Explore Workflows

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

Path: task_types/tt_kmer_top_n.cwl

Branch/Commit ID: 90a321ecf2d049330bcf0657cc4d764d2c3f42dd

Experimental pipeline for Cut-n-Run analysis. Uses mapping results from the following experiment types: - `chipseq-pe.cwl` - `trim-chipseq-pe.cwl` - `trim-atacseq-pe.cwl` Note, the upstream analyses should not have duplicates removed

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

Path: workflows/trim-chipseq-pe-cut-n-run.cwl

Branch/Commit ID: 9b4dc225c537685b9c9a32d931d3892d20953dd7

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

Path: task_types/tt_kmer_seq_entry_extract_wnode.cwl

Branch/Commit ID: 9e43bc5cff985574e1f8135d4c50b5a347517c9e

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

Path: task_types/tt_blastn_wnode.cwl

Branch/Commit ID: af468ae34c82dc88399aeedfd8f12f1e87052367

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

Path: task_types/tt_assm_assm_blastn_wnode.cwl

Branch/Commit ID: af468ae34c82dc88399aeedfd8f12f1e87052367

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

Path: definitions/pipelines/germline_exome.cwl

Branch/Commit ID: 67f56d3b9c70ad56019ed8aa8d50a128e02be43b

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

Path: definitions/pipelines/chipseq_alignment_mouse.cwl

Branch/Commit ID: 457e101e3fb87e7fd792357afce00ed8ccbfbcdb

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

Path: task_types/tt_extract_gencoll_ids.cwl

Branch/Commit ID: 54c5074587af001a44eccb4762a4cb25fa24cb3e

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. The pipeline was adapted for ATAC-Seq paired-end data analysis by updating genome coverage step. _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. To adapt the pipeline for ATAC-Seq data analysis we calculate genome coverage using only the first 9 bp from every read. 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-atacseq-pe.cwl

Branch/Commit ID: d6f58c383d0676269afb519399061191a1144a6a

https://github.com/common-workflow-language/cwl-v1.1.git

Path: tests/count-lines16-wf.cwl

Branch/Commit ID: 86c46cb397de029e4c91f02cca40fa2b54d22f37