r - 我如何才能发现Rscript已由CWL在docker上成功运行？

Question

我已经编写了在Docker容器中运行Rscript命令的CWL代码。我有两个cwl和yaml文件，并通过以下命令运行它们:

cwltool --debug a_code.cwl a_input.yaml

我得到的输出表示过程状态为成功，但是没有输出文件，并且结果为“输出”:报告为null。我想知道是否有一种方法可以找到Rscript文件已在docker上成功运行。我实际上想知道输出文件为null的原因。

结果的最后一部分是:

[job a_code.cwl] {
    "output": null, 
    "errorFile": null
}
[job a_code.cwl] Removing input staging directory /tmp/tmpUbyb7k
[job a_code.cwl] Removing input staging directory /tmp/tmpUbyb7k
[job a_code.cwl] Removing temporary directory /tmp/tmpkUIOnw
[job a_code.cwl] Removing temporary directory /tmp/tmpkUIOnw
Removing intermediate output directory /tmp/tmpCG9Xs1
Removing intermediate output directory /tmp/tmpCG9Xs1
{
    "output": null, 
    "errorFile": null
}
Final process status is success
Final process status is success

R代码:

library(cummeRbund)
cuff<-readCufflinks( dbFile = "cuffData.db", gtfFile = NULL, runInfoFile = "run.info", repTableFile = "read_groups.info", geneFPKM = "genes.fpkm_trac .... )
#setwd("/scripts")
sink("cuff.txt")
print(cuff)
sink()

我的cwl文件代码是:

class: CommandLineTool
cwlVersion: v1.0
id: cummerbund
baseCommand:
  - Rscript
inputs:
  - id: Rfile
    type: File?
    inputBinding:
      position: 0
  - id: cuffdiffout
    type: 'File[]?'
    inputBinding:
      position: 1
  - id: errorout
    type: File?
    inputBinding:
      position: 99
      prefix: 2>
      valueFrom: |
        error.txt
outputs:
  - id: output
    type: File?
    outputBinding:
      glob: cuff.txt
  - id: errorFile
    type: File?
    outputBinding:
      glob: error.txt
label: cummerbund
requirements:
  - class: DockerRequirement
    dockerPull: cummerbund_0

我的输入文件(yaml文件)为:

 inputs:
    Rfile:
      basename: run_cummeR.R
      class: File
      nameext: .R
      nameroot: run_cummeR
      path: run_cummeR.R
    cuffdiffout:
      - class: File
        path: cuffData.db
      - class: File
        path: genes.fpkm_tracking
      - class: File
        path: read_groups.info
      - class: File
        path: genes.count_tracking
      - class: File
        path: genes.read_group_tracking
      - class: File
        path: isoforms.fpkm_tracking
      - class: File
        path: isoforms.read_group_tracking
      - class: File
        path: isoforms.count_tracking
      - class: File
        path: isoform_exp.diff
      - class: File
        path: gene_exp.diff
    errorout:
      - class: File
        path: error.txt

另外，这是我用于创建镜像的Dockerfile:

FROM r-base
COPY . /scripts
RUN apt-get update
RUN apt-get install -y \
    libcurl4-openssl-dev\
    libssl-dev\
    libmariadb-client-lgpl-dev\
    libmariadbclient-dev\
    libxml2-dev\
    r-cran-plyr\
    r-cran-reshape2
WORKDIR /scripts
RUN Rscript /scripts/build.R
ENTRYPOINT /bin/bash

Answer 1

我得到了答案!
我的程序中存在一些问题。
1. docker 未正确拉出，那么cwl无法产生任何输出。
2.输入和输出未定义为强制性的。因此，在没有适当输入和输出的情况下，我获得了成功状态。