while trying to run scrnaseq pipeline, here is the error I get:

-- Check script 'nf-core-scrnaseq_4.1.0/4_1_0/subworkflows/nf-core/utils_nfcore_pipeline/main.nf' at line: 82 or see '.nextflow.log' file for more details

executor >  slurm (3)
[a8/3bfa59] NFC…TQC (MFI141_ds17_S21_L001) | 21 of 21, cached: 21 ✔
[53/36cdbc] NFC…laris_6.0.dna.toplevel.fa) | 1 of 1, cached: 1 ✔
[20/fd9b04] NFC…laris_6.0.dna.toplevel.fa) | 1 of 1, cached: 1 ✔
[1e/7b33c6] NFC…LIGN (MFI124_cs17_S4_L001) | 1 of 21, cached: 1
[-        ] NFC…NASEQ:SCRNASEQ:MTX_TO_H5AD -
[-        ] NFC…ELLBENDER_REMOVEBACKGROUND -
[-        ] NFC…R_ANNDATA:ANNDATA_BARCODES -
[-        ] NFC…5AD_CONVERSION:CONCAT_H5AD -
[-        ] NFC…ONVERSION:ANNDATAR_CONVERT -
[-        ] NFC…_SCRNASEQ:SCRNASEQ:MULTIQC -
-[nf-core/scrnaseq] Pipeline completed with errors-
WARN: Killing running tasks (2)
ERROR ~ while scanning a simple key
 in 'reader', line 3, column 4:
       END_VERSIONS
       ^
could not find expected ':'
 in 'reader', line 4, column 1:

In the .nextflow.log file, I see the following error:

Feb.-10 11:45:35.125 [main] WARN  nextflow.trace.ReportObserver - Failed to render execution report -- see the log file for details
nextflow.exception.AbortOperationException: Report file already exists: ../analysis/GSE130114/pipeline_info/execution_report_2026-02-10_11-45-09.html -- enable the 'report.overwrite' option in your con
fig file to overwrite existing files
        at nextflow.trace.TraceHelper.newFileWriter(TraceHelper.groovy:67)
        at nextflow.trace.ReportObserver.renderHtml(ReportObserver.groovy:243)
        at nextflow.trace.ReportObserver.onFlowComplete(ReportObserver.groovy:129)
        at nextflow.Session$_notifyFlowComplete_lambda39.doCall(Session.groovy:1121)
        at nextflow.Session.notifyEvent(Session.groovy:1151)
        at nextflow.Session.notifyFlowComplete(Session.groovy:1121)
        at nextflow.Session.shutdown0(Session.groovy:779)
        at nextflow.Session.destroy(Session.groovy:724)
        at nextflow.script.ScriptRunner.shutdown(ScriptRunner.groovy:263)
        at nextflow.script.ScriptRunner.execute(ScriptRunner.groovy:147)
        at nextflow.cli.CmdRun.run(CmdRun.groovy:429)
        at nextflow.cli.Launcher.run(Launcher.groovy:515)
        at nextflow.cli.Launcher.main(Launcher.groovy:675)
Caused by: java.nio.file.FileAlreadyExistsException: ../analysis/GSE130114/pipeline_info/execution_report_2026-02-10_11-45-09.html
        at java.base/sun.nio.fs.UnixException.translateToIOException(UnixException.java:94)
        at java.base/sun.nio.fs.UnixException.rethrowAsIOException(UnixException.java:106)
        at java.base/sun.nio.fs.UnixException.rethrowAsIOException(UnixException.java:111)
        at java.base/sun.nio.fs.UnixFileSystemProvider.newByteChannel(UnixFileSystemProvider.java:218)
        at java.base/java.nio.file.spi.FileSystemProvider.newOutputStream(FileSystemProvider.java:484)
        at java.base/java.nio.file.Files.newOutputStream(Files.java:228)
        at java.base/java.nio.file.Files.newBufferedWriter(Files.java:3008)
        at nextflow.trace.TraceHelper.newFileWriter(TraceHelper.groovy:64)
        ... 12 common frames omitted
Feb.-10 11:45:35.125 [main] DEBUG nextflow.trace.TimelineObserver - Workflow completed -- rendering execution timeline
Feb.-10 11:45:35.200 [main] WARN  nextflow.trace.TimelineObserver - Failed to render execution timeline -- see the log file for details
nextflow.exception.AbortOperationException: Timeline file already exists: ../analysis/GSE130114/pipeline_info/execution_timeline_2026-02-10_11-45-09.html -- enable the 'timeline.overwrite' option in your config file to overwrite existing files
        at nextflow.trace.TraceHelper.newFileWriter(TraceHelper.groovy:67)
        at nextflow.trace.TimelineObserver.renderHtml(TimelineObserver.groovy:164)
        at nextflow.trace.TimelineObserver.onFlowComplete(TimelineObserver.groovy:91)
        at nextflow.Session$_notifyFlowComplete_lambda39.doCall(Session.groovy:1121)
        at nextflow.Session.notifyEvent(Session.groovy:1151)
        at nextflow.Session.notifyFlowComplete(Session.groovy:1121)
        at nextflow.Session.shutdown0(Session.groovy:779)
        at nextflow.Session.destroy(Session.groovy:724)
        at nextflow.script.ScriptRunner.shutdown(ScriptRunner.groovy:263)
        at nextflow.script.ScriptRunner.execute(ScriptRunner.groovy:147)
        at nextflow.cli.CmdRun.run(CmdRun.groovy:429)
        at nextflow.cli.Launcher.run(Launcher.groovy:515)
        at nextflow.cli.Launcher.main(Launcher.groovy:675)
Caused by: java.nio.file.FileAlreadyExistsException: ../analysis/GSE130114/pipeline_info/execution_timeline_2026-02-10_11-45-09.html
        at java.base/sun.nio.fs.UnixException.translateToIOException(UnixException.java:94)
        at java.base/sun.nio.fs.UnixException.rethrowAsIOException(UnixException.java:106)
        at java.base/sun.nio.fs.UnixException.rethrowAsIOException(UnixException.java:111)
        at java.base/sun.nio.fs.UnixFileSystemProvider.newByteChannel(UnixFileSystemProvider.java:218)
        at java.base/java.nio.file.spi.FileSystemProvider.newOutputStream(FileSystemProvider.java:484)
        at java.base/java.nio.file.Files.newOutputStream(Files.java:228)
        at java.base/java.nio.file.Files.newBufferedWriter(Files.java:3008)
        at nextflow.trace.TraceHelper.newFileWriter(TraceHelper.groovy:64)
        ... 12 common frames omitted

