"Permission denied" error.

[edmundmiller]

The pipeline needs to by synchronised with the latest nf-core template (#525) to avoid the following error:

Original Slack Message:

---

hello guys,

I am trying to run the nf-core methylseq pipeline but i run into a "Permission denied" error. It appears that the command is failing when trying to access the fastqs, but the fastqs should be accessible to the methylseq pipeline. However, I am wondering if it is having trouble accessing a command in the work area. The error message is below. Thanks for your help!

$ /igo/work/nabors/tools/nextflow run nf-core/methylseq -profile singularity --input /igo/work/nabors/fastq/Project_12582_CA/samplesheet.csv --outdir /igo/staging/stats/naborsd_workspace/METHYLSEQ/methylseq_12582_CA --bismark_index /igo/work/igo/BismarkIndex --fasta /igo/work/igo/BismarkIndex/hg38.fa --fasta_index /igo/work/igo/BismarkIndex/hg38.fa.fai --igenomes_ignore

 N E X T F L O W   ~  version 25.04.2

Launching <https://github.com/nf-core/methylseq>` [berserk_murdock] DSL2 - revision: 4415e90a60 [master]


------------------------------------------------------
                                        ,--./,-.
        ___     __   __   __   ___     /,-._.--~'
  |\ | |__  __ /    /  \ |__) |__         }  {
  | \| |       \__, \__/ |  \ |___     \`-._,-`-,
                                        `._,._,'
  nf-core/methylseq 3.0.0
------------------------------------------------------
Input/output options
  input              : /igo/work/nabors/fastq/Project_12582_CA/samplesheet.csv
  outdir             : /igo/staging/stats/naborsd_workspace/METHYLSEQ/methylseq_12582_CA

Reference genome options
  fasta              : /igo/work/igo/BismarkIndex/hg38.fa
  fasta_index        : /igo/work/igo/BismarkIndex/hg38.fa.fai
  bismark_index      : /igo/work/igo/BismarkIndex
  igenomes_ignore    : true

Generic options
  trace_report_suffix: 2025-05-22_12-27-36

Core Nextflow options
  revision           : master
  runName            : berserk_murdock
  containerEngine    : singularity
  launchDir          : /igo/staging/stats/naborsd_workspace/METHYLSEQ/methylseq_12582_CA
  workDir            : /igo/staging/stats/naborsd_workspace/METHYLSEQ/methylseq_12582_CA/work
  projectDir         : /home/nabors/.nextflow/assets/nf-core/methylseq
  userName           : nabors
  profile            : singularity
  configFiles        :

!! Only displaying parameters that differ from the pipeline defaults !!
------------------------------------------------------* The pipeline
  <https://doi.org/10.5281/zenodo.1343417>

* The nf-core framework
    <https://doi.org/10.1038/s41587-020-0439-x>

* Software dependencies
    <https://github.com/nf-core/methylseq/blob/master/CITATIONS.md>

executor &gt;  local (10)
[-        ] process &gt; NFCORE_METHYLSEQ:METHYLSEQ:CAT_FASTQ                                              -
executor &gt;  local (10)
[-        ] process &gt; NFCORE_METHYLSEQ:METHYLSEQ:CAT_FASTQ                                              -
executor &gt;  local (10)
[-        ] process &gt; NFCORE_METHYLSEQ:METHYLSEQ:CAT_FASTQ                                              -
[9d/87e1fe] process &gt; NFCORE_METHYLSEQ:METHYLSEQ:FASTQC (DS-bla-628_NOS_T1_IGO_12582_CA_4)              [  0%] 0 of 10
executor &gt;  local (10)
[-        ] process &gt; NFCORE_METHYLSEQ:METHYLSEQ:CAT_FASTQ                                              -
[9d/87e1fe] process &gt; NFCORE_METHYLSEQ:METHYLSEQ:FASTQC (DS-bla-628_NOS_T1_IGO_12582_CA_4)              [  0%] 0 of 10
[45/562405] process &gt; NFCORE_METHYLSEQ:METHYLSEQ:TRIMGALORE (DS-bla-486_SQUAM_T1_IGO_12582_CA_5)        [  0%] 0 of 10
[-        ] process &gt; NFCORE_METHYLSEQ:METHYLSEQ:FASTQ_ALIGN_DEDUP_BISMARK:BISMARK_ALIGN                -
[-        ] process &gt; NFCORE_METHYLSEQ:METHYLSEQ:FASTQ_ALIGN_DEDUP_BISMARK:BISMARK_DEDUPLICATE          -
[-        ] process &gt; NFCORE_METHYLSEQ:METHYLSEQ:FASTQ_ALIGN_DEDUP_BISMARK:SAMTOOLS_SORT                -
[-        ] process &gt; NFCORE_METHYLSEQ:METHYLSEQ:FASTQ_ALIGN_DEDUP_BISMARK:SAMTOOLS_INDEX               -
[-        ] process &gt; NFCORE_METHYLSEQ:METHYLSEQ:FASTQ_ALIGN_DEDUP_BISMARK:BISMARK_METHYLATIONEXTRACTOR -
[-        ] process &gt; NFCORE_METHYLSEQ:METHYLSEQ:FASTQ_ALIGN_DEDUP_BISMARK:BISMARK_REPORT               -
[-        ] process &gt; NFCORE_METHYLSEQ:METHYLSEQ:FASTQ_ALIGN_DEDUP_BISMARK:BISMARK_SUMMARY              -
[-        ] process &gt; NFCORE_METHYLSEQ:METHYLSEQ:MULTIQC                                                -
Execution cancelled -- Finishing pending tasks before exit
-[nf-core/methylseq] Pipeline completed with errors-
WARN: Directive process.shell` cannot contain new-line characters - offending value: [bash

