Commit ID: 686b570a9fa46f3ace3f8e9935490b75df86a1fc
workflow graph Filter Protein Alignments I

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

Path: protein_alignment/wf_align_filter.cwl

Branch/Commit ID: 16d1198871195e2229fd44dd0ad94a4ed6a87caf
workflow graph 02-trim-pe.cwl

ChIP-seq 02 trimming - reads: PE

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

Path: v1.0/ChIP-seq_pipeline/02-trim-pe.cwl

Branch/Commit ID: 33385c6a820a9d4d18cff6fc3a533ec8e3c11c6e
workflow graph Seed Search Compartments

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

Path: protein_alignment/wf_seed.cwl

Branch/Commit ID: 16d1198871195e2229fd44dd0ad94a4ed6a87caf