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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/Barski-lab/workflows.git

Path: tools/bam-bedgraph-bigwig.cwl

Branch/Commit ID: c82a2e766abba032f0bbe2aa76e0176e69064569
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: e668f9c4047f1971ae53040a5af3eccc4bfc3c53
workflow graph maf2vcf_gz_workflow.cwl

Workflow to convert a maf file into a vcf.gz with .tbi index

https://github.com/mskcc/pluto-cwl.git

Path: cwl/maf2vcf_gz_workflow.cwl

Branch/Commit ID: 462f6015c9268a4205b6e81de018a470b8a4a153
workflow graph blastp_wnode_naming

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

Path: task_types/tt_blastp_wnode_naming.cwl

Branch/Commit ID: e668f9c4047f1971ae53040a5af3eccc4bfc3c53
workflow graph RNA-seq alelle specific pipeline for single-read data

Allele specific RNA-Seq single-read workflow

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

Path: workflows/allele-rnaseq-se.cwl

Branch/Commit ID: 4106b7dc96e968db291b7a61ecd1641aa3b3dd6d
workflow graph samples_fillout_workflow.cwl

https://github.com/mskcc/pluto-cwl.git

Path: cwl/samples_fillout_workflow.cwl

Branch/Commit ID: 462f6015c9268a4205b6e81de018a470b8a4a153
workflow graph trim-chipseq-pe.cwl

Runs ChIP-Seq BioWardrobe basic analysis with paired-end input data files.

https://github.com/Barski-lab/workflows.git

Path: workflows/trim-chipseq-pe.cwl

Branch/Commit ID: c82a2e766abba032f0bbe2aa76e0176e69064569
workflow graph RNA-Seq pipeline paired-end stranded mitochondrial

Slightly changed original [BioWardrobe's](https://biowardrobe.com) [PubMed ID:26248465](https://www.ncbi.nlm.nih.gov/pubmed/26248465) **RNA-Seq** basic analysis for **strand specific pair-end** experiment. An additional steps were added to map data to mitochondrial chromosome only and then merge the output. Experiment files in [FASTQ](http://maq.sourceforge.net/fastq.shtml) format either compressed or not can be used. Current workflow should be used only with the pair-end strand specific RNA-Seq data. It performs the following steps: 1. `STAR` to align reads from input FASTQ file according to the predefined reference indices; generate unsorted BAM file and alignment statistics file 2. `fastx_quality_stats` to analyze input FASTQ file and generate quality statistics file 3. `samtools sort` to generate coordinate sorted BAM(+BAI) file pair from the unsorted BAM file obtained on the step 1 (after running STAR) 5. Generate BigWig file on the base of sorted BAM file 6. Map input FASTQ file to predefined rRNA reference indices using Bowtie to define the level of rRNA contamination; export resulted statistics to file 7. Calculate isoform expression level for the sorted BAM file and GTF/TAB annotation file using `GEEP` reads-counting utility; export results to file

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

Path: workflows/rnaseq-pe-dutp-mitochondrial.cwl

Branch/Commit ID: 36fd18f11e939d3908b1eca8d2939402f7a99b0f
workflow graph mut3.cwl

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

Path: tests/wf/mut3.cwl

Branch/Commit ID: 9a8e654a91ea5d26e8452dd1cecf3faf22b7a12e
workflow graph WGS QC workflow

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

Path: definitions/subworkflows/qc_wgs.cwl

Branch/Commit ID: 735be84cdea041fcc8bd8cbe5728b29ca3586a21