Explore Workflows

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

Graph Name Retrieved From View
workflow graph Xenbase RNA-Seq pipeline single-read

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-se.cwl

Branch/Commit ID: b141f7e73005227d6d02fa03a47151836dd4109b
workflow graph transform.cwl

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

Path: workflows/bamfastq_align/transform.cwl

Branch/Commit ID: 2f7c0e92e7b88b57b86602f11c595661c374008a
workflow graph fastqtosam_se.cwl

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

Path: workflows/fastqtosam/fastqtosam_se.cwl

Branch/Commit ID: a3eec6c1081d28efe00a0d269fb41303acc4ccdd
workflow graph scatter-valuefrom-wf2.cwl

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

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

Branch/Commit ID: 478c2ffc09fb189c4f36ccb82aad945b3db5f9b3
workflow graph protein_extract

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

Path: progs/protein_extract.cwl

Branch/Commit ID: 66b5bc323dcd23e1b2c14bf4783babf0f15ca43b
workflow graph 05-quantification.cwl

ChIP-seq - Quantification - samples: treatment

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

Path: v1.0/ChIP-seq_pipeline/05-quantification.cwl

Branch/Commit ID: 13826f526a99e151e9cf5f22e70bdcf4feea73f4
workflow graph xenbase-fastq-bowtie-bigwig-se-pe.cwl

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

Path: subworkflows/xenbase-fastq-bowtie-bigwig-se-pe.cwl

Branch/Commit ID: b141f7e73005227d6d02fa03a47151836dd4109b
workflow graph 05-quantification-with-control.cwl

ChIP-seq - Quantification - samples: treatment and control

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

Path: v1.0/ChIP-seq_pipeline/05-quantification-with-control.cwl

Branch/Commit ID: 13826f526a99e151e9cf5f22e70bdcf4feea73f4
workflow graph any-type-compat.cwl

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

Path: cwltool/schemas/v1.0/v1.0/any-type-compat.cwl

Branch/Commit ID: 4c905b830371eee45188a53510ba0ee9113fd4c8
workflow graph 01-qc-se.cwl

ChIP-seq 01 QC - reads: SE

 https://github.com/Duke-GCB/GGR-cwl.git

Path: v1.0/ChIP-seq_pipeline/01-qc-se.cwl

Branch/Commit ID: a502ff01b0857f8067aa541effc46a4c8b10d90f