Explore Workflows

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

Path: definitions/subworkflows/sv_depth_caller_filter.cwl

Branch/Commit ID: 1750cd5cc653f058f521b6195e3bec1e7df1a086

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

Path: task_types/tt_kmer_cache_store.cwl

Branch/Commit ID: 9ff3e17888a15f4691ba82380472317214e20a1c

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

Path: cwltool/schemas/v1.0/v1.0/count-lines5-wf.cwl

Branch/Commit ID: 3e9bca4e006eae7e9febd76eb9b8292702eba2cb

abundace profiles from annotated files, for protein and/or rna

https://github.com/MG-RAST/pipeline.git

Path: CWL/Workflows/abundance-clca.workflow.cwl

Branch/Commit ID: 662d424d2e433e636f46a79025325d5daaca6271

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

Path: definitions/subworkflows/phase_vcf.cwl

Branch/Commit ID: a7838a5ca72b25db5c2af20a15f34303a839980e

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

Path: task_types/tt_kmer_build_tree.cwl

Branch/Commit ID: bba6c580ab88e077f6aa2c2ee7c73159f3f9156e

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

Path: task_types/tt_format_rrnas_from_seq_entry.cwl

Branch/Commit ID: 449f87c8365637e803ba66f83367e96f98c88f5c

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. A [FASTQ](http://maq.sourceforge.net/fastq.shtml) input file has to be provided. The pipeline produces a sorted BAM file alongside with index BAI file, quality statistics of the input FASTQ file, coverage by estimated fragments as a 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. Workflow starts with step *fastx\_quality\_stats* from FASTX-Toolkit to calculate quality statistics for input FASTQ file. At the same time `bowtie` is used to align reads from input FASTQ file to reference genome *bowtie\_aligner*. The output of this step is an unsorted SAM file which is being sorted and indexed by `samtools sort` and `samtools index` *samtools\_sort\_index*. Depending on workflow’s input parameters indexed and sorted BAM file can be processed by `samtools rmdup` *samtools\_rmdup* to get rid of duplicated reads. If removing duplicates is not required the original BAM and BAI files are returned. Otherwise step *samtools\_sort\_index\_after\_rmdup* repeat `samtools sort` and `samtools index` with BAM and BAI files without duplicates. Next `macs2 callpeak` performs peak calling *macs2\_callpeak* and the next step reports *macs2\_island\_count* the number of islands and estimated fragment size. If the latter is less that 80bp (hardcoded in the workflow) `macs2 callpeak` is rerun again with forced fixed fragment size value (*macs2\_callpeak\_forced*). It is also possible to force MACS2 to use pre set fragment size in the first place. Next 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 (*bamtools\_stats* and *bam\_to\_bigwig*) are used to calculate coverage from BAM file and save it in BigWig format. For that purpose bamtools stats returns the number of mapped reads which is then used as scaling factor by bedtools genomecov when it performs coverage calculation and saves it as a BEDgraph file whichis then 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 nearest 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 from the BAM file.

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

Path: workflows/chipseq-pe.cwl

Branch/Commit ID: 12c29f88855329192bfff977f046990031f04931

https://github.com/hubmapconsortium/spatial-transcriptomics-pipeline.git

Path: steps/spaceTxConversion.cwl

Branch/Commit ID: 03b8da4ede3afcbf97b4e780c153155f33e76c84

https://github.com/mskcc/roslin-variant.git

Path: setup/cwl/conpair/0.2/conpair-master.cwl

Branch/Commit ID: f3f070b4c0cce2cbcdab78c10f2f88abfb78586a