Workflows

What is a Workflow?
537 Workflows visible to you, out of a total of 579
Stable

Cite with Zenodo Nextflow run with conda run with docker ...

Type: Nextflow

Creators: Damon-Lee Pointon, William Eagles, Ying Sims

Submitter: Damon-Lee Pointon

COVID-19: variation analysis on ARTIC PE data

The workflow for Illumina-sequenced ampliconic data builds on the RNASeq workflow for paired-end data using the same steps for mapping and variant calling, but adds extra logic for trimming amplicon primer sequences off reads with the ivar package. In addition, this workflow uses ivar also to identify amplicons affected by primer-binding site mutations and, if possible, excludes reads derived from such ...

No description specified

Type: Galaxy

Creators: None

Submitter: Markus Konkol

Stable

Calculates the Fibonacci series up to a specified length.

Type: COMPSs

Creator: Uploading this Workflow under the guidance of Raül Sirvent.

Submitter: Ashish Bhawel

Contiging Solo w/HiC:

Generate phased assembly based on PacBio Hifi Reads using HiC data from the same individual for phasing.

Inputs

  1. Hifi long reads [fastq]
  2. HiC forward reads (if multiple input files, concatenated in same order as reverse reads) [fastq]
  3. HiC reverse reads (if multiple input files, concatenated in same order as forward reads) [fastq]
  4. K-mer database [meryldb]
  5. Genome profile summary generated by Genomescope [txt]
  6. Name of first assembly
  7. Name of second ...

Type: Galaxy

Creator: Galaxy, VGP

Submitter: WorkflowHub Bot

Scaffolding using HiC data with YAHS.

Type: Galaxy

Creator: VGP, Galaxy

Submitter: WorkflowHub Bot

Purge contigs marked as duplicates by purge_dups (could be haplotypic duplication or overlap duplication). This workflow is the 6th workflow of the VGP pipeline. It is meant to be run after one of the contigging steps (Workflow 3, 4, or 5)

Type: Galaxy

Creator: Galaxy, VGP

Submitter: WorkflowHub Bot

Assembly with Hifi reads and Trio Data

Generate phased assembly based on PacBio Hifi Reads using parental Illumina data for phasing

Inputs

  1. Hifi long reads [fastq]
  2. Concatenated Illumina reads : Paternal [fastq]
  3. Concatenated Illumina reads : Maternal [fastq]
  4. K-mer database [meryldb]
  5. Paternal hapmer database [meryldb]
  6. Maternal hapmer database [meryldb]
  7. Genome profile summary generated by Genomescope [txt]
  8. Bloom Filter
  9. Name of first haplotype
  10. Name of second haplotype ...

Type: Galaxy

Creator: Galaxy, VGP

Submitter: WorkflowHub Bot

Purge Duplicate Contigs

Purge contigs marked as duplicates by purge_dups in a single haplotype(could be haplotypic duplication or overlap duplication) This workflow is the 6th workflow of the VGP pipeline. It is meant to be run after one of the contigging steps (Workflow 3, 4, or 5)

Inputs

  1. Genomescope model parameters [txt] (Generated by the k-mer profiling workflow)
  2. Hifi long reads - trimmed [fastq] (Generated by Cutadapt in the contigging workflow)
  3. Assembly to purge (e.g. hap1) ...

Type: Galaxy

Creator: Galaxy, VGP

Submitter: WorkflowHub Bot

Stable

Name: Matmul GPU Case 1 Cache-ON Contact Person: cristian.tatu@bsc.es Access Level: public License Agreement: Apache2 Platform: COMPSs Machine: Minotauro-MN4

Matmul running on the GPU leveraging COMPSs GPU Cache for deserialization speedup. Launched using 32 GPUs (16 nodes). Performs C = A @ B Where A: shape (320, 56_900_000) block_size (10, 11_380_000)             B: shape (56_900_000, 10)   block_size (11_380_000, 10)             C: shape (320, 10)                block_size ...

Type: COMPSs

Creators: Cristian Tatu, The Workflows and Distributed Computing Team (https://www.bsc.es/discover-bsc/organisation/scientific-structure/workflows-and-distributed-computing/)

Submitter: Cristian Tatu

DOI: 10.48546/workflowhub.workflow.798.1

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