samples获取

在samples.json文件中写入样本信息。

{
    "A" :
    {
        "R1" : "/local_data1/project/A_Q20L50_1.fastq.gz",
        "R2": "/local_data1/project/A_Q20L50_2.fastq.gz"
    },
    "B" :
    {
        "R1" : " /local_data1/project//B_Q20L50_1.fastq.gz",
        "R2" : " /local_data1/project/B_Q20L50_2.fastq.gz"
    }
}

读入json文件。
FILES = json.load(open("test.json"))

FILES是一个字典

{'A': {'R1': '/local_data1/project/A_Q20L50_1.fastq.gz',
  'R2': '/local_data1/project/A_Q20L50_2.fastq.gz'},
 'B': {'R1': ' /local_data1/project//B_Q20L50_1.fastq.gz',
  'R2': ' /local_data1/project/B_Q20L50_2.fastq.gz'}}

image

ALL_SAMPLES得到列表 ['A','B']
ALL_FASTQ的expand为snakemake中的用法。这里相当于得到

image

shell脚本和python结合

rule kallisto_quant:
    input:
        r1 = lambda wildcards: FILES[wildcards.sample]['R1'],
        r2 = lambda wildcards: FILES[wildcards.sample]['R2'],
        index = rules.kallisto_index.output.index
    output:
        join(OUT_DIR, '{sample}', 'abundance.tsv'),
        join(OUT_DIR, '{sample}', 'run_info.json')
    version:
        KALLISTO_VERSION
    threads:
        4
    resources:
        mem = 4000
    run:
        fastqs = ' '.join(chain.from_iterable(zip(input.r1, input.r2)))
        shell('kallisto quant'
              ' --threads={threads}'
              ' --index={input.index}'
              ' --output-dir=' + join(OUT_DIR, '{wildcards.sample}') +
              ' ' + fastqs)

cluster wrapper

当用--cluster参数时，snakemake处理顺序

直接提交

snakemake --snakefile res-snake.py --cluster "qsub -l p=2 -q res -o o.logs -e e.logs -cwd" --jobs 8

qsub提交脚本

snakemake -j 2 --cluster-config cluster.json --cluster './bsub_cluster.py {dependencies}'

dependencies

如果在这里'./bsub_cluster.py -p 2'，脚本增加如下

bsub ... -w 'done(-p) && done(2)' .sh

http://www.glue.umd.edu/lsf-docs/man/bsub.html

bsub的w参数

specifies the dependency condition of a batch job. Only when depend_cond is satisfied (TRUE), will the job be considered for dispatch.

似乎是设置job之间的联系。仅用于bsub。

snakemake根据snakefile的rule和sample拆分job，每一个job生成一个jobscript,放在临时目录中。比如
01snaketest/.snakemake/tmp.o81t2076/snakejob.fastqc_clean.1.sh。

每一个jobscript通过qsub提交，生成qsub命令时候，读取cluster引号内容，jobscirpt作为最后一个参数。

bsub -n 1 -W 00:15 -u XXXX -q res -J trimming-17 -o bsub_log/trimming-17.out -e bsub_log/trimming-17.err -M 16384 -R rusage[mem=16384] projects/01snaketest/.snakemake/tmp.5qjmx_9i/snakejob.trimming.17.sh | tail -1 | cut -f 2 -d \< | cut -f 1 -d \>

这是一个jobscriptsnakejob.trimming.17.sh的内容。

其中cluster的配置由cluster.json设置，--cluster-config cluster.json读入。

#!/bin/sh
# properties = {"type": "single", "rule": "trimming", "local": false, "input": ["rawData/reads/WR180002S_R1.fastq.gz", "rawData/reads/WR180002S_R2.fastq.gz"], "output": ["outData/trimmed/WR180002S_clean_R1.fq.gz", "outData/trimmed/WR180002S_clean_R2.fq.gz", "outData/trimmed/unpaired_WR180002S_R1.fq.gz", "outData/trimmed/unpaired_WR180002S_R2.fq.gz"], "wildcards": {"sample": "WR180002S"}, "params": {"trimmomatic": "/local_data1/software/Trimmomatic/Trimmomatic-0.38/trimmomatic-0.38.jar"}, "log": [], "threads": 10, "resources": {}, "jobid": 17, "cluster": {"time": "00:15", "cpu": 1, "email": "XXX", "EmailNotice": "N", "MaxMem": 16384, "queue": "res"}}

cd projects/01snaketest && \
software/anaconda3/bin/python3.6 \
-m snakemake outData/trimmed/WR180002S_clean_R1.fq.gz --snakefile /projects/01snaketest/Snakefile \
--force -j --keep-target-files --keep-remote \
--wait-for-files /projects/01snaketest/.snakemake/tmp.t8ndnw4x rawData/reads/WR180002S_R1.fastq.gz rawData/reads/WR180002S_R2.fastq.gz --latency-wait 5 \
 --attempt 1 --force-use-threads \
--wrapper-prefix https://bitbucket.org/snakemake/snakemake-wrappers/raw/ \
   --allowed-rules trimming --nocolor --notemp --no-hooks --nolock \
--mode 2  && touch "/projects/01snaketest/.snakemake/tmp.t8ndnw4x/17.jobfinished" || (touch "/projects/01snaketest/.snakemake/tmp.t8ndnw4x/17.jobfailed"; exit 1)

简单的wrapper函数

read_job_properties是snakemake自带函数，可以读取jobscript中的properties，得到一个字典。

#!/usr/bin/env python3
import os
import sys

from snakemake.utils import read_job_properties

jobscript = sys.argv[1]
job_properties = read_job_properties(jobscript)

# do something useful with the threads
threads = job_properties[threads]

# access property defined in the cluster configuration file (Snakemake ≥3.6.0)
job_properties["cluster"]["time"]

print("qsub -t {threads} {script}".format(threads=threads, script=jobscript))