TMPDIR :unbound variable

[erinyoung]

Describe the Bug

I think I almost have this workflow working.

To Reproduce

Steps to reproduce the behavior, including:

1. Command(s) run: Provide the exact command(s) used.

nextflow run CDCgov/neissflow -profile singularity --outdir neisslow --name UT-SH00354-251007 --input samplesheet.csv --pubmlst mlst_db --blastdb blastdb -resume --mash_db $(pwd)/RefSeqSketchesDefaults.msh

2. Input files: Describe or attach relevant input files (e.g., FASTQ, FASTA).

This was my sample sheet

sample,fastq_1,fastq_2
2114118,reads/2114118_S26_L001_R1_001.fastq.gz,reads/2114118_S26_L001_R2_001.fastq.gz
2114122,reads/2114122_S27_L001_R1_001.fastq.gz,reads/2114122_S27_L001_R2_001.fastq.gz

3. Environment:

I was using Singularity

4. Error message: Copy and paste the exact error message or traceback.

 N E X T F L O W   ~  version 25.04.7

Launching `https://github.com/CDCgov/neissflow` [distracted_faraday] DSL2 - revision: a9b8658a64 [main]



------------------------------------------------------
             _          __ _               
  _ __   ___(_)___ ___ / _| | _____      __
 | '_ \ / _ \ / __/ __| |_| |/ _ \ \ /\ / /
 | | | |  __/ \__ \__ \  _| | (_) \ V  V / 
 |_| |_|\___|_|___/___/_| |_|\___/ \_/\_/  

  neissflow/main.nf v2.0.0-ga9b8658
------------------------------------------------------
Core Nextflow options
  revision                  : main
  runName                   : distracted_faraday
  containerEngine           : singularity
  launchDir                 : /Volumes/NGS_2/pulsenet_and_arln/UT-SH00354-251007
  workDir                   : /Volumes/NGS_2/pulsenet_and_arln/UT-SH00354-251007/work
  projectDir                : /home/eriny/.nextflow/assets/CDCgov/neissflow
  userName                  : eriny
  profile                   : singularity
  configFiles               : 

Input/output options
  input                     : samplesheet.csv
  outdir                    : neisslow
  name                      : UT-SH00354-251007

Species ID parameters
  mash_db                   : /Volumes/NGS_2/pulsenet_and_arln/UT-SH00354-251007/RefSeqSketchesDefaults.msh
  FA19_ref                  : /home/eriny/.nextflow/assets/CDCgov/neissflow/assets/FA19.gb

Assembly Parameters
  FA19cg                    : /home/eriny/.nextflow/assets/CDCgov/neissflow/assets/FA19cg.fa

AMR Profiler parameters
  amr_ref                   : /home/eriny/.nextflow/assets/CDCgov/neissflow/assets/amr_genes.gbk
  loci                      : /home/eriny/.nextflow/assets/CDCgov/neissflow/assets/FA19_loci.tsv
  default_amr               : /home/eriny/.nextflow/assets/CDCgov/neissflow/assets/AMR_defaults.tsv
  columns                   : /home/eriny/.nextflow/assets/CDCgov/neissflow/assets/amr_columns.txt
  mtrR_mosaic_ref           : /home/eriny/.nextflow/assets/CDCgov/neissflow/assets/gene_refs/mosaic-mtrR.fasta
  a_blastdb                 : /home/eriny/.nextflow/assets/CDCgov/neissflow/assets/blastdb
  pubmlst                   : mlst_db
  blastdb                   : blastdb
  ngmasterdb                : /home/eriny/.nextflow/assets/CDCgov/neissflow/assets/alleledb/ngmaster/
  ngstar                    : /home/eriny/.nextflow/assets/CDCgov/neissflow/assets/alleledb/ngmaster/pubmlst/ngstar/ngstar.txt
  ngmast                    : /home/eriny/.nextflow/assets/CDCgov/neissflow/assets/alleledb/ngmaster/pubmlst/ngmast/ngmast.txt

