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8. Exercise 6

Move into the exercise 6 directory and execute the script.

cd /workspace/gitpod/troubleshoot/exercise6
nextflow run

Error message

ERROR ~ No such file or directory: /workspace/gitpod/troubleshoot/exercise6/data/samplesheet.csv

-- Check '.nextflow.log' file for details

The error message suggests that the path to the samplesheet.csv is incorrect.

Searching the file directory, indeed, /workspace/gitpod/troubleshoot/exercise6/data/samplesheet.csv does not exist.

The complete path should be /workspace/gitpod/troubleshoot/data/samplesheet.csv.

By examining how the path to samplesheet.csv is derived it can be seen that there is no obvious path error.
// Execution environment setup
params.baseDir = "/workspace/gitpod/troubleshoot"
$baseDir = params.baseDir

// Primary input
params.reads_bam = "${baseDir}/data/samplesheet.csv"

However, it can be noted that there is a $ before baseDir on line 7 which would suggest it is a variable.

$baseDir was once an implicit variable, and its usage here is causing the wrong path.

By removing the $ the proper path should be resolved.
baseDir = params.baseDir