Explore Workflows

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

Graph Name Retrieved From View
workflow graph 04-quantification-se-unstranded.cwl

RNA-seq 04 quantification

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

Path: v1.0/RNA-seq_pipeline/04-quantification-se-unstranded.cwl

Branch/Commit ID: 1a0dd34d59ec983d1f7ad77bff35da2f016e3134
workflow graph 03-map-se-blacklist-removal.cwl

ATAC-seq 03 mapping - reads: SE - blacklist removal

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

Path: v1.0/ATAC-seq_pipeline/03-map-se-blacklist-removal.cwl

Branch/Commit ID: 487af88ef0b971f76ecd1a215639bb47e3ee94e1
workflow graph chipseq-header.cwl

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

Path: metadata/chipseq-header.cwl

Branch/Commit ID: c9e7f3de7f6ba38ee663bd3f9649e8d7dbac0c86
workflow graph Read quality control, trimming and contamination filter.

Workflow for (paired) read quality control, trimming and contamination filtering. Will output a merged set of read pairs, when multiple datasets are used. Steps: - FastQC (read quality control) - fastp (read quality trimming) - bbduk used for rrna filtering - bbmap for contamination filter

https://git.wageningenur.nl/unlock/cwl.git

Path: cwl/workflows/workflow_quality.cwl

Branch/Commit ID: d6893a25b58b9b25fb76c5e060974b54d9eabc41
workflow graph rnaseq-header.cwl

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

Path: metadata/rnaseq-header.cwl

Branch/Commit ID: 480e99a4bb3046e0565113d9dca294e0895d3b0c
workflow graph spurious_annot

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

Path: spurious_annot/wf_spurious_annot_pass1.cwl

Branch/Commit ID: a402541b8530f30eab726c160da90a23036847a1
workflow graph bam to trimmed fastqs

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

Path: definitions/subworkflows/bam_to_trimmed_fastq.cwl

Branch/Commit ID: 457e101e3fb87e7fd792357afce00ed8ccbfbcdb
workflow graph assemble.cwl

Assemble a set of reads using SKESA

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

Path: assemble.cwl

Branch/Commit ID: e2a6cbcc36212433d8fbc804919442787a5e2a49
workflow graph Cell Ranger Count Gene Expression

Cell Ranger Count Gene Expression =================================

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

Path: workflows/single-cell-preprocess-cellranger.cwl

Branch/Commit ID: 480e99a4bb3046e0565113d9dca294e0895d3b0c
workflow graph THOR - differential peak calling of ChIP-seq signals with replicates

What is THOR? -------------- THOR is an HMM-based approach to detect and analyze differential peaks in two sets of ChIP-seq data from distinct biological conditions with replicates. THOR performs genomic signal processing, peak calling and p-value calculation in an integrated framework. For more information please refer to: ------------------------------------- Allhoff, M., Sere K., Freitas, J., Zenke, M., Costa, I.G. (2016), Differential Peak Calling of ChIP-seq Signals with Replicates with THOR, Nucleic Acids Research, epub gkw680.

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

Path: workflows/rgt-thor.cwl

Branch/Commit ID: 09267e79fd867aa68a219c69e6db7d8e2e877be2