Helloo, my CI tests failed and I was wondering if ...
# methylong
j
Helloo, my CI tests failed and I was wondering if this is due to some docker permissions error? the below is the error shown: permission denied
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Run nextflow run ${GITHUB_WORKSPACE} -profile test,docker docker --outdir ./results
N E X T F L O W  ~  version 25.02.3-edge
Launching `/home/runner/work/methylong/methylong/main.nf` [disturbed_khorana] DSL2 - revision: cccd09db65
Downloading plugin nf-schema@2.1.1

------------------------------------------------------
                                        ,--./,-.
        ___     __   __   __   ___     /,-._.--~'
  |\ | |__  __ /  ` /  \ |__) |__         }  {
  | \| |       \__, \__/ |  \ |___     \`-._,-`-,
                                        `._,._,'
  nf-core/methylong 1.0.0
------------------------------------------------------
Input/output options
  input                     : <https://raw.githubusercontent.com/nf-core/test-datasets/refs/heads/methylong/test_data/test_samplesheet.csv>
  outdir                    : ./results

Institutional config options
  config_profile_name       : Test profile
  config_profile_description: Minimal test dataset to check pipeline function

Core Nextflow options
  runName                   : disturbed_khorana
  containerEngine           : docker
  launchDir                 : /home/runner/work/methylong/methylong
  workDir                   : /home/runner/work/methylong/methylong/work
  projectDir                : /home/runner/work/methylong/methylong
  userName                  : runner
  profile                   : test,docker
  configFiles               : 

!! Only displaying parameters that differ from the pipeline defaults !!
------------------------------------------------------
* The nf-core framework
    <https://doi.org/10.1038/s41587-020-0439-x>

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

WARN: nf-core pipelines do not accept positional arguments. The positional argument `docker` has been detected.
HINT: A common mistake is to provide multiple values separated by spaces e.g. `-profile test, docker`.

WARN: The `when` process section is deprecated -- use conditional logic in the calling workflow instead
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.
]
[da/36deee] Submitted process > NFCORE_METHYLONG:METHYLONG:FASTQ_UNZIP:GUNZIP (Col-CEN_v1.2.Chr1_5MB-7MB.fasta.gz)
[a3/f441fe] Submitted process > NFCORE_METHYLONG:METHYLONG:FASTQ_UNZIP:GUNZIP (Col-CEN_v1.2.Chr1_5MB-7MB.fasta.gz)
ERROR ~ Error executing process > 'NFCORE_METHYLONG:METHYLONG:FASTQ_UNZIP:GUNZIP (Col-CEN_v1.2.Chr1_5MB-7MB.fasta.gz)'

Caused by:
  Process `NFCORE_METHYLONG:METHYLONG:FASTQ_UNZIP:GUNZIP (Col-CEN_v1.2.Chr1_5MB-7MB.fasta.gz)` terminated with an error exit status (126)


Command executed:

  # Not calling gunzip itself because it creates files
  # with the original group ownership rather than the
  # default one for that user / the work directory
  gzip \
      -cd \
       \
      Col-CEN_v1.2.Chr1_5MB-7MB.fasta.gz \
      > Col-CEN_v1.2.Chr1_5MB-7MB.fasta
  
  cat <<-END_VERSIONS > versions.yml
  "NFCORE_METHYLONG:METHYLONG:FASTQ_UNZIP:GUNZIP":
      gunzip: $(echo $(gunzip --version 2>&1) | sed 's/^.*(gzip) //; s/ Copyright.*$//')
  END_VERSIONS

Command exit status:
  126

Command output:
  (empty)

Command error:
  9f0d519e5362: Pulling fs layer
  2fc3b27fe229: Pulling fs layer
  4f4fb700ef54: Waiting
  17dc7ea432cc: Waiting
  92dc97a3ef36: Waiting
  403f74b0f85e: Waiting
  bb36d6c3110d: Waiting
  10b8c00c10a5: Waiting
  030a47592a0a: Waiting
  0ea1a16bbe82: Waiting
  9f0d519e5362: Waiting
  2fc3b27fe229: Waiting
  dec6b097362e: Verifying Checksum
  dec6b097362e: Download complete
  f88da01cff0b: Verifying Checksum
  f88da01cff0b: Download complete
  dafa2b0c44d2: Verifying Checksum
  dafa2b0c44d2: Download complete
  4f4fb700ef54: Download complete
  92dc97a3ef36: Download complete
  403f74b0f85e: Verifying Checksum
  403f74b0f85e: Download complete
  10b8c00c10a5: Verifying Checksum
  10b8c00c10a5: Download complete
  17dc7ea432cc: Download complete
  bb36d6c3110d: Verifying Checksum
  bb36d6c3110d: Download complete
  0ea1a16bbe82: Verifying Checksum
  0ea1a16bbe82: Download complete
  dafa2b0c44d2: Pull complete
  030a47592a0a: Download complete
  9f0d519e5362: Verifying Checksum
  9f0d519e5362: Download complete
  2fc3b27fe229: Verifying Checksum
  2fc3b27fe229: Download complete
  dec6b097362e: Pull complete
  f88da01cff0b: Pull complete
  4f4fb700ef54: Pull complete
  92dc97a3ef36: Pull complete
  403f74b0f85e: Pull complete
  10b8c00c10a5: Pull complete
  17dc7ea432cc: Pull complete
  bb36d6c3110d: Pull complete
  0ea1a16bbe82: Pull complete
  030a47592a0a: Pull complete
  9f0d519e5362: Pull complete
  2fc3b27fe229: Pull complete
  Digest: sha256:63c2c6b22e83b2f656e88fbb1553e595da4e9e58794e3bfcb98b20b3837f328a
  Status: Downloaded newer image for <http://community.wave.seqera.io/library/coreutils_grep_gzip_lbzip2_pruned:838ba80435a629f8|community.wave.seqera.io/library/coreutils_grep_gzip_lbzip2_pruned:838ba80435a629f8>
  /bin/bash: line 10: .command.run: Permission denied

Work dir:
  /home/runner/work/methylong/methylong/work/a3/f441fe3ce24371e2940f1e402a266b

Container:
  <http://community.wave.seqera.io/library/coreutils_grep_gzip_lbzip2_pruned:838ba80435a629f8|community.wave.seqera.io/library/coreutils_grep_gzip_lbzip2_pruned:838ba80435a629f8>

Tip: you can replicate the issue by changing to the process work dir and entering the command `bash .command.run`

 -- Check '.nextflow.log' file for details
Execution cancelled -- Finishing pending tasks before exit
ERROR ~ Pipeline failed. Please refer to troubleshooting docs: <https://nf-co.re/docs/usage/troubleshooting>

 -- Check '.nextflow.log' file for details
-[nf-core/methylong] Pipeline completed with errors-
Error: Process completed with exit code 1.