Explore Workflows

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

Path: bacterial_kmer/wf_bacterial_kmer.cwl

Branch/Commit ID: test

https://github.com/mr-c/h3agatk.git

Path: workflows/GATK/GATK-Sub-Workflow-h3abionet-snp.cwl

Branch/Commit ID: cwl_v1_0

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/mr-c/datirium-workflows.git

Path: tools/bam-bedgraph-bigwig.cwl

Branch/Commit ID: license_test

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

Path: tests/sum-wf-noET.cwl

Branch/Commit ID: main

An example workflow created using Autosubmit's basic a000 workflow as reference. The `platform.yml` is ignored as it contains only information about platforms (e.g. it could be given to a tool like Troika as-is). `expdef.yml` and `autosubmit.yml` basically provide CWL inputs. `jobs.yml` contains the steps of the CWL workflow, with their dependencies. In CWL dependencies are specified via inputs and outputs. When task A outputs a value X, and task B has an input of type A/X, then the dependency A -> B is created in CWl. This is different than Autosubmit, and needs some care to guarantee the correct order in the workflow graph of start dates, members, chunks, etc.

https://github.com/kinow/kinoshita.eti.br.git

Path: notes/autosubmit/autosubmit.cwl

Branch/Commit ID: c3a46afaa5caa48b20882bdc7d5658d2dea935ee

https://github.com/fstrozzi/scalability-reproducibility-chapter.git

Path: CWL/workflow.cwl

Branch/Commit ID: master

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

Path: tests/wf/js_output_workflow.cwl

Branch/Commit ID: 766d58b47180d92618074679eb9f3c6c30acf638

https://github.com/andurill/ACCESS-Pipeline.git

Path: workflows/marianas/collapsed_fastq_to_bam.cwl

Branch/Commit ID: 0.0.33_dmp

https://github.com/lux563624348/WDL-HuBMAP-salmon-rnaseq.git

Path: pipeline_cavatica.cwl

Branch/Commit ID: main

Whole Exome Sequence analysis using GATK4 - v2.2.0

https://github.com/bespin-workflows/exomeseq-gatk4.git

Path: exomeseq-gatk4.cwl

Branch/Commit ID: develop