Institutional config options
  config_profile_description: null
  config_profile_url        : null

Generic options
  version                   : 2.0

!! Only displaying parameters that differ from the pipeline defaults !!
------------------------------------------------------
If you use neissflow/main.nf for your analysis please cite:

* The pipeline

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

* Software dependencies
  https://github.com/CDCgov/neissflow/main.nf/-/blob/main/CITATIONS.md
------------------------------------------------------
executor >  local (5)
[ad/788341] process > NFCORE_NEISSFLOW:NEISSFLOW:CHECK_FASTQS (2114118)                      [100%] 2 of 2, cached: 2 ✔
[4a/559cfc] process > NFCORE_NEISSFLOW:NEISSFLOW:PREPROCESSING:FASTP (2114118)               [100%] 2 of 2, cached: 2 ✔
[b1/e796b0] process > NFCORE_NEISSFLOW:NEISSFLOW:PREPROCESSING:PARSE_FASTP_REPORTS (2114118) [100%] 2 of 2, cached: 2 ✔
[61/dce4ce] process > NFCORE_NEISSFLOW:NEISSFLOW:PREPROCESSING:COMBINE_FASTP_REPORTS         [100%] 1 of 1, cached: 1 ✔
[68/39aca8] process > NFCORE_NEISSFLOW:NEISSFLOW:PREPROCESSING:FASTP_QC_CHECK                [100%] 1 of 1, cached: 1 ✔
[6e/9d14b4] process > NFCORE_NEISSFLOW:NEISSFLOW:SNIPPY (2114122)                            [  0%] 0 of 2 ✘
[-        ] process > NFCORE_NEISSFLOW:NEISSFLOW:ASSEMBLY:ASSEMBLY_STATS                     -
[-        ] process > NFCORE_NEISSFLOW:NEISSFLOW:ASSEMBLY:QUAST                              -
[e6/3805a9] process > NFCORE_NEISSFLOW:NEISSFLOW:SPECIES_CHECK:MASH (2114118)                [100%] 2 of 2 ✔
[b4/07cbda] process > NFCORE_NEISSFLOW:NEISSFLOW:SPECIES_CHECK:COMBINE_MASH_REPORTS          [100%] 1 of 1 ✔
[-        ] process > NFCORE_NEISSFLOW:NEISSFLOW:SPECIES_CHECK:STATS                         -
[-        ] process > NFCORE_NEISSFLOW:NEISSFLOW:SPECIES_CHECK:COVERAGE                      -
[-        ] process > NFCORE_NEISSFLOW:NEISSFLOW:INITIAL_MERGE                               -
[-        ] process > NFCORE_NEISSFLOW:NEISSFLOW:QC_CHECK                                    -
[-        ] process > NFCORE_NEISSFLOW:NEISSFLOW:AMR_PROFILER:SNIPPY_AMR                     -
[-        ] process > NFCORE_NEISSFLOW:NEISSFLOW:AMR_PROFILER:DEPTH                          -
[-        ] process > NFCORE_NEISSFLOW:NEISSFLOW:AMR_PROFILER:VARIANT_ANALYSIS               -
[-        ] process > NFCORE_NEISSFLOW:NEISSFLOW:AMR_PROFILER:MLST                           -
[-        ] process > NFCORE_NEISSFLOW:NEISSFLOW:AMR_PROFILER:NGMASTER                       -
[-        ] process > NFCORE_NEISSFLOW:NEISSFLOW:AMR_PROFILER:BLASTN                         -
[-        ] process > NFCORE_NEISSFLOW:NEISSFLOW:AMR_PROFILER:MERGE_SINGLE_AMR               -
[-        ] process > NFCORE_NEISSFLOW:NEISSFLOW:AMR_PROFILER:MERGE_AMR                      -
[-        ] process > NFCORE_NEISSFLOW:NEISSFLOW:MERGE_REPORTS                               -
[-        ] process > NFCORE_NEISSFLOW:NEISSFLOW:PHYLOGENY:SNIPPY_CORE                       -
[-        ] process > NFCORE_NEISSFLOW:NEISSFLOW:PHYLOGENY:SNIPPY_CLEAN                      -
[-        ] process > NFCORE_NEISSFLOW:NEISSFLOW:PHYLOGENY:GUBBINS                           -
[-        ] process > NFCORE_NEISSFLOW:NEISSFLOW:PHYLOGENY:COUNT_MONO_NUC                    -
[-        ] process > NFCORE_NEISSFLOW:NEISSFLOW:PHYLOGENY:SNPDISTS                          -
[-        ] process > NFCORE_NEISSFLOW:NEISSFLOW:PHYLOGENY:OUTBREAK_DETECTION                -
[-        ] process > NFCORE_NEISSFLOW:NEISSFLOW:PHYLOGENY:CLUSTER_COLORING                  -
[-        ] process > NFCORE_NEISSFLOW:NEISSFLOW:PHYLOGENY:MAKE_PARTITION_GUIDE              -
[-        ] process > NFCORE_NEISSFLOW:NEISSFLOW:PHYLOGENY:RAXML                             -
[-        ] process > NFCORE_NEISSFLOW:NEISSFLOW:PHYLOGENY:REROOT                            -
[-        ] process > NFCORE_NEISSFLOW:NEISSFLOW:PHYLOGENY:PHYLOGENY_QC                      -
[-        ] process > NFCORE_NEISSFLOW:NEISSFLOW:PHYLOGENY:GOTREE_PNG                        -
[-        ] process > NFCORE_NEISSFLOW:NEISSFLOW:PHYLOGENY:REPORT                            -
[-        ] process > NFCORE_NEISSFLOW:NEISSFLOW:MULTIQC                                     -
Execution cancelled -- Finishing pending tasks before exit
-[neissflow/main.nf] Pipeline completed with errors-
ERROR ~ Error executing process > 'NFCORE_NEISSFLOW:NEISSFLOW:SNIPPY (2114118)'

