Explore Workflows

https://github.com/tmooney/cancer-genomics-workflow.git

Path: definitions/pipelines/somatic_exome_cle.cwl

Branch/Commit ID: 0db1a5f1ceedd4416ac550787c27b99c87dbe985

https://github.com/nal-i5k/organism_onboarding.git

Path: flow_create_genomics-workspace_yml/flow_create_yml/workflow.cwl

Branch/Commit ID: add45db6f08de518e224bdc3c04094fd69cad2d2

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: 3fc68366adb179927af5528c27b153abaf94494d

Workflow converts input BAM file into bigWig and bedGraph files

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

Path: subworkflows/bam-bedgraph-bigwig.cwl

Branch/Commit ID: 9ee330737f4603e4e959ffe786fbb2046db70a00

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

Path: bacterial_noncoding/wf_bacterial_noncoding.cwl

Branch/Commit ID: 369e2b6c7f4db75099d258729dec1326f55d2cc5

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

Path: tests/wf/1st-workflow.cwl

Branch/Commit ID: ec2cf2da6c31ffedf827a0fb213b5204e172f510

Workflow runs group-isoforms.cwl tool using scatter for isoforms_file input. genes_filename and common_tss_filename inputs are ignored.

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

Path: tools/group-isoforms-batch.cwl

Branch/Commit ID: 4dcc405133f22c63478b6091fb5f591b6be8950f

The original [BioWardrobe's](https://biowardrobe.com) [PubMed ID:26248465](https://www.ncbi.nlm.nih.gov/pubmed/26248465) **RNA-Seq** basic analysis for a **paired-end** experiment. A corresponded input [FASTQ](http://maq.sourceforge.net/fastq.shtml) file has to be provided. Current workflow should be used only with the paired-end RNA-Seq data. It performs the following steps: 1. Use STAR to align reads from input FASTQ files according to the predefined reference indices; generate unsorted BAM file and alignment statistics file 2. Use fastx_quality_stats to analyze input FASTQ files and generate quality statistics files 3. Use samtools sort to generate coordinate sorted BAM(+BAI) file pair from the unsorted BAM file obtained on the step 1 (after running STAR) 4. Generate BigWig file on the base of sorted BAM file 5. Map input FASTQ files to predefined rRNA reference indices using Bowtie to define the level of rRNA contamination; export resulted statistics to file 6. 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.cwl

Branch/Commit ID: a0b22644ca178b640fb74849d23b7c631022f0b5

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

Path: definitions/subworkflows/bam_to_trimmed_fastq_and_biscuit_alignments.cwl

Branch/Commit ID: e2a34d2b8c406db9aed8e49e8bdcf36f51444379

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

Path: definitions/subworkflows/qc_wgs.cwl

Branch/Commit ID: 44ada20f3eeb59005d5bd999d2435102e9bae991