FASTP module not finding input paths

[hazlemhub]

Description of the bug

Hello, after the most recent updates, I've been unable to run my pipeline. It stops right after the processes are shown on the check list.

The .nextflow.log returns not valid path value error for FASTP (see below).
However, I've already confirmed that the directory and data are correctly located, and that I'm running the command in the correct directory to access the fastq.gz properly through ./data

I'm trying to track if this problem is related to my pipeline implementation/input or specifically to FASTP. Thank you!

NOTE: this same command, input tsv file and fastq.gz data worked fine with: nf-core/bacass v.2.3.1, Nextflow 24.04.4
(last successful run: Nov-4-24)

Script_f0c9be7d13f120a6: /home/user/.nextflow/assets/nf-core/bacass/./workflows/../modules/nf-core/cat/fastq/main.nf
Nov-22 19:06:15.800 [main] DEBUG nextflow.script.ScriptRunner - > Awaiting termination
Nov-22 19:06:15.800 [main] DEBUG nextflow.Session - Session await

Nov-22 19:06:15.870 [Actor Thread 19] DEBUG nextflow.processor.TaskProcessor - Handling unexpected condition for
task: name=NFCORE_BACASS:BACASS:FASTQ_TRIM_FASTP_FASTQC:FASTP (1); work-dir=null
error [nextflow.exception.ProcessUnrecoverableException]: Not a valid path value: './data/SRR30237409_1.fastq.gz'
Nov-22 19:06:15.870 [Actor Thread 31] DEBUG nextflow.processor.TaskProcessor - Handling unexpected condition for
task: name=NFCORE_BACASS:BACASS:FASTQ_TRIM_FASTP_FASTQC:FASTQC_RAW (1); work-dir=null
error [nextflow.exception.ProcessUnrecoverableException]: Not a valid path value: './data/SRR30237409_1.fastq.gz'
Nov-22 19:06:15.884 [Actor Thread 28] DEBUG nextflow.processor.TaskProcessor - Handling unexpected condition for
task: name=NFCORE_BACASS:BACASS:FASTQ_TRIM_FASTP_FASTQC:FASTP; work-dir=null
error [java.lang.InterruptedException]: java.lang.InterruptedException
Nov-22 19:06:15.893 [Actor Thread 20] DEBUG nextflow.sort.BigSort - Sort completed -- entries: 1; slices: 1; internal sort time: 0.001 s; external sort time: 0.012 s; total time: 0.013 s
Nov-22 19:06:15.896 [Actor Thread 31] ERROR nextflow.processor.TaskProcessor - Execution aborted due to an unexpected error
java.lang.NullPointerException: Cannot get property 'containerEngine' on null object

Command used and terminal output

Using the environment described below, I run:
(Current directory contains: /data  SRR30237409.tsv)
(./data directory contains: SRR30237409_1.fastq.gz  SRR30237409_2.fastq.gz)

$ nextflow run nf-core/bacass -profile docker --input SRR30237409.tsv --skip_kraken2 --outdir test_bacass_env_nf --skip_kmerfinder True



Output:
... [-        ] process > NFCORE_BACASS:BACASS:MULTIQC_CUSTOM                      -
Execution cancelled -- Finishing pending tasks before exit
-[nf-core/bacass] Pipeline completed with errors-
ERROR ~ Execution aborted due to an unexpected error
 -- Check script '/home/user/.nextflow/assets/nf-core/bacass/./workflows/../modules/nf-core/fastqc/main.nf' at line: 6 or see '.nextflow.log' file for more details
ERROR ~ Pipeline failed. Please refer to troubleshooting docs: https://nf-co.re/docs/usage/troubleshooting

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

Relevant files

Input file:
SRR30237409.txt

System information

nextflow=24.10.1
nf-core=3.0.2
nf-core/bacass=2.4.0

Linux, on a Google Cloud VM

[m-jahn]

I can confirm this; pipeline runs when using absolute instead of relative paths.

I tried different relative paths but none seemed to work. I didn't exactly know which dir the pipeline assumes as work dir to construct relative paths, but neither the location of the pipeline itself (I cloned from github) nor the location of the samplesheet worked.

[Daniel-VM]

Hi @m-jahn !,

Thank you for testing. It seems to be an issue related to the symlinks. I’ve been busy and haven’t had time to fix it, but I’d be happy to review it if you’d like to contribute.