Explore Workflows

Reverse the lines in a document, then sort those lines.

https://github.com/Duke-GCB/calrissian.git

Path: input-data/revsort-single-no-docker.cwl

Branch/Commit ID: ceb1c2731dd4c3c20229a5cad06a64a487103c21

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

Path: task_types/tt_kmer_top_n_extract.cwl

Branch/Commit ID: ac387721a55fd91df3dcdf16e199354618b136d1

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

Path: testdata/record-output-wf_v1_0.cwl

Branch/Commit ID: e949503ac0dd7e22ba9b04ac51926d13780f9cee

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 **single-read** 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. In outputs it returns coordinate sorted BAM file alongside with index BAI file, quality statistics of the input FASTQ file, 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 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 unsorted SAM file which is being sorted and indexed by `samtools sort` and `samtools index` *samtools\_sort\_index*. Based 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 input BAM and BAI files return. Otherwise step *samtools\_sort\_index\_after\_rmdup* repeat `samtools sort` and `samtools index` with BAM and BAI files. Right after that `macs2 callpeak` performs peak calling *macs2\_callpeak*. On the base of returned outputs the next step *macs2\_island\_count* calculates the number of islands and estimated fragment size. If the last one is less that 80bp (hardcoded in the workflow) `macs2 callpeak` is rerun again with forced fixed fragment size value (*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 estimates fragment size (*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 (*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 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-se.cwl

Branch/Commit ID: ddc35c559d1ac6aab4972fe1a2b63300c4373f54

https://github.com/bcbio/bcbio_validation_workflows.git

Path: NA12878-chr20/NA12878-platinum-chr20-workflow/wf-variantcall.cwl

Branch/Commit ID: c4592973b1580e3ff44cb697f64b12345b91e6f5

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

Path: definitions/subworkflows/pindel_cat.cwl

Branch/Commit ID: c6bbd4cdd612b3b5cc6e9000df4800c21e192bf5

Perform pairwise alignment of protein sequences for pairs identified by structural similarity search. retrieve sequence from blastdbcmd result makeblastdb: ../Tools/14_makeblastdb.cwl blastdbcmd: ../Tools/15_blastdbcmd.cwl seqretsplit: ../Tools/16_seqretsplit.cwl needle (Global alignment): ../Tools/17_needle.cwl water (Local alignment): ../Tools/17_water.cwl

https://github.com/yonesora56/plant2human.git

Path: Workflow/11_retrieve_sequence_wf.cwl

Branch/Commit ID: 1d9df140de0ffc7d22b6d151b98b59de162e7c37

https://github.com/d3b-center/canine-dev.git

Path: subworkflows/canine_vep_module.cwl

Branch/Commit ID: 7da5645975f5712362cce7908d2ab138e05876fb

https://github.com/tmooney/cancer-genomics-workflow.git

Path: definitions/pipelines/somatic_exome_cle_gathered.cwl

Branch/Commit ID: 0db1a5f1ceedd4416ac550787c27b99c87dbe985

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

Path: tests/wf/mut2.cwl

Branch/Commit ID: 63f539ba60e91f0cb3ce7cda2c5da5c65525c375