Explore Workflows

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

Graph Name Retrieved From View
workflow graph bam-bedgraph-bigwig.cwl

Workflow converts input BAM file into bigWig and bedGraph files. Input BAM file should be sorted by coordinates (required by `bam_to_bedgraph` step). If `split` input is not provided use true by default. Default logic is implemented in `valueFrom` field of `split` input inside `bam_to_bedgraph` step to avoid possible bug in cwltool with setting default values for workflow inputs. `scale` has higher priority over the `mapped_reads_number`. The last one is used to calculate `-scale` parameter for `bedtools genomecov` (step `bam_to_bedgraph`) only in a case when input `scale` is not provided. All logic is implemented inside `bedtools-genomecov.cwl`. `bigwig_filename` defines the output name only for generated bigWig file. `bedgraph_filename` defines the output name for generated bedGraph file and can influence on generated bigWig filename in case when `bigwig_filename` is not provided. All workflow inputs and outputs don't have `format` field to avoid format incompatibility errors when workflow is used as subworkflow.

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

Path: tools/bam-bedgraph-bigwig.cwl

Branch/Commit ID: a8eaf61c809d76f55780b14f2febeb363cf6373f
workflow graph Cut-n-Run pipeline paired-end

Experimental pipeline for Cut-n-Run analysis. Uses mapping results from the following experiment types: - `chipseq-pe.cwl` - `trim-chipseq-pe.cwl` - `trim-atacseq-pe.cwl` Note, the upstream analyses should not have duplicates removed

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

Path: workflows/trim-chipseq-pe-cut-n-run.cwl

Branch/Commit ID: b1a5dabeeeb9079b30b2871edd9c9034a1e00c1c
workflow graph SoupX Estimate

SoupX Estimate ==============

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

Path: workflows/soupx.cwl

Branch/Commit ID: b1a5dabeeeb9079b30b2871edd9c9034a1e00c1c
workflow graph Build Bismark indices

Copy fasta_file file to the folder and run run bismark_genome_preparation script to prepare indices for Bismark Methylation Analysis. Bowtie2 aligner is used by default. The name of the output indices folder is equal to the genome input.

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

Path: workflows/bismark-index.cwl

Branch/Commit ID: 7fb8a1ebf8145791440bc2fed9c5f2d78a19d04c
workflow graph tt_fscr_calls_pass1

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

Path: task_types/tt_fscr_calls_pass1.cwl

Branch/Commit ID: 92118627c800e4addb7e29b9dabcca073a5bae71
workflow graph final_filtering

Final filtering

https://gitlab.bsc.es/lrodrig1/structuralvariants_poc.git

Path: structuralvariants/cwl/subworkflows/final_filtering.cwl

Branch/Commit ID: 32a040f94e9798bf91858da51598f0d68c35797d
workflow graph samtools_sort

https://gitlab.bsc.es/lrodrig1/structuralvariants_poc.git

Path: structuralvariants/cwl/subworkflows/samtools_sort.cwl

Branch/Commit ID: 32a040f94e9798bf91858da51598f0d68c35797d
workflow graph bam to trimmed fastqs and biscuit alignments

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

Path: definitions/subworkflows/bam_to_trimmed_fastq_and_biscuit_alignments.cwl

Branch/Commit ID: da335d9963418f7bedd84cb2791a0df1b3165ffe
workflow graph Cellranger Reanalyze

Cellranger Reanalyze ====================

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

Path: workflows/cellranger-reanalyze.cwl

Branch/Commit ID: 581156366f91861bd4dbb5bcb59f67d468b32af3
workflow graph Single-Cell Preprocessing Pipeline

Devel version of Single-Cell Preprocessing Pipeline ===================================================

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

Path: workflows/single-cell-preprocess.cwl

Branch/Commit ID: 581156366f91861bd4dbb5bcb59f67d468b32af3