The message mentions a missing file. Wasn't there a discussion regarding something like this recently? If it's serious I suppose you'll run into it too.

Here's the long message:

Assertion failed: 
  
  assert workflow.success
         |        |
         workflow false
  
  Nextflow stdout:
  
  ERROR ~ Error executing process > 'NFCORE_AMPLISEQ:AMPLISEQ:SUMMARY_REPORT (1)'
  
  Caused by:
    Process `NFCORE_AMPLISEQ:AMPLISEQ:SUMMARY_REPORT (1)` terminated with an error exit status (1)
  
  
  Command executed:
  
    #!/usr/bin/env Rscript
    library(rmarkdown)
    
    # Work around  <https://github.com/rstudio/rmarkdown/issues/1508>
    # If the symbolic link is not replaced by a physical file
    # output- and temporary files will be written to the original directory.
    file.copy("./report_template.Rmd", "./template.Rmd", overwrite = TRUE)
    
    rmarkdown::render("template.Rmd", output_file = "summary_report.html", params = list(css='nf-core_style.css',report_logo='nf-core-ampliseq_logo_light_long.png',workflow_manifest_version='2.16.0dev',workflow_scriptid='989f5de55d',report_title='Summary of analysis results',metadata='Metadata.tsv',input_samplesheet='Samplesheet.tsv',cutadapt_summary='cutadapt_summary.tsv',truncq=2,trunc_qmin=25,trunc_rmin=0.75,trunclenf='null',trunclenr='null',max_ee=2,dada_qc_f_path='FW_qual_stats.svg',dada_qc_r_path='RV_qual_stats.svg',dada_pp_qc_f_path='FW_preprocessed_qual_stats.svg',dada_pp_qc_r_path='RV_preprocessed_qual_stats.svg',dada_filtntrim_args='filterAndTrim.args.txt',dada_sample_inference='independent',dada_err_path='1_1.err.svg,1_2.err.svg',dada_err_run='1',asv_table_path='ASV_table.tsv',path_asv_fa='ASV_seqs.fasta',path_dada2_tab='DADA2_table.tsv',dada_stats_path='DADA2_stats.tsv',mergepairs_strategy='merge',path_barrnap_sum='summary.tsv',filter_ssu_stats='stats.ssu.tsv',filter_ssu_asv='ASV_seqs.ssu.fasta',filter_ssu='bac',min_len_asv=0,max_len_asv=0,dada_min_boot=50,pplace_taxonomy='test_pplace.taxonomy.tsv',pplace_heattree='test_pplace.heattree.tree.svg',qiime2_taxonomy='taxonomy.tsv',qiime2_ref_tax_title='Greengenes 16S - Version 13_8 - clustered at 85% similarity - for testing purposes only',qiime2_ref_tax_file='[<https://data.qiime2.org/2023.7/tutorials/training-feature-classifiers/85_otus.fasta>, <https://data.qiime2.org/2023.7/tutorials/training-feature-classifiers/85_otu_taxonomy.txt]',qiime2_ref_tax_citation='McDonald>, D., Price, M., Goodrich, J. et al. An improved Greengenes taxonomy with explicit ranks for ecological and evolutionary analyses of bacteria and archaea. ISME J 6, 610–618 (2012). <https://doi.org/10.1038/ismej.2011.139',val_used_taxonomy='phylogenetic> placement',filter_stats_tsv='count_table_filter_stats.tsv',qiime2_filtertaxa='276,48',exclude_taxa='mitochondria,chloroplast',min_frequency='10',min_samples='2',barplot=TRUE,abundance_tables=TRUE,diversity_indices_depth='WARNING\ The\ sampling\ depth\ of\ 500\ seems\ too\ small\ for\ rarefaction.txt',diversity_indices_alpha=TRUE,diversity_indices_beta='beta_diversity/unweighted_unifrac_distance_matrix-treatment1,beta_diversity/jaccard_distance_matrix-mix8,beta_diversity/bray_curtis_distance_matrix-treatment1,beta_diversity/jaccard_distance_matrix-treatment1,beta_diversity/weighted_unifrac_distance_matrix-treatment1,beta_diversity/weighted_unifrac_distance_matrix-mix8,beta_diversity/unweighted_unifrac_distance_matrix-mix8,beta_diversity/bray_curtis_distance_matrix-mix8',phyloseq='phyloseq/qiime2_phyloseq.rds,phyloseq/pplace_phyloseq.rds',tse='tse/qiime2_TreeSummarizedExperiment.rds,tse/pplace_TreeSummarizedExperiment.rds'), envir = new.env())
    
    writeLines(c("\"NFCORE_AMPLISEQ:AMPLISEQ:SUMMARY_REPORT\":",
        paste0("    R: ", paste0(R.Version()[c("major","minor")], collapse = ".")),
        paste0("    rmarkdown: ", packageVersion("rmarkdown")),
        paste0("    knitr: ", packageVersion("knitr")) ),
        "versions.yml")
  
