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Seminar 4 Coding Material

nf-core/smrnaseq

Run command from Introduction

nextflow run nf-core/smrnaseq \
    -profile <docker/singularity/.../institute> \
    --input samplesheet.csv \
    --genome 'GRCh37' \
    --mirtrace_species 'hsa' \
    --protocol 'illumina' \
    --outdir <OUTDIR>

Sample sheet (samplesheet.csv)

sample,fastq_1
Clone1_N1,s3://ngi-igenomes/test-data/smrnaseq/C9-N1-R1_S7_L001_R1_001.fastq.gz
Clone1_N2,s3://ngi-igenomes/test-data/smrnaseq/C9-N2-R1_S8_L001_R1_001.fastq.gz
Control_N1,s3://ngi-igenomes/test-data/smrnaseq/Ctl-N1-R1_S1_L001_R1_001.fastq.gz
Control_N2,s3://ngi-igenomes/test-data/smrnaseq/Ctl-N2-R1_S2_L001_R1_001.fastq.gz

Parameters (myParams.json)

{
    "max_cpus": 4,
    "max_memory": "12.GB",
    "max_time": "6.h",
    "input": "https://github.com/nf-core/test-datasets/raw/smrnaseq/samplesheet/v2.0/samplesheet.csv",
    "fasta":"https://github.com/nf-core/test-datasets/raw/smrnaseq/reference/genome.fa",
    "mature": "https://github.com/nf-core/test-datasets/raw/smrnaseq/reference/mature.fa",
    "hairpin": "https://github.com/nf-core/test-datasets/raw/smrnaseq/reference/hairpin.fa",
    "mirna_gtf": "https://github.com/nf-core/test-datasets/raw/smrnaseq/reference/hsa.gff3",
    "mirtrace_species": "hsa",
    "protocol": "illumina",
    "skip_mirdeep": true  
}

Run command

nextflow run smrnaseq/ -profile docker --input samplesheet.csv -params-file myParams.json --outdir results

Tower

Instructions

Tutorial here.

Follow the instructions in the Tower documentation to launch the pipeline.

export TOWER_ACCESS_TOKEN=<token>

export TOWER_WORKSPACE_ID=<id>

Can store in $HOME/.nextflow/config

tower {
  enabled = true
  accessToken = '<token>'
  workspaceId = '<id>'
}

Notes found here.