Truwl

BETA

Workflows

  • hello world script with checker

    This demonstrates how to wrap a "real" tool with a checker workflow that runs both the tool and a tool that performs verification of results.

  • cat_sort.cwl

    A toy workflow used for testing. Concatenates two text files and sorts the combined file.

  • ATAC-seq pipeline

    The prototype ATAC-seq pipeline was developed by Anshul Kundaje's lab at Stanford University. Upon revision and full implementation, it will be a part of the ENCODE Uniform Processing Pipelines series. The full ATAC-seq pipeline code is available on Github. The ENCODE ATAC-seq pipeline is used for quality control and statistical signal processing of short-read sequencing data, producing alignments and measures of enrichment.

  • lrnaWorkflow.cwl

    ENCODE pipeline for paired-ended and stranded long RNA-seq data. RNA libraries generated from mRNAs (poly-A(+)), rRNA-depleted total RNA, or poly-A(-) populations that are size-selected to be longer than approximately 200 bp may be run through this pipeline. More information regarding references used for this pipeline and exogenous RNA spike-in controls are described in the pipelines overview document.

  • chip-seq pipeline2

    ENCODE defined analysis pipeline for ChIP-seq read mapping

  • ATAC-seq pipeline v2

    The prototype ATAC-seq pipeline was developed by Anshul Kundaje's lab at Stanford University. Upon revision and full implementation, it will be a part of the ENCODE Uniform Processing Pipelines series. The full ATAC-seq pipeline code is available on Github. The ENCODE ATAC-seq pipeline is used for quality control and statistical signal processing of short-read sequencing data, producing alignments and measures of enrichment. The pipeline shown here assumes the following defaults: align_only is false, pipeline_type is 'atac', all fastq and adapter files are defined in a single files, true_rep_only is false, disable_xcor is false, disable_ataqc is false, enable_idr is true (false is the default value, but set to true so all the possible steps are shown).

  • md5sum with checker workflow

    This demonstrates how to wrap a "real" tool with a checker workflow that runs both the tool and a tool that performs verification of results.