Compilation error - token recognition

[davidaray]

I'm receiving this error when I try to run a workflow.

N E X T F L O W  ~  version 22.04.2
Launching `TEcurate.LINE.nf` [irreverent_sanger] DSL1 - revision: 06b6093663
Script compilation error
- file : /lustre/scratch/daray/ixodes/iRic1_nextflow/TEcurate.LINE.nf
- cause: token recognition error at: '(' @ line 60, column 13.
   	LINECOUNT=$(awk 'END{ print NR }' $params.WORKDIR/prioritize/${params.NAME}_LINEs.txt)
               ^

1 error

If it helps, the objective is to generate an array job but the number of jobs that will be required is variable. Thus, I'm attempting to gather information about the number of lines in the input file, which I then use to modify the array submission script. Unfortunately, the interpreter is having trouble with the line I'm using to generate that value. The larger workflow is copied below. Any help would be appreciated.

#!/usr/bin/env nextflow
 
/*
 * Defines the pipeline inputs parameters (giving a default value for each for them)
 * Each of the following parameters can be specified as command line options
 */

params.NAME = "iRic1"
params.MINORF = 500
params.MINCOPY = 10
params.WORKDIR = "/lustre/scratch/daray/ixodes/iRic1_nextflow"
params.TARGET = "iRic1_extended_rep.fa.classified"
params.EXTENSIONSDIR = "/lustre/scratch/daray/ixodes/iRic1_nextflow/extensions"
params.PFAM = "/lustre/work/daray/software/pfam_db"
params.AIDPATH = "/lustre/work/daray/software/TE-Aid"
params.ASSEMBLIESDIR = "/lustre/scratch/daray/ixodes/assemblies"
params.AIDOUT = "/lustre/scratch/daray/ixodes/iRic1_nextflow/te-aid"

/*
 *Call TEcurate_setup to generate the initial table and output directories.
 */
 
process TECURATE_SETUP {
	output:
	stdout into SETUP

	shell:
	"""
	#!/bin/bash 
	
	sh $params.WORKDIR/TEcurate_setup.sh \
		$params.NAME \
		$params.MINORF \
		$params.MINCOPY \
		$params.WORKDIR \
		$params.TARGET \
		$params.EXTENSIONSDIR \
		$params.PFAM \
		$params.AIDPATH \
		$params.ASSEMBLIESDIR \
	"""
	}

/*
 *Call RC_array.sh to check orientation of ORF-containing hits and 
 *reverse complement if necessary using array jobs.
 */

process RC_ARRAY_LINE {
	input:
	stdin from SETUP
	
	output:
	stdout into RC

	shell:
	"""
	#!/bin/bash 
	
	LINECOUNT=$(wc -l $params.WORKDIR/prioritize/${params.NAME}_LINEs.txt | awk '{print $1}')
	
	echo "LINECOUNT="$LINECOUNT
	
	sed "s|<COUNT>|$LINECOUNT|g" RC_array_template.sh >RC_array_LINE.sh
	
	sed -i "s|<TECLASS>|LINE|g" RC_array_LINE.sh
	
	#sbatch $params.WORKDIR/RC_array_LINE.sh \
	#	$params.NAME \
	#	$params.WORKDIR \
	#	$params.AIDOUT \
	#	$params.AIDPATH 
	"""
	}
	

[davidaray]

Would anyone have a suggestion on how to resolve this problem?

[phue]

Looks like a problem with string interpolation for bash vs nextflow variables.
See https://www.nextflow.io/docs/latest/process.html#shell

[davidaray]

Yes. After a little investigation, I found that was the case. Thank you.

While I was unable to determine which variable was causing the problem, I worked around the problem by creating a stand-alone bash script to do the substitutions for me and just invoked that as a separate process.

[bentsherman]

For what it's worth, you should only need to escape the dollar sign here:

LINECOUNT=\$(wc -l ...

Basically any dollar sign that isn't for a Nextflow variable should be escaped, when using a script block.