Explore Workflows

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

Path: testdata/workflow_input_sf_expr_v1_2.cwl

Branch/Commit ID: 124a08ce3389eb49066c34a4163cbbed210a0355

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: 7ced5a5259dbd8b3fc64456beaeffd44f4a24081

The original [BioWardrobe's](https://biowardrobe.com) [PubMed ID:26248465](https://www.ncbi.nlm.nih.gov/pubmed/26248465) **ChIP-Seq** basic analysis workflow for a **paired-end** experiment with Trim Galore. _Trim Galore_ is a wrapper around [Cutadapt](https://github.com/marcelm/cutadapt) and [FastQC](http://www.bioinformatics.babraham.ac.uk/projects/fastqc/) to consistently apply adapter and quality trimming to FastQ files, with extra functionality for RRBS data. A [FASTQ](http://maq.sourceforge.net/fastq.shtml) input file has to be provided. In outputs it returns coordinate sorted BAM file alongside with index BAI file, quality statistics for both the input FASTQ files, reads coverage in a form of BigWig file, peaks calling data in a form of narrowPeak or broadPeak files, islands with the assigned nearest genes and region type, data for average tag density plot (on the base of BAM file). Workflow starts with running fastx_quality_stats (steps fastx_quality_stats_upstream and fastx_quality_stats_downstream) from FASTX-Toolkit to calculate quality statistics for both upstream and downstream input FASTQ files. At the same time Bowtie is used to align reads from input FASTQ files to reference genome (Step bowtie_aligner). The output of this step is unsorted SAM file which is being sorted and indexed by samtools sort and samtools index (Step samtools_sort_index). Depending on workflow’s input parameters indexed and sorted BAM file could be processed by samtools rmdup (Step samtools_rmdup) to remove all possible read duplicates. In a case when removing duplicates is not necessary the step returns original input BAM and BAI files without any processing. If the duplicates were removed the following step (Step samtools_sort_index_after_rmdup) reruns samtools sort and samtools index with BAM and BAI files, if not - the step returns original unchanged input files. Right after that macs2 callpeak performs peak calling (Step macs2_callpeak). On the base of returned outputs the next step (Step macs2_island_count) calculates the number of islands and estimated fragment size. If the last one is less that 80 (hardcoded in a workflow) macs2 callpeak is rerun again with forced fixed fragment size value (Step macs2_callpeak_forced). If at the very beginning it was set in workflow input parameters to force run peak calling with fixed fragment size, this step is skipped and the original peak calling results are saved. In the next step workflow again calculates the number of islands and estimated fragment size (Step macs2_island_count_forced) for the data obtained from macs2_callpeak_forced step. If the last one was skipped the results from macs2_island_count_forced step are equal to the ones obtained from macs2_island_count step. Next step (Step macs2_stat) is used to define which of the islands and estimated fragment size should be used in workflow output: either from macs2_island_count step or from macs2_island_count_forced step. If input trigger of this step is set to True it means that macs2_callpeak_forced step was run and it returned different from macs2_callpeak step results, so macs2_stat step should return [fragments_new, fragments_old, islands_new], if trigger is False the step returns [fragments_old, fragments_old, islands_old], where sufix \"old\" defines results obtained from macs2_island_count step and sufix \"new\" - from macs2_island_count_forced step. The following two steps (Step bamtools_stats and bam_to_bigwig) are used to calculate coverage on the base of input BAM file and save it in BigWig format. For that purpose bamtools stats returns the number of mapped reads number which is then used as scaling factor by bedtools genomecov when it performs coverage calculation and saves it in BED format. The last one is then being sorted and converted to BigWig format by bedGraphToBigWig tool from UCSC utilities. Step get_stat is used to return a text file with statistics in a form of [TOTAL, ALIGNED, SUPRESSED, USED] reads count. Step island_intersect assigns genes and regions to the islands obtained from macs2_callpeak_forced. Step average_tag_density is used to calculate data for average tag density plot on the base of BAM file.

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

Path: workflows/trim-chipseq-pe.cwl

Branch/Commit ID: 4a80f5b8f86c83af39494ecc309b789aeda77964

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

Path: definitions/pipelines/gathered_cle_aml_trio.cwl

Branch/Commit ID: a93be3183c2218ee50f13ae2675dd1cde563fdbc

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

Path: tests/scatter-valuefrom-wf1.cwl

Branch/Commit ID: 1f3ef888d9ef2306c828065c460c1800604f0de4

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

Path: tests/record-output-wf.cwl

Branch/Commit ID: 1f3ef888d9ef2306c828065c460c1800604f0de4

https://github.com/PNNL-CompBio/decomprolute.git

Path: localData/05-plot-immune-figs.cwl

Branch/Commit ID: 6351764c74a44fc4fa2042d31c0cedde5a5bdbe9

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

Path: cwltool/schemas/v1.0/v1.0/search.cwl

Branch/Commit ID: 203797516329f7fb8aa5e763e6f9b331c63c3060

Packed ID: main

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

Path: definitions/subworkflows/pindel.cwl

Branch/Commit ID: b7d9ace34664d3cedb16f2512c8a6dc6debfc8ca

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

Path: definitions/subworkflows/molecular_qc.cwl

Branch/Commit ID: 72c4c3115956340f35e72cda1fd46ec276f1ca03