Explore Workflows

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: 2d54a7edc45b7dfbee41ecef200a634fd0cd5e97

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

Path: workflows/bamfastq_align/extract_readgroups_bam.cwl

Branch/Commit ID: 20a901f44c9fb0e6f4ee3c40ec33fa4b1c8ef005

Mark duplicates

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

Path: structuralvariants/cwl/abstract_operations/subworkflows/picard_markduplicates.cwl

Branch/Commit ID: f4c51a054b1ec51d07d89c6a8218e610653675f3

FastQC - a quality control tool for high throughput sequence data ===================================== FastQC aims to provide a simple way to do some quality control checks on raw sequence data coming from high throughput sequencing pipelines. It provides a modular set of analyses which you can use to give a quick impression of whether your data has any problems of which you should be aware before doing any further analysis. The main functions of FastQC are: - Import of data from FastQ files (any variant) - Providing a quick overview to tell you in which areas there may be problems - Summary graphs and tables to quickly assess your data - Export of results to an HTML based permanent report - Offline operation to allow automated generation of reports without running the interactive application

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

Path: workflows/fastqc.cwl

Branch/Commit ID: 2caa50434966ebdf4b33e5ca689c2e4df32f9058

https://github.com/common-workflow-language/cwl-v1.2.git

Path: tests/count-lines3-wf.cwl

Branch/Commit ID: ad91c844b5adfef514c059af364e20afc935e598

https://github.com/uc-cdis/genomel_pipelines.git

Path: genomel/cwl/workflows/utils/duplicated_readgroup_fix.cwl

Branch/Commit ID: 13c106834d6c9031de08496faeff521740a0c95f

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

Path: definitions/subworkflows/qc_wgs_nonhuman.cwl

Branch/Commit ID: 0d2f354af9192a56af258a7d2426c7c160f4ec1a

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

Path: tests/wf/wffail.cwl

Branch/Commit ID: fd6e054510e2bb65eed4069a3a88013d7ecbb99c

CNV ExomeDepth calling

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

Path: structuralvariants/cwl/subworkflows/cnv_exome_depth.cwl

Branch/Commit ID: 93fbc4e51770d953fc44104a7b09436f75719470

https://github.com/apaul7/cancer-genomics-workflow.git

Path: definitions/subworkflows/vcf_readcount_annotator.cwl

Branch/Commit ID: bfcb5ffbea3d00a38cc03595d41e53ea976d599d