vmikk / vmikk/NextITS

rename issue in nextflow

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R
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Description

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

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First steps

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  2. Comment on the issue to say you are picking it up — it saves two people doing the same work.
  3. Fork the repository and make your change on a branch.
  4. Open a pull request that references the issue number.

Research direction

Start with the test script and its .nextflow.log output, then inspect the rename command shown for the demultiplexed files and compare it with the Perl rename available at ~/miniconda/bin/rename. Done means the test script completes the LIMA demultiplexing step and renames the generated .fq.gz files without the Perl evaluation errors.

Written by the indexing model from the issue text.

Assessment

Tech stack
perl, shell
Domain
bioinformatics
Issue type
Bug
Difficulty
3/5
Estimated time
1-2 days
Activity status
Quiet
Clarity
Needs clarification
Newbie friendliness
45/100

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