Cannot find any reads matching

[abbyevewilliams]

I'm having difficulties running the nf-polish pipeline due to issues finding my reads. Here is the log:

N E X T F L O W  ~  version 23.04.2
Launching `/data/biol-silvereye/ball6625/pipeline/nf-polish/main.nf` [adoring_fermat] DSL2 - revision: 907f6d3146
POLISH MY READS! - N F   P I P E L I N E    
===================================
reads        : /data/biol-silvereye/norfolk_wgs/arbor/*_R{1,2}.fastq.gz
outdir       : /data/biol-silvereye/ball6625/pipeline/nf-out

WARN: Process with name 'merge' overrides a built-in operator with the same name
ERROR ~ No such variable: read_pairs_ch

 -- Check script 'nf-polish/main.nf' at line: 40 or see '.nextflow.log' file for more details
Cannot find any reads matching: /data/biol-silvereye/norfolk_wgs/arbor/*.fastq.gz

Though the files definitely exist:

ls /data/biol-silvereye/norfolk_wgs/arbor/*_R{1,2}.fastq.gz
/data/biol-silvereye/norfolk_wgs/arbor/AEB01_L0001_R1.fastq.gz  /data/biol-silvereye/norfolk_wgs/arbor/AEB01_L0006_R1.fastq.gz
/data/biol-silvereye/norfolk_wgs/arbor/AEB01_L0001_R2.fastq.gz  /data/biol-silvereye/norfolk_wgs/arbor/AEB01_L0006_R2.fastq.gz
/data/biol-silvereye/norfolk_wgs/arbor/AEB01_L0002_R1.fastq.gz  /data/biol-silvereye/norfolk_wgs/arbor/AEB01_L0007_R1.fastq.gz
/data/biol-silvereye/norfolk_wgs/arbor/AEB01_L0002_R2.fastq.gz  /data/biol-silvereye/norfolk_wgs/arbor/AEB01_L0007_R2.fastq.gz
/data/biol-silvereye/norfolk_wgs/arbor/AEB01_L0003_R1.fastq.gz  /data/biol-silvereye/norfolk_wgs/arbor/AEB01_L0008_R1.fastq.gz
/data/biol-silvereye/norfolk_wgs/arbor/AEB01_L0003_R2.fastq.gz  /data/biol-silvereye/norfolk_wgs/arbor/AEB01_L0008_R2.fastq.gz
/data/biol-silvereye/norfolk_wgs/arbor/AEB01_L0004_R1.fastq.gz  /data/biol-silvereye/norfolk_wgs/arbor/AEB01_L0009_R1.fastq.gz
/data/biol-silvereye/norfolk_wgs/arbor/AEB01_L0004_R2.fastq.gz  /data/biol-silvereye/norfolk_wgs/arbor/AEB01_L0009_R2.fastq.gz
/data/biol-silvereye/norfolk_wgs/arbor/AEB01_L0005_R1.fastq.gz  /data/biol-silvereye/norfolk_wgs/arbor/AEB01_L0010_R1.fastq.gz
/data/biol-silvereye/norfolk_wgs/arbor/AEB01_L0005_R2.fastq.gz  /data/biol-silvereye/norfolk_wgs/arbor/AEB01_L0010_R2.fastq.gz

I'm running the script like so:

nextflow run /data/biol-silvereye/ball6625/pipeline/nf-polish/main.nf \
	-profile slurm

And here are my params in nextflow.config:

params {

    reads = "/data/biol-silvereye/norfolk_wgs/arbor/*_R{1,2}.fastq.gz"
    outdir = "/data/biol-silvereye/ball6625/pipeline/nf-out"

I have tried many different configurations of this (using quotes, without quotes, removing the curly braces and just checking for `.fastq.gz, specifying the reads in my command line...) but nothing is working.

A similar issue was raised here but I haven't found any of the solutions helpful.

Log below.

.nextflow.log

[mribeirodantas]

This pipeline uses DSL1, a no longer supported Nextflow Domain-Specific Language (DSL) version. You can either update the code to DSL2 or use the last Nextflow DSL version to support DSL1, which is 22.04.0 (run your pipeline like NXF_VER=22.04.0 nextflow run.... Be aware you must add nextflow.enable.dsl = 1 at the top of the workflow script.