  Command exit status:
    1
  
  Command output:
    [1] TRUE
    1/159                            
    2/159 [libraries]                
    3/159                            
    4/159 [setup]                    
    5/159                            
    6/159 [unnamed-chunk-1]          
    7/159                            
    8/159 [unnamed-chunk-2]          
    9/159                            
    10/159 [unnamed-chunk-3]          
    11/159                            
    12/159 [unnamed-chunk-4]          
    13/159                            
    14/159 [unnamed-chunk-5]          
    15/159                            
    16/159 [unnamed-chunk-6]          
    17/159                            
    18/159 [unnamed-chunk-7]          
    19/159                            
    20/159 [unnamed-chunk-8]          
    21/159 [!isFALSE(params$mqc_plot)]
  
  Command error:
    [1] TRUE
    
    
    processing file: template.Rmd
    1/159                            
    2/159 [libraries]                
    3/159                            
    4/159 [setup]                    
    5/159                            
    6/159 [unnamed-chunk-1]          
    7/159                            
    8/159 [unnamed-chunk-2]          
    9/159                            
    10/159 [unnamed-chunk-3]          
    11/159                            
    12/159 [unnamed-chunk-4]          
    13/159                            
    14/159 [unnamed-chunk-5]          
    15/159                            
    16/159 [unnamed-chunk-6]          
    17/159                            
    18/159 [unnamed-chunk-7]          
    19/159                            
    20/159 [unnamed-chunk-8]          
    21/159 [!isFALSE(params$mqc_plot)]
    
    Quitting from lines 256-262 [!isFALSE(params$mqc_plot)] (template.Rmd)
    Error in `file.exists()`:
    ! invalid 'file' argument
    Backtrace:
     1. base::file.exists(params$mqc_plot)
    Execution halted
  
  Work dir:
    /home/daluab/dev/nf-core-ampliseq/.nf-test/tests/c6949535cc2e539d759ad6735ccd5062/work/11/19aa79766d62b7c304e463224eac97
  
  Container:
    <http://quay.io/biocontainers/mulled-v2-b2ec1fea5791d428eebb8c8ea7409c350d31dada:a447f6b7a6afde38352b24c30ae9cd6e39df95c4-1|quay.io/biocontainers/mulled-v2-b2ec1fea5791d428eebb8c8ea7409c350d31dada:a447f6b7a6afde38352b24c30ae9cd6e39df95c4-1>
  
  Tip: you can try to figure out what's wrong by changing to the process work dir and showing the script file named `.command.sh`
  
   -- Check '/home/daluab/dev/nf-core-ampliseq/.nf-test/tests/c6949535cc2e539d759ad6735ccd5062/meta/nextflow.log' file for details
  ERROR ~ Pipeline failed. Please refer to troubleshooting docs: <https://nf-co.re/docs/usage/troubleshooting>
  
   -- Check '/home/daluab/dev/nf-core-ampliseq/.nf-test/tests/c6949535cc2e539d759ad6735ccd5062/meta/nextflow.log' file for details
  Nextflow stderr:

The

file.exists(params$mqc_plot)

seems to be funny in your error message above.

Hm got the same error now on github when doing the template update. I can replicate the issue also locally. No idea why that is suddenly appearing.

MultiQC doesnt produce plots any more at all... that was always buggy, seems like its back 😱 Edit: or not... seems to be other stuff 😄

lines 189-226

seem to be related to input samplesheet & metadata.

! line 1 did not have 4 elements

sounds like 4 columns were expected but not found. However, I do not know if its the sample sheet or the metadata that the script complains about. Is there any unusual sign or similar in the first line? Probably the files are not tab separated? (Because that seems needed, but the sample sheet can be other formats...)

That was the case, the first line of samplesheet did not have an extra tab 😄