Caused by:
  Process `NFCORE_NEISSFLOW:NEISSFLOW:SNIPPY (2114118)` terminated with an error exit status (1)


Command executed:

  filename=FA19.gb
  outdir="${filename%.*}"
  
  snippy --cpus 12 --prefix 2114118 --outdir ${outdir}/2114118 --ref FA19.gb --R1 2114118_S26_L001_R1_001.fastq.gz --R2 2114118_S26_L001_R2_001.fastq.gz --tmpdir $TMPDIR --minfrac 0.9 --basequal 20
  
  cat <<-END_VERSIONS > versions.yml
  "NFCORE_NEISSFLOW:NEISSFLOW:SNIPPY":
      snippy: $(echo $(snippy --version 2>&1) | sed 's/snippy //')
  END_VERSIONS

Command exit status:
  1

Command output:
  (empty)

Command error:
  .command.sh: line 5: TMPDIR: unbound variable

Work dir:
  /Volumes/NGS_2/pulsenet_and_arln/UT-SH00354-251007/work/ea/b714b50f6e89316184e91597d08839

Container:
  /Volumes/NGS_2/singularity/depot.galaxyproject.org-singularity-snippy%3A4.6.0--0.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

Expected Behavior

A clear and concise description of what should happen.

I imagine the workflow should have gone to completion.

Screenshots (if applicable)

If applicable, attach screenshots, plots, or error outputs.

I have pasted the error message and attached the nextflow.log.

Logs & Debug Info

• Attach relevant log files (.log, .err, .out). To save logs <command> 2>&1 | tee -a log.txt
• Run the script with --verbose or --debug (if applicable) and attach the output.

Here is the nextflow log file
nextflow.log

Possible fixes

It looks like there's a variable (TMPDIR) that doesn't have a set value in the singularity container for the SNIPPY process.

Additional Context

Any other relevant details, such as links to related issues or discussions.

I think I've set up the pubmlst scheme and mash references correctly.

