nmdp-bioinformatics/flow

Name: flow

Owner: NMDP/Be The Match Bioinformatics Research

Description: Consensus assembly and variant calling workflow.

Created: 2014-12-15 21:50:08.0

Updated: 2017-10-18 08:07:01.0

Pushed: 2015-05-26 16:45:44.0

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Size: 682

Language: null

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README

flow

Consensus assembly and variant calling workflow.

Hacking flow

Install Nextflow

rl -fsSL get.nextflow.io | bash 

  N E X T F L O W
  Version 0.13.5 build 2985
  last modified 07-05-2015 12:30 UTC (07:30 CDT)
  http://nextflow.io

flow installation completed.

Run workflow locally (requires workflow dependencies to be installed locally)

nextflow run main.nf 
X T F L O W  ~  version 0.13.5
ching main.nf
m up] executor > local
654161] Submitted process > interleave (example)
88ef80] Submitted process > fastqToSsake (example)
c3d689] Submitted process > reformat (example)
21d368] Submitted process > alignReads (example)
a1c58f] Submitted process > ssake (example)
ing example.reads.bwa.sorted.bam (readsBam) into: tutorial/final
ing example.reads.bwa.sorted.vcf.gz (readsVcf) into: tutorial/final
e1a618] Submitted process > alignContigs (example)
ing example.contigs (contigsFasta) into: tutorial/final
ing example.contigs.bwa.sorted.bam (contigsBam) into: tutorial/final
ing example.contigs.bwa.sorted.vcf.gz (configVcf) into: tutorial/final

Run workflow locally using Docker image (requires only Docker to be installed locally)

nextflow run main.nf -with-docker nmdpbioinformatics/docker-flow:1.0-snapshot-2
X T F L O W  ~  version 0.13.5
ching main.nf
m up] executor > local
d7bd89] Submitted process > fastqToSsake (example)
b6cf05] Submitted process > interleave (example)
86ea16] Submitted process > reformat (example)
3370df] Submitted process > alignReads (example)
f4bbf7] Submitted process > ssake (example)
ing example.reads.bwa.sorted.bam (readsBam) into: tutorial/final
ing example.reads.bwa.sorted.vcf.gz (readsVcf) into: tutorial/final
fbdffd] Submitted process > alignContigs (example)
ing example.contigs (contigsFasta) into: tutorial/final
ing example.contigs.bwa.sorted.bam (contigsBam) into: tutorial/final
ing example.contigs.bwa.sorted.vcf.gz (configVcf) into: tutorial/final

Use SLURM executor, with or without Docker

ho "process.executor = 'slurm'" > nextflow.config
nextflow run main.nf -with-docker nmdpbioinformatics/docker-flow:1.0-snapshot-2
X T F L O W  ~  version 0.13.5
m up] executor > slurm
882358] Submitted process > fastqToSsake (example)
d3ac82] Submitted process > interleave (example)
9cbbaf] Submitted process > reformat (example)
2f652d] Submitted process > alignReads (example)
270f79] Submitted process > ssake (example)
ing example.reads.bwa.sorted.bam (readsBam) into: tutorial/final
ing example.reads.bwa.sorted.vcf.gz (readsVcf) into: tutorial/final
55682c] Submitted process > alignContigs (example)
ing example.contigs (contigsFasta) into: tutorial/final
ing example.contigs.bwa.sorted.bam (contigsBam) into: tutorial/final
ing example.contigs.bwa.sorted.vcf.gz (configVcf) into: tutorial/final

Note that when using the SLURM executor, the Nextflow working directory must be mounted on a volume shared to all SLURM nodes.