set -e # Exit if a tool returns a non-zero status/exit code
set -u # Treat unset variables and parameters as an error
set -o pipefail # Returns the status of the last command to exit with a non-zero status or zero if all successfully execute
set -C # No clobber - prevent output redirection from overwriting files.
]
ERROR ~ Error executing process &gt; 'NFCORE_METHYLSEQ:METHYLSEQ:TRIMGALORE (DS-bla-408_NOS_T1_IGO_12582_CA_6)'

Caused by:
  Process NFCORE_METHYLSEQ:METHYLSEQ:TRIMGALORE (DS-bla-408_NOS_T1_IGO_12582_CA_6)` terminated with an error exit status (126)


Command executed:

  [ ! -f  DS-bla-408_NOS_T1_IGO_12582_CA_6_1.fastq.gz ] &amp;&amp; ln -s DS-bla-408_NOS_T1_IGO_12582_CA_6_S274_R1_001.fastq.gz DS-bla-408_NOS_T1_IGO_12582_CA_6_1.fastq.gz
  [ ! -f  DS-bla-408_NOS_T1_IGO_12582_CA_6_2.fastq.gz ] &amp;&amp; ln -s DS-bla-408_NOS_T1_IGO_12582_CA_6_S274_R2_001.fastq.gz DS-bla-408_NOS_T1_IGO_12582_CA_6_2.fastq.gz
  trim_galore \
      --fastqc \
      --cores 8 \
      --paired \
      --gzip \
      DS-bla-408_NOS_T1_IGO_12582_CA_6_1.fastq.gz \
      DS-bla-408_NOS_T1_IGO_12582_CA_6_2.fastq.gz

  cat &lt;&lt;-END_VERSIONS &gt; versions.yml
  "NFCORE_METHYLSEQ:METHYLSEQ:TRIMGALORE":
      trimgalore: $(echo $(trim_galore --version 2&gt;&amp;1) | sed 's/^.*version //; s/Last.*$//')
      cutadapt: $(cutadapt --version)
      pigz: $( pigz --version 2&gt;&amp;1 | sed 's/pigz //g' )
  END_VERSIONS

Command exit status:
  126

Command output:
  (empty)

Command error:
  /bin/bash: line 10: .command.run: Permission denied

Work dir:
  /igo/staging/stats/naborsd_workspace/METHYLSEQ/methylseq_12582_CA/work/95/73d0bf6c4b6f179eece8fdc106d15a

Container:
  /igo/work/nabors/cache/community-cr-prod.seqera.io-docker-registry-v2-blobs-sha256-9b-9becad054093ad4083a961d12733f2a742e11728fe9aa815d678b882b3ede520-data.img

Tip: view the complete command output by changing to the process work dir and entering the command cat .command.out`

 -- Check '.nextflow.log' file for details
ERROR ~ Pipeline failed. Please refer to troubleshooting docs: <https://nf-co.re/docs/usage/troubleshooting>

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