Pipeline cannot be converted due to script errors

nextflow lint

StackOverflowError

nextflow.file.http.XPath.iterator(XPath.groovy:242)
    at groovy.json.DefaultJsonGenerator.writeObject(DefaultJsonGenerator.java:206)
    at groovy.json.DefaultJsonGenerator.writeObject(DefaultJsonGenerator.java:168)
    at groovy.json.DefaultJsonGenerator.writeIterator(DefaultJsonGenerator.java:416)
    at groovy.json.DefaultJsonGenerator.writeObject(DefaultJsonGenerator.java:206)

Canceling since a higher priority waiting request for Run nf-test-759 exists

>       ERROR conda.core.link:_execute(1014): An error occurred while installing package 'bioconda::spades-3.15.5-h95f258a_1'.
      >       Rolling back transaction:
      >       LinkError: post-link script failed for package bioconda::spades-3.15.5-h95f258a_1
      >       location of failed script: /home/runner/work/modules/modules/.nf-test/tests/769e57f0e7d8bc77bee19f97fef1c9d9/work/conda/env-27f8de4e77d219b103e2d1302f904167/bin/.spades-post-link.sh
      >       ==> script messages <==
      >       <None>
      >       ==> script output <==
      >       stdout:
      >       stderr: /home/runner/work/modules/modules/.nf-test/tests/769e57f0e7d8bc77bee19f97fef1c9d9/work/conda/env-27f8de4e77d219b103e2d1302f904167/etc/conda/deactivate.d/deactivate-gxx_linux-64.sh: line 68: CONDA_BACKUP_CXX: unbound variable

> Command error:
      >   WARNING: DEPRECATED USAGE: Forwarding SINGULARITYENV_NXF_TASK_WORKDIR as environment variable will not be supported in the future, use APPTAINERENV_NXF_TASK_WORKDIR instead
      >   WARNING: DEPRECATED USAGE: Forwarding SINGULARITYENV_NXF_DEBUG as environment variable will not be supported in the future, use APPTAINERENV_NXF_DEBUG instead
      >   ERROR  : Failed to create container process: Operation not permitted

modules/nf-core/vuegen/.conda-lock/linux_amd64-bd-9eebdec0448f6563_1.txt

process {
    withName: 'BOWTIE2_ALIGN' {
        ext.args = {
            [
                meta.read_group ? "--rg-id ${meta.id} --rg SM:${meta.id - ~/_T\\d+$/} --rg PL:ILLUMINA --rg LB:${meta.id} --rg PU:1" : '',
                params.seq_center ? "--rg CN:${params.seq_center}" : '',
                '-X 1000'
            ].join(' ').trim()
        }
    }

    withName: 'BAMTOOLS_FILTER' {
        ext.args = {
            [
                meta.single_end ? '-F 0x004' : '-F 0x004 -F 0x0008 -f 0x001',
                params.keep_dups ? '' : '-F 0x0400',
                params.keep_multi_map ? '' : '-q 30'
            ].join(' ').trim()
        }
    }

fast

Workflow execution completed unsuccessfully!
The exit status of the task that caused the workflow execution to fail was: null.

The full error message was:

Error executing process > 'NFCORE_MAG:MAG:ANCIENT_DNA_ASSEMBLY_VALIDATION:PYDAMAGE_ANALYZE (SPAdes-22ds)'

