Explore Workflows

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Graph	Name	Retrieved From	View
	kmer_cache_retrieve	https://github.com/ncbi/pgap.git Path: task_types/tt_kmer_cache_retrieve.cwl Branch/Commit ID: 41d14ec5e2dfa0fac7eebeefda1f26ccea14c9a0
	align_merge_sas	https://github.com/ncbi/pgap.git Path: task_types/tt_align_merge_sas.cwl Branch/Commit ID: da35c7b700912dd3643e3dd2c5c96b7be3a4edad
	ChIP-Seq pipeline paired-end 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: 4a5c59829ff8b9f3c843e66e3c675dcd9c689ed5
	gcaccess_from_list	https://github.com/ncbi/pgap.git Path: task_types/tt_gcaccess_from_list.cwl Branch/Commit ID: 90a321ecf2d049330bcf0657cc4d764d2c3f42dd
	ani_top_n	https://github.com/ncbi/pgap.git Path: task_types/tt_ani_top_n.cwl Branch/Commit ID: 4def84df33963fc9ac9d5c5f804b911d01a0d9ad
	Exome QC workflow	https://github.com/genome/analysis-workflows.git Path: definitions/subworkflows/qc_exome.cwl Branch/Commit ID: 889a077a20c0fdb01f4ed97aa4bc40f920c37a1a
	EMG pipeline v3.0 (paired end version)	https://github.com/ProteinsWebTeam/ebi-metagenomics-cwl.git Path: workflows/emg-pipeline-v3-paired.cwl Branch/Commit ID: 9c57dba558a4e04a1884eae1df8431dcaccafc1e
	harmonization_bwa_mem_no_trim.cwl	https://github.com/uc-cdis/genomel_pipelines.git Path: genomel/cwl/workflows/harmonization/harmonization_bwa_mem_no_trim.cwl Branch/Commit ID: 7eb6b9f75db20866611a3bc55bee28746e84c1b6
	revsort.cwl Reverse the lines in a document, then sort those lines.	https://github.com/common-workflow-language/cwltool.git Path: tests/wf/revsort.cwl Branch/Commit ID: 4635090ef98247b1902b3c7a25c007d9db1cb883
	WGS QC workflow	https://github.com/genome/analysis-workflows.git Path: definitions/subworkflows/qc_wgs.cwl Branch/Commit ID: 1249b5d4e23d57ca5e3b8ad6d8e5f10ddb019f68