Explore Workflows

1. Convert input SRA file into FASTQ file (run fastq-dump) 2. Analyze quality of FASTQ file (run fastqc) 3. If any of the following fields in fastqc generated report is marked as failed: \"Per base sequence quality\", \"Per sequence quality scores\", \"Overrepresented sequences\", \"Adapter Content\", - trim adapters (run trimmomatic) 4. Align original or trimmed FASTQ file to reference genome (run Bowtie2) 5. Sort and index generated by Bowtie2 BAM file (run samtools sort, samtools index) 6. Remove duplicates in sorted BAM file (run picard) 7. Sort and index BAM file after duplicates removing (run samtools sort, samtools index) 8. Count mapped reads number in sorted BAM file (run bamtools stats) 9. Generate genome coverage BED file (run bedtools genomecov) 10. Sort genearted BED file (run sort) 11. Generate genome coverage bigWig file from BED file (run bedGraphToBigWig)

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

Path: workflows/xenbase-chipseq-se.cwl

Branch/Commit ID: 9ee330737f4603e4e959ffe786fbb2046db70a00

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

Path: task_types/tt_kmer_compare_wnode.cwl

Branch/Commit ID: b4a6e46405c08e0b14ad92f0ab38bcc4a69caa5c

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

Path: cwltool/schemas/v1.0/v1.0/js-expr-req-wf.cwl

Branch/Commit ID: 2256a30d0c1365b30e0a7338fb883c74674fcd25

Packed ID: wf

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

Path: testdata/step-valuefrom2-wf_v1_2.cwl

Branch/Commit ID: e78db9870cb744fe36674f43b3223c688e9989e1

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

Path: task_types/tt_cache_asnb_entries.cwl

Branch/Commit ID: e9cc6de8cd1e00345969c646e5e6f27d7d10420f

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: 211ded59fb0c05ff0a5eb4b56c5cb5addf56d8b7

Principal Component Analysis --------------- Principal component analysis (PCA) is a statistical procedure that uses an orthogonal transformation to convert a set of observations of possibly correlated variables (entities each of which takes on various numerical values) into a set of values of linearly uncorrelated variables called principal components. The calculation is done by a singular value decomposition of the (centered and possibly scaled) data matrix, not by using eigen on the covariance matrix. This is generally the preferred method for numerical accuracy.

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

Path: workflows/pca.cwl

Branch/Commit ID: 30031ca5e69cec603c4733681de54dc7bffa20a3

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

Path: tests/count-lines16-wf.cwl

Branch/Commit ID: e62f99dd79d6cb9c157cceb458f74200da84f6e9

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

Path: tests/count-lines12-wf.cwl

Branch/Commit ID: e62f99dd79d6cb9c157cceb458f74200da84f6e9

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

Path: cwltool/schemas/v1.0/v1.0/count-lines10-wf.cwl

Branch/Commit ID: 2256a30d0c1365b30e0a7338fb883c74674fcd25