Syntax conflict for "{" using Nextflow - bioinformatics

Question

New to nextflow, attempted to run a loop in nextflow chunk to remove extension from sequence file names and am running into a syntax error.
params.rename = "sequences/*.fastq.gz"
workflow {
rename_ch = Channel.fromPath(params.rename)
RENAME(rename_ch)
RENAME.out.view()
}
process RENAME {
input:
path read
output:
stdout
script:
"""
for file in $baseDir/sequences/*.fastq.gz;
do
mv -- '$file' '${file%%.fastq.gz}'
done
"""
}
Error:
- cause: Unexpected input: '{' # line 25, column 16.
process RENAME {
^
Tried to use other methods such as basename, but to no avail.

Answer 1

Inside a script block, you just need to escape the Bash dollar-variables and use double quotes so that they can expand. For example:
params.rename = "sequences/*.fastq.gz"
workflow {
RENAME()
}
process RENAME {
debug true
"""
for fastq in ${baseDir}/sequences/*.fastq.gz;
do
echo mv -- "\$fastq" "\${fastq%%.fastq.gz}"
done
"""
}
Results:
$ nextflow run main.nf
N E X T F L O W ~ version 22.04.0
Launching `main.nf` [crazy_brown] DSL2 - revision: 71ada7b0d5
executor > local (1)
[71/4321e6] process > RENAME [100%] 1 of 1 ✔
mv -- /path/to/sequences/A.fastq.gz /path/to/sequences/A
mv -- /path/to/sequences/B.fastq.gz /path/to/sequences/B
mv -- /path/to/sequences/C.fastq.gz /path/to/sequences/C
Also, if you find escaping the Bash variables tedious, you may want to consider using a shell block instead.