Explore Workflows

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

Path: genomel/cwl/workflows/harmonization/alignment_prep.cwl

Branch/Commit ID: 13c106834d6c9031de08496faeff521740a0c95f

https://github.com/chgarth/cwl-openfoam.git

Path: cwl/fortunecow.cwl

Branch/Commit ID: 2fbe585034c501b7cc8a20ad495d8eeb86b7ba3d

https://github.com/EBI-Metagenomics/pipeline-v5.git

Path: workflows/subworkflows/final_chunking.cwl

Branch/Commit ID: a83ee883bb3c7480010fa952939fac771491ddf4

https://github.com/EBI-Metagenomics/pipeline-v5.git

Path: workflows/subworkflows/assembly/CGC-subwf.cwl

Branch/Commit ID: a83ee883bb3c7480010fa952939fac771491ddf4

https://github.com/EBI-Metagenomics/pipeline-v5.git

Path: workflows/subworkflows/other_ncrnas.cwl

Branch/Commit ID: a83ee883bb3c7480010fa952939fac771491ddf4

Workflow for genome annotation from EMBL format

https://git.wageningenur.nl/unlock/cwl.git

Path: cwl/workflows/workflow_sapp_microbes.cwl

Branch/Commit ID: b9097b82e6ab6f2c9496013ce4dd6877092956a0

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: 1a46cb0e8f973481fe5ae3ae6188a41622c8532e

Wrapper to run bam indexing on all bams before submitting for samples fillout Also includes steps to pre-filter some maf input files NOTE: each sample in a sample_group must have a .bam file, and there must be a minumum of 1 .maf file amoungst samples in the same sample_group this means that for each sample in the sample_group, a .bam is required but a .maf is optional as long as one sample in the group has a .maf this also means that singleton sample groups, or a sample group with only one sample, MUST include a .maf file; singletons cannot lack a .maf NOTE: all .maf files must be valid, at a minimum they must have a header and at least one variant if a sample has no variants in its .maf file, or has an empty .maf file, then it should NOT have a maf_file entry associated with it

https://github.com/mskcc/pluto-cwl.git

Path: cwl/samples_fillout_index_batch_workflow.cwl

Branch/Commit ID: 59b69eed7ffefcffd81313ec8ffb84c0d716b933

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

Path: progs/protein_extract.cwl

Branch/Commit ID: c7c674b873b9925b28ffbd602974eec4bfe78cf9

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

Path: task_types/tt_blastp_wnode_struct.cwl

Branch/Commit ID: c009eeba7379efbbd37b8d5013a83f161f06939b