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 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 (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-pe.cwl

Branch/Commit ID: 4106b7dc96e968db291b7a61ecd1641aa3b3dd6d
workflow graph List ZIP content for zenodo community

For a given Zenodo community, list file content of its downloadable *.zip files

https://github.com/stain/ro-index-paper.git

Path: code/data-gathering/workflows/zenodo-zip-content.cwl

Branch/Commit ID: a3ce8d810d16111d695a04316ef55671d2d38ee5
workflow graph iwdr_with_nested_dirs.cwl

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

Path: v1.0/v1.0/iwdr_with_nested_dirs.cwl

Branch/Commit ID: 22490926651174c6cbe01c76c2ded3c9e8d0ee6f
workflow graph snps_and_indels.cwl

https://github.com/mskcc/innovation-pipeline.git

Path: workflows/subworkflows/snps_and_indels.cwl

Branch/Commit ID: b0f226a9ac5152f3afe0d38c8cd54aa25b8b01cf
workflow graph assm_assm_blastn_wnode

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

Path: task_types/tt_assm_assm_blastn_wnode.cwl

Branch/Commit ID: 733ab7198a66a0153d0f03c3022ab53c17325ff8
workflow graph scatter-wf3.cwl#main

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

Path: cwltool/schemas/v1.0/v1.0/scatter-wf3.cwl

Branch/Commit ID: c6cced7a2e6389d2eb43342e702677ccb7c7497c

Packed ID: main
workflow graph Single-cell Differential Abundance Analysis

Single-cell Differential Abundance Analysis Detects cell subpopulations with differential abundance between datasets split by biological condition.

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

Path: workflows/sc-rna-da-cells.cwl

Branch/Commit ID: 12e5256de1b680c551c87fd5db6f3bc65428af67
workflow graph env-wf2.cwl

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

Path: cwltool/schemas/v1.0/v1.0/env-wf2.cwl

Branch/Commit ID: 7ec307b01442936fad9b1149f4500496557505ff
workflow graph scatter-wf2.cwl

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

Path: cwltool/schemas/v1.0/v1.0/scatter-wf2.cwl

Branch/Commit ID: bfe56f3138e9e6fc0b9b8c06447553d4cea03d59
workflow graph kmer_cache_retrieve

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

Path: task_types/tt_kmer_cache_retrieve.cwl

Branch/Commit ID: 733ab7198a66a0153d0f03c3022ab53c17325ff8