rename issue in nextflow

[FrankBerninger]

Hello,

I encountered an issue with nextflow on a HPC system (Roihu) and I am not sure how to solve it.

The error (from the .nextflow.log) file while running the test script is

Demultiplexing with LIMA (dual symmetric barcodes)

..Renaming demultiplexed files
Perl evaluation error: Can't modify constant item in predecrement (--) at (eval 1) line 1, at EOF
Bareword "filename" not allowed while "strict subs" in use at (eval 1) line 1.
Aug-20 11:42:56.546 [main] DEBUG nextflow.Session - Session await > all processes finished
Aug-20 11:42:56.546 [main] DEBUG nextflow.Session - Session await > all barriers passed
Aug-20 11:42:56.549 [main] DEBUG n.trace.WorkflowStatsObserver - Workflow completed > WorkflowStats[succeededCount=3; failedCount=1; ignoredCount=0; cachedCount=0; pendingCount=2; submittedCount=0; runningCount=0; retriesCount=0; abortedCount=0; succeedDuration=11.1s; failedDuration=1.7s; cachedDuration=0ms;loadCpus=0; loadMemory=0; peakRunning=2; peakCpus=4; peakMemory=0; ]

The issue seems to point to this line:
echo -e "\n..Renaming demultiplexed files"
rename --filename
's/^lima.//g; s/--.$/.fq.gz/'
$(find LIMA -name ".fq.gz")

fi

I changed the rename from the linux utils (which does not work) and to the perl rename....

(base) [berninge@rc5144 ~]$ which rename
~/miniconda/bin/rename

[vmikk]

Hello @FrankBerninger ,

It looks like the pipeline may be running without a container profile, so it is picking up the rename command from your local Conda environment instead of the version expected by NextITS.

For that, NextITS supports both Docker and Singularity.
You can activate either with -profile docker or -profile singularity (in most cases, the later is preffered on HPC systems).
On the first run, NextITS will pull the required container image.
Depending on the HPC configuration, you may first need to load Singularity, for example:

module load singularity

For Singularity, it is also useful to define a cache directory so that the downloaded image can be reused in subsequent runs:

export NXF_SINGULARITY_CACHEDIR="$HOME/Singularity_images/"

I would suggest trying the pipeline using the provided containers, as there are a lot of other dependencies which might be missing on your system.