nextflow process to download a fastq file from TCGA

[sam benneti]

Hello, I am a French student, please help me, I am new to bioinformatics and I start using nextflow to do my pipeline. I'm trying to do a process that downloads the TCGA data from a manifest. first, I'm doing a process that extracts the uids from the manifesto. Then in the second process I wanted to download the fastq but on nextflow I can not read the file containing my uuids. I put what I did so that someone could help me.

here is the mistake I have :

Command output:
  WARNING: Your token file 'gdc-user-token.2018-10-08T11_11_53.504Z.txt' is not properly secured. Please secure your token file by ensuring that it is not readable or writeable by anyone other than the owner of the file. On Linux: chmod 600 gdc-user-token.2018-10-08T11_11_53.504Z.txt
  ERROR: filecontain_uuids: 404 Client Error: NOT FOUND: {
    "message": "filecontain_uuids not found"
  }
  ERROR: filecontain_uuids: 404 Client Error: NOT FOUND: {
    "message": "filecontain_uuids not found"
  }
  ERROR: Unable to download file https://api.gdc.cancer.gov/data/filecontain_uuids
  Successfully downloaded: 0
  Failed downloads: 1

Command wrapper:
  WARNING: Your token file 'gdc-user-token.2018-10-08T11_11_53.504Z.txt' is not properly secured. Please secure your token file by ensuring that it is not readable or writeable by anyone other than the owner of the file. On Linux: chmod 600 gdc-user-token.2018-10-08T11_11_53.504Z.txt
  ERROR: filecontain_uuids: 404 Client Error: NOT FOUND: {
    "message": "filecontain_uuids not found"
  }
  ERROR: filecontain_uuids: 404 Client Error: NOT FOUND: {
    "message": "filecontain_uuids not found"
  }
  ERROR: Unable to download file https://api.gdc.cancer.gov/data/filecontain_uuids
  Successfully downloaded: 0
  Failed downloads: 1

[Steve]

Hi Sam, I have adjusted the pipeline you posted to match the syntax I usually use and changed some things that might be causing the errors:

params.manifest = "/home/guest/sam_tmp/Test/gdc_manifest.2018-04-23_withIDs.csv"
params.token = "/home/guest/sam_tmp/Test/gdc-user-token.2018-10-08T11_11_53.504Z.txt"
Channel.fromPath(params.token).set { token_ch }


process extract {
  input:
  file(manifest) from Channel.fromPath(params.manifest)

  output:
  file("uuids.txt") into sampleID

  script:
  """
  cut -d ';' -f2 "${manifest}" > uuids.txt
  """

}

process downloadFastq{
  publishDir "/home/guest/sam_tmp/Test/FastqFile" , mode:'copy'

  input:
  set file(filecontain_uuids), file(keys) from sampleID.combine(token_ch)

  output:
  file('*.fastq')

  script:
  """
  gdc-client download "${filecontain_uuids}" -t "${keys}"
  """
}

Without example manifest and key files its hard to tell if this will work, but you might give it a shot.