[kitkatm16]

Hi! This is actually something I'm addressing in updates for the docs. This is the byproduct of a quirk of running Snippy (and other similar tools) on HPC nodes where Snippy attempts to write files to temp space on the nodes that may be full. By setting this environment variable, it allows for the user to control where temp files are written to, preventing memory issues. I recommend updating the profile you are using to run neissflow to include the "env" block seen in the following sample profile:
local {
executor {
name = 'local'
queueSize = 6
}
process {
memory = '16.GB'
cpus = 1
time = '12.h'
}
env {
// TODO: Replace these paths with where you would like your temp files to go
TMP = "/scratch/nextflow/tmp"
TMPDIR = "/scratch/nextflow/tmp"
}
}

Replacing the sample TMP and TMPDIR paths with locations on your machine/system will allow neissflow to run smoothly :)

[erinyoung]

Thank you for the suggestion. I set those variables, and can get the workflow to run this far

$ nextflow run CDCgov/neissflow -profile singularity --outdir neisslow --name UT-SH00354-251007 --input samplesheet.csv --pubmlst mlst_db --blastdb blastdb -resume --mash_db $(pwd)/RefSeqSketchesDefaults.msh -c test_config.config

 N E X T F L O W   ~  version 25.10.0

Launching `https://github.com/CDCgov/neissflow` [compassionate_jepsen] DSL2 - revision: a9b8658a64 [main]



------------------------------------------------------
             _          __ _
  _ __   ___(_)___ ___ / _| | _____      __
 | '_ \ / _ \ / __/ __| |_| |/ _ \ \ /\ / /
 | | | |  __/ \__ \__ \  _| | (_) \ V  V /
 |_| |_|\___|_|___/___/_| |_|\___/ \_/\_/

  neissflow/main.nf v2.0.0-ga9b8658
------------------------------------------------------
Core Nextflow options
  revision                  : main
  runName                   : compassionate_jepsen
  containerEngine           : singularity
  launchDir                 : /Volumes/NGS_2/pulsenet_and_arln/UT-SH00354-251007
  workDir                   : /Volumes/NGS_2/pulsenet_and_arln/UT-SH00354-251007/work
  projectDir                : /home/eriny/.nextflow/assets/CDCgov/neissflow
  userName                  : eriny
  profile                   : singularity
  configFiles               :

Input/output options
  input                     : samplesheet.csv
  outdir                    : neisslow
  name                      : UT-SH00354-251007

Species ID parameters
  mash_db                   : /Volumes/NGS_2/pulsenet_and_arln/UT-SH00354-251007/RefSeqSketchesDefaults.msh
  FA19_ref                  : /home/eriny/.nextflow/assets/CDCgov/neissflow/assets/FA19.gb

Assembly Parameters
  FA19cg                    : /home/eriny/.nextflow/assets/CDCgov/neissflow/assets/FA19cg.fa

AMR Profiler parameters
  amr_ref                   : /home/eriny/.nextflow/assets/CDCgov/neissflow/assets/amr_genes.gbk
  loci                      : /home/eriny/.nextflow/assets/CDCgov/neissflow/assets/FA19_loci.tsv
  default_amr               : /home/eriny/.nextflow/assets/CDCgov/neissflow/assets/AMR_defaults.tsv
  columns                   : /home/eriny/.nextflow/assets/CDCgov/neissflow/assets/amr_columns.txt
  mtrR_mosaic_ref           : /home/eriny/.nextflow/assets/CDCgov/neissflow/assets/gene_refs/mosaic-mtrR.fasta
  a_blastdb                 : /home/eriny/.nextflow/assets/CDCgov/neissflow/assets/blastdb
  pubmlst                   : mlst_db
  blastdb                   : blastdb
  ngmasterdb                : /home/eriny/.nextflow/assets/CDCgov/neissflow/assets/alleledb/ngmaster/
  ngstar                    : /home/eriny/.nextflow/assets/CDCgov/neissflow/assets/alleledb/ngmaster/pubmlst/ngstar/ngstar.txt
  ngmast                    : /