I added overwrite = true in config file like so:

timeline {
    enabled = true
    file    = "${params.outdir}/pipeline_info/execution_timeline_${params.trace_report_suffix}.html"
    overwrite = true
}
report {
    enabled = true
    file    = "${params.outdir}/pipeline_info/execution_report_${params.trace_report_suffix}.html"
    overwrite = true
}
trace {
    enabled = true
    file    = "${params.outdir}/pipeline_info/execution_trace_${params.trace_report_suffix}.txt"
    overwrite = true
}

Enabling this the overwrite errors don't occur but the "ERROR ~ while scanning the simple key" still persists.

Hello, hope some of these comments can help you, if you haven't solved it yet (I have used this pipeline, both cellranger and starsolo mode for processing, and never facing the error like you experienced) About the overwrite, the file param actually configured to write a different name for the report each time you run (even with -resume), so its feel a bit strange to me that you facing that, but if you dont need to lookback at the old report for resource optimization or for the record, you can use the current solution About the remaining error, because I dont have your code (I dont know if you have change anything that might effect), so you can try this first and tell me if its work: Check this script for me: scrnaseq/modules/local/star_align.nf at 4.1.0 · nf-core/scrnaseq (find this module in your local machine), roll to the end, and see whether before END_VERSION have any space, its supposed to be in same column (margin, line, etc., dont know how to explain this in english) with the "STAR", "def", or "if"

thank you for your reply @Huy Trần; here is what the code block looks like in star_align.nf:

cat <<-END_VERSIONS > versions.yml
    "${task.process}":
        star: \$(STAR --version | sed -e "s/STAR_//g")
    END_VERSIONS

How would you solve it? I'm curious about the error, too, so it would be nice if you could share it