Explore Workflows

Remove sequences which align against a reference set using bowtie2. The references are preformatted (index files)

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

Path: CWL/Workflows/organism-screening.workflow.cwl

Branch/Commit ID: d9cf22cd615542c94f7974e8bce4cf29b24d985f

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: d9cf22cd615542c94f7974e8bce4cf29b24d985f

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

Path: tests/count-lines11-null-step-wf-noET.cwl

Branch/Commit ID: 707ebcd2173889604459c5f4ffb55173c508abb3

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. 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-se.cwl

Branch/Commit ID: bfa3843bcf36125ff258d6314f64b41336f06e6b

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

Path: protein_alignment/wf_seed_1.cwl

Branch/Commit ID: 656113dcac0de7cef6cff6c688f61441ee05872a

Allele specific RNA-Seq (using vcf) single-read workflow

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

Path: workflows/allele-vcf-rnaseq-se.cwl

Branch/Commit ID: b141f7e73005227d6d02fa03a47151836dd4109b

Pairwise genomic regions intersection ============================================= Overlaps peaks from two ChIP/ATAC experiments

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

Path: workflows/peak-intersect.cwl

Branch/Commit ID: 57437c1e9f881411b65f79acd64b7cf14df5b901

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

Path: tests/wf-loadContents4.cwl

Branch/Commit ID: a5073143db4155e05df8d2e7eb59d9e62acd65a5

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

Path: definitions/subworkflows/gatk_haplotypecaller_iterator.cwl

Branch/Commit ID: 6949082038c1ad36d6e9848b97a2537aef2d3805

Workflow runs homer-make-tag-directory.cwl tool using scatter for the following inputs - bam_file - fragment_size - total_reads `dotproduct` is used as a `scatterMethod`, so one element will be taken from each array to construct each job: 1) bam_file[0] fragment_size[0] total_reads[0] 2) bam_file[1] fragment_size[1] total_reads[1] ... N) bam_file[N] fragment_size[N] total_reads[N] `bam_file`, `fragment_size` and `total_reads` arrays should have the identical order.

https://github.com/Barski-lab/workflows.git

Path: subworkflows/heatmap-prepare.cwl

Branch/Commit ID: 915ea871cc28f7b666a4d7b476fdaa7b454ce7c3