Caused by:
  process hasn't exited

nextflow pull nf-core/mag
nextflow run nf-core/mag -r 5.5.0 \
-c custom.config \
-profile singularity \
--input /projects/standard/mnievesc/zolik006/01_projects/01_PIALQ/02_analysis/03_Metagenomics/01_analysis/04_Denovo/sam$
--clip_tool adapterremoval \
--host_fasta /projects/standard/mnievesc/shared/ref_seqs/human_g1k_v37.fasta \
--host_fasta_bowtie2index /projects/standard/mnievesc/shared/ref_seqs \
--spades_fix_cpus 32 \
--megahit_fix_cpu_1 \
--reads_minlength 30 \
--binning_map_mode own \
--min_contig_size 500 \
--save_assembly_mapped_reads \
--exclude_unbins_from_postbinning \
--skip_prokka \
--run_checkm \
--run_busco \
--checkm_db /projects/standard/mnievesc/zolik006/02_refseqs/09_metaWARP/CheckM_DB \
--refine_bins_dastool \
--refine_bins_dastool_threshold 0.3 \
--postbinning_input refined_bins_only \
--run_gunc \
--gunc_db /projects/standard/mnievesc/zolik006/02_refseqs/11_gunc/gunc_db_progenomes2.1.dmnd \
--gtdb_db /projects/standard/mnievesc/zolik006/gtdbtk/share/gtdbtk-2.6.1/db \
--ancient_dna \
--outdir /projects/standard/mnievesc/zolik006/01_projects/01_PIALQ/02_analysis/03_Metagenomics/01_analysis/04_Denovo/

process {
        withName: GTDBTK_CLASSIFYWF {
                cpus = 32
                memory = 256.GB
        }
        withName: CHECKM_QC {
                cpus = 32
                memory = 256.GB
        }
        withName: PYDAMAGE_ANALYZE {
                cpus = 32
                memory = 256.GB
        }
}

nf-core pipelines sync \
   --dir /Users/luisheinzlmeier/Desktop/Repos/hadge \
   --from-branch dev \
   --pull-request \
   --username LuisHeinzlmeier \
   --github-repository <https://github.com/nf-core/hadge.git>


                                          ,--./,-.
          ___     __   __   __   ___     /,-._.--~\
    |\ | |__  __ /  ` /  \ |__) |__         }  {
    | \| |       \__, \__/ |  \ |___     \`-._,-`-,
                                          `._,._,'

    nf-core/tools version 4.1.0 - <https://nf-co.re>


WARNING  Could not find GitHub authentication token. Some API requests may fail.
WARNING  Could not find GitHub authentication token. Some API requests may fail.
INFO     Pipeline directory: /Users/luisheinzlmeier/Desktop/Repos/hadge
INFO     Using branch 'dev' to fetch workflow variables
INFO     Will attempt to automatically create a pull request
INFO     Original pipeline repository branch is 'dev'
INFO     Deleting tracked files in 'TEMPLATE' branch
INFO     Making a new template pipeline using pipeline variables
INFO     Using found ORCID for Fabiola Curion. Please double-check: <https://orcid.org/0000-0003-2502-8803>
INFO     Saving metadata file to '/Users/luisheinzlmeier/Desktop/Repos/hadge'
INFO     Generated container configs for the pipeline.
INFO     Committed changes to 'TEMPLATE' branch
INFO     Pushing TEMPLATE branch to remote: 'hadge'
INFO     Checking out original branch: 'dev'
ERROR    Could not push TEMPLATE branch:
           Cmd('git') failed due to: exit code(1)
           cmdline: git push
           stderr: 'remote: error: GH013: Repository rule violations found for refs/heads/TEMPLATE.
         remote: Review all repository rules at <https://github.com/nf-core/hadge/rules?ref=refs%2Fheads%2FTEMPLATE>
         remote:
         remote: - Cannot update this protected ref.
         remote:
         To <https://github.com/nf-core/hadge.git>
          !  TEMPLATE -> TEMPLATE (push declined due to repository rule violations)
         error: failed to push some refs to '<https://github.com/nf-core/hadge.git''>

aws.batch.platformType

ec2

fargate

platformType

job-definition://

aws.batch.platformType

ERROR    Could not parse Nextflow config for
         '/home/runner/work/funcscan/funcscan'. Possibly because of a Nextflow
         version mismatch?
         Command 'nextflow config -o json /home/runner/work/funcscan/funcscan'
         failed with exit code 1
         Downloading plugin nf-schema@2.7.2
         ERROR ~ No such variable: meta
Error: Process completed with exit code 1.