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PesKchan's questions

Martin Hope
PesKchan
Asked: 2023-09-24 05:18:10 +0800 CST
  • 5

Meu objetivo é aumentar o número de novas tentativas para esta validação fastq que às vezes falha devido a problemas de rede, embora haja dados para o ID NCBI SRA fornecido, mas falha. Portanto, preciso aumentar a repetição pelo menos 5 vezes antes de abortar.

Como faço o mesmo?

set -x
PS4='[\\d \\t] '

# Check parameter for error
check=0
# Print fastq-dump executable path
echo \$(which fastq-dump)

# Loop through all parameters to check validity
for file in \$@;
do
    cp \${file} .
    # Extract filename for sampleID
    file_basename=\$(basename \${file})
    id=\${file_basename%".id"}
    # Start validation
    echo "Checking \${id}..."
    # Download start of fastq
    fastq-dump $(get_ngc()) -X 1 -Z --split-spot \${id} > \${id}.test.fastq 2> \${id}.test.log
    # Get number of lines downloaded to valildate for error
    numLines=\$(cat \${id}.test.fastq | wc -l)
    if [ \$numLines -gt 0 ]; then
        echo "\${id} has data... OK"
    else
        echo "\${id} does not have data... ERROR"
        check=1
    fi
done
# Exit with error if some fastqs not accessible
if [ \$check -gt 0 ]; then
    echo "ERROR: One or more samples have inaccessible fastqs.. exiting"
    exit 1
fi

############ ATUALIZAR ###############

#!/usr/bin/env cwl-runner

cwlVersion: cwl:v1.0
class: CommandLineTool
requirements:
- class: DockerRequirement
  dockerPull: kcm1400/validate_fastq_ncbi_sra:v1
- class: InlineJavascriptRequirement
  expressionLib:
  - var get_ngc= function(){ if(inputs["ngc_file"]==null){ return " "; }else{ return
    "--ngc "+inputs["ngc_file"].path+" "; } }
- class: InitialWorkDirRequirement
  listing:
  - entry: |-
      set -x
      PS4='[\\d \\t] '

      # Check parameter for error
      check=0
      # Print fastq-dump executable path
      echo \$(which fastq-dump)

      # Loop through all parameters to check validity
      for file in \$@;
      do
          cp \${file} .
          # Extract filename for sampleID
          file_basename=\$(basename \${file})
          id=\${file_basename%".id"}
          # Start validation
          echo "Checking \${id}..."
          # Download start of fastq
          fastq-dump $(get_ngc()) -X 1 -Z --split-spot \${id} > \${id}.test.fastq 2> \${id}.test.log
          # Get number of lines downloaded to valildate for error
          numLines=\$(cat \${id}.test.fastq | wc -l)
          if [ \$numLines -gt 0 ]; then
              echo "\${id} has data... OK"
          else
              echo "\${id} does not have data... ERROR"
              check=1
          fi
      done
      # Exit with error if some fastqs not accessible
      if [ \$check -gt 0 ]; then
          echo "ERROR: One or more samples have inaccessible fastqs.. exiting"
          exit 1
      fi
    entryname: validate_fastq.sh
    writable: false
label: validate_fastq_ncbi_sra
stdout: validate_fastq.log.txt
inputs:
  sra_ID:
    type:
    - type: array
      items: string
    - 'null'
    inputBinding:
      position: 1
  id_file:
    type:
    - type: array
      items: File
    - 'null'
    inputBinding:
      position: 2
  ngc_file:
    type:
    - File
    - 'null'
    inputBinding:
      position: 3
outputs:
  output_log:
    type: stdout
    label: output log file
  ncbi_ids:
    type:
      type: array
      items: File
    outputBinding:
      glob:
      - '*.id'
baseCommand:
- sh
- validate_fastq.sh

O arquivo CWL para o mesmo

shell