nf-core / neutronstar Goto Github PK

ref:
https://conda.io/docs/user-guide/tasks/manage-environments.html#creating-an-environment-file-manually

Shouldn't it be possible to run the test execution using singularity instead of docker?
Using singularity,test isn't possible right now.

Use tigmint for assembly error correction using linked-read information, usually before ar{c,k}s scaffolding.

Same use cases as related issue #16.

Have a think about integrating EMA mapping + Arcs (or EMA bc whitelisting + Arks) to do additional and more aggressive scaffolding than than Supernova does.

With the coming of DSL 2. It could be a good idea to write this out to a sub-workflow with its own entrypoint. A common use-case would also be running these tools on an existing long-read assembly (e.g. PacBio).

These tools exist on bioconda! 👍

From @remiolsen on December 11, 2017 17:4

For transparency, here's my "design document"

Main requirements

• Nextflow? yes
• Supernova running in $SNIC_TMP (Irma compatible?)
  • 1.20 compatible — multiple input parameter assemblies
  • [ ] Use nextflow publishdata in stead of rsync couldn't make it work. Use rsync!
  • Make a this optional
• Rsync supernova assembly back to workdir
• supernova mkoutput - pseudohap, megabubbles
  • gunzip
  • parameter of additional outputs — always output .phased.fasta
  • parameter for minimum length
• QUAST
  • make it run on Irma
• BUSCO
  • UPPMAX — beforeScript
• MultiQC
  • Needs testing
• support for --no-preflight flag
• Documentation
  • Readme.md
• dump software versions & commands that were run
• Send mail when done pipeline is finished
• Clean up and generalize the configs
  • Common HPC config
  • Common Uppmax config
  • Make a general local run config
• Release tags

Docker / Singularity

• Supernova (copyright issues?)
• Quast
• BUSCO
• Script for automatic singularity/docker download / installation

NX script

• input configuration:
  • id
    • fastqs
    • sample
    • maxreads
    • bcfrac
  • genomesize
• memory parameter
• cpu parameter
• make Longranger / fastqc optional

Input_validation

• id — only numbers, letters, dash, and underscore allowed
• bcfrac (0,1)
• maxreads - num

MultiQC

• Fix when having empty molecule.yaml files
• Does having “ASSEMBLER_CS” folders break multiqc?
• Fix QUAST module. It breaks when running with -s option

Testing

• Test data from NA12878 run.
• Travis-CI integration

Could haves

• Tigmint evaluation
• Delivery template mail / output folder structure
• BWA align
  • picard-tools
  • remove dups
  • collectinsertsize
• qaTools-singularity
• FRC-singularity
• BUSCOv2 datasets in config
  • auto-script to download datasets

Copied from original issue: SciLifeLab#3