Workflows

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738 Workflows visible to you, out of a total of 793
Metabolome Annotation Workflow (MAW)
Stable

This repository hosts Metabolome Annotation Workflow (MAW). The workflow takes MS2 .mzML format data files as an input in R. It performs spectral database dereplication using R Package Spectra and compound database dereplication using SIRIUS OR MetFrag . Final candidate selection is done in Python using RDKit and PubChemPy.

Type: Common Workflow Language

Creators: Mahnoor Zulfiqar, Michael R. Crusoe, Luiz Gadelha, Christoph Steinbeck, Maria Sorokina, Kristian Peters

Submitter: Mahnoor Zulfiqar

DOI: 10.48546/workflowhub.workflow.510.2

ARA (Automated Record Analysis)
Stable

ARA (Automated Record Analysis) : An automatic pipeline for exploration of SRA datasets with sequences as a query

Requirements

or

  • Mamba package manager

  • Please checkout the mamba or micromamba official installation guide.

  • We prefer mamba over conda since it is faster and uses ...

Type: Perl

Creators: Anand Maurya, Maciej Szymanski, Wojciech Karlowski

Submitter: Anand Maurya

DOI: 10.48546/workflowhub.workflow.546.1

Timing of spring events changes under modelled future climate scenarios in a mesotrophic lake
Stable

Simulations and figures supporting the manuscript "Timing of spring events changes under modelled future climate scenarios in a mesotrophic lake"

Type: Unrecognized workflow type

Creators: Jorrit Mesman, Inmaculada Jiménez-Navarro, Ana Ayala, Javier Senent-Aparicio, Dennis Trolle, Don Pierson

Submitter: Jorrit Mesman

DOI: 10.48546/workflowhub.workflow.511.5

Sample workflow that combines simulations with data analytics.
Stable

Sample workflow template that combines simulations with data analytics. It is not a real workflow, but it mimics this type of workflows. It illustrates how COMPSs invokes binaries. It can be extended to invoke MPI applications.

Type: COMPSs

Creators: Rosa M Badia, Javier Conejero

Submitter: Rosa M Badia

DOI: 10.48546/workflowhub.workflow.541.1

BackTrackBB: Multi-band array detection and location of seismic sources
Stable

BackTrackBB is a program for detection and space-time location of seismic sources based on multi-scale, frequency-selective statistical coherence of the wave field recorded by dense large-scale seismic networks and local antennas. The method is designed to enhance coherence of the signal statistical features across the array of sensors and consists of three steps. They are signal processing, space-time imaging and detection and location.

Source with inputs and outputs included (too big for ...

Type: COMPSs

Creators: Natalia Poiata, Claudio Satriano, Javier Conejero

Submitter: Raül Sirvent

DOI: 10.48546/workflowhub.workflow.386.2

prepareChIPs:
Work-in-progress

prepareChIPs

This is a simple snakemake workflow template for preparing single-end ChIP-Seq data. The steps implemented are:

  1. Download raw fastq files from SRA
  2. Trim and Filter raw fastq files using AdapterRemoval
  3. Align to the supplied genome using bowtie2
  4. Deduplicate Alignments using Picard MarkDuplicates
  5. Call Macs2 Peaks using macs2

A pdf of the rulegraph is available here

Full details for each step are given below. Any additional ...

Type: Snakemake

Creator: Stevie Pederson

Submitter: Stevie Pederson

DOI: 10.48546/workflowhub.workflow.528.1

BatchConvert
Work-in-progress

BatchConvert DOI:10.5281

A command line tool for converting image data into either of the standard file formats OME-TIFF or OME-Zarr.

The tool wraps the dedicated file converters bfconvert and bioformats2raw to convert into OME-TIFF or OME-Zarr, respectively. The workflow management system NextFlow is used to perform conversion in parallel for batches of images.

The tool also wraps s3 and Aspera clients (go-mc and aspera-cli, respectively). ...

Type: Nextflow

Creator: Bugra Oezdemir

Submitter: bugra oezdemir

DOI: 10.48546/workflowhub.workflow.453.3

CWL-based (single-sample) workflow for germline variant calling
Stable

A CWL-based pipeline for calling small germline variants, namely SNPs and small INDELs, by processing data from Whole-genome Sequencing (WGS) or Targeted Sequencing (e.g., Whole-exome sequencing; WES) experiments.

On the respective GitHub folder are available:

  • The CWL wrappers and subworkflows for the workflow
  • A pre-configured YAML template, based on validation analysis of publicly available HTS data

Briefly, the workflow performs the following steps:

  1. Quality control of Illumina reads ...

Type: Common Workflow Language

Creators: Konstantinos Kyritsis, Nikolaos Pechlivanis, Fotis Psomopoulos

Submitter: Konstantinos Kyritsis

DOI: 10.48546/workflowhub.workflow.527.1

CWL-based (multi-sample) workflow for germline variant calling
Stable

A CWL-based pipeline for calling small germline variants, namely SNPs and small INDELs, by processing data from Whole-genome Sequencing (WGS) or Targeted Sequencing (e.g., Whole-exome sequencing; WES) experiments.

On the respective GitHub folder are available:

  • The CWL wrappers and subworkflows for the workflow
  • A pre-configured YAML template, based on validation analysis of publicly available HTS data

Briefly, the workflow performs the following steps:

  1. Quality control of Illumina reads ...

Type: Common Workflow Language

Creators: Konstantinos Kyritsis, Nikolaos Pechlivanis, Fotis Psomopoulos

Submitter: Konstantinos Kyritsis

DOI: 10.48546/workflowhub.workflow.526.1

CWL-based ChIP-Seq workflow
Stable

A CWL-based pipeline for processing ChIP-Seq data (FASTQ format) and performing:

  • Peak calling
  • Consensus peak count table generation
  • Detection of super-enhancer regions
  • Differential binding analysis

On the respective GitHub folder are available:

  • The CWL wrappers for the workflow
  • A pre-configured YAML template, based on validation analysis of publicly available HTS data
  • Tables of metadata (EZH2_metadata_CLL.csv and H3K27me3_metadata_CLL.csv), based on the same validation ...

Type: Common Workflow Language

Creators: Konstantinos Kyritsis, Nikolaos Pechlivanis, Fotis Psomopoulos

Submitter: Konstantinos Kyritsis

DOI: 10.48546/workflowhub.workflow.525.1

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