nanopore_workflow_scripts

Set Up

1. このリポジトリをダウンロード

wget https://github.com/ncc-ccat-gap/nanopore_workflow_scripts/archive/refs/heads/main.zip
unzip main.zip

2. pull singularity image

singularity pull docker://aokad/minimap2:2.24
singularity pull docker://aokad/nanopolish:0.14.0
singularity pull docker://friend1ws/nanomonsv:v0.5.0
singularity pull docker://kishwars/pepper_deepvariant:r0.8
singularity pull docker://aokad/ensembl-vep:20220216
singularity pull docker://aokad/whatshap:1.5

3. リファレンスゲノムをダウンロード

4. 設定ファイルを編集

conf/param.sh

CONF_XXX_IMG=/path/to/image.sif
CONF_XXX_REFERENCE=/path/to/reference.fasta

Run

実行フロー

※1 guppyは終了しているものとする

run.sh を使用する場合

conf/sample.sh (1ファイル1ペアのみ)

PARAM_TUMOR=TUMOR_NAME
PARAM_CONTL=CONTROL_NAME

PARAM_TUMOR_FASTQ=/path/to/tumor.fastq.gz
PARAM_CONTL_FASTQ=/path/to/control.fastq.gz

PARAM_TUMOR_FAST5=/path/to/tumor/fast5_directory

ジョブ投入

cd {this repository}
bash run.sh conf/sample.sh

snakemake を使用する場合

config.yml (複数サンプル登録可能)

pair:
  TUMOR_NAME1: CONTROL_NAME1
  TUMOR_NAME2: CONTROL_NAME2
  TUMOR_NAME3: CONTROL_NAME2     # CONTROLの重複可能

fastq:
  TUMOR_NAME1:
  - /path/to/tumor1.fastq.gz
  TUMOR_NAME2:
  - /path/to/tumor2.fastq.gz
  TUMOR_NAME3:
  - /path/to/tumor3.fastq.gz
  CONTROL_NAME1:
  - /path/to/control1.fastq.gz
  CONTROL_NAME2:
  - /path/to/control2.fastq.gz

fast5:
  TUMOR_NAME1:
  - /path/to/tumor1/fast5_directory
  TUMOR_NAME2:
  - /path/to/tumor2/fast5_directory
  TUMOR_NAME3:
  - /path/to/tumor3/fast5_directory
  CONTROL_NAME1:
  - /path/to/control1/fast5_directory
  CONTROL_NAME2:
  - /path/to/control2/fast5_directory

snakemake実行

cd {this repository}
snakemake --cores 8 -k

Output Files

{This repository}
#   Files originally in this repository
|-- config.yml
|-- snakefile.txt
|-- conf/
|   |-- param.sh
|   `-- sample.sh
|-- script/
|
#   Output
|-- log/
|   |-- CONTROL_NAME/
|   `-- TUMOR_NAME/
|-- minimap2/
|   |-- CONTROL_NAME/
|   |   |-- CONTROL_NAME.bam
|   |   `-- CONTROL_NAME.bam.bai
|   `-- TUMOR_NAME/
|       |-- TUMOR_NAME.bam
|       `-- TUMOR_NAME.bam.bai
|-- nanomonsv/
|   |-- CONTROL_NAME/
|   `-- TUMOR_NAME/
|       |-- TUMOR.nanomonsv.result.txt
|       |-- TUMOR.nanomonsv.result.vcf
|       |-- TUMOR.nanomonsv.sbnd.result.txt
|       `-- TUMOR.nanomonsv.supporting_read.txt
|-- nanopolish
|   `-- CONTROL_NAME/
|       `-- methylation_calls.tsv.gz
|   `-- TUMOR_NAME/
|       `-- methylation_calls.tsv.gz
|-- vep/
|   `-- CONTROL_NAME/
|       |-- PMDV.annot.vcf.gz
|       `-- PMDV.annot.vcf.gz.tbi
|-- whatshap/
|   |-- CONTROL_NAME/
|   |   |-- phased.vcf.gz
|   |   |-- phased.vcf.gz.tbi
|   |   |-- CONTROL_NAME.bam
|   |   `-- haplotag.txt
|   `-- TUMOR_NAME/
|       |-- TUMOR_NAME.bam
|       `-- haplotag.txt
|
#   Temporary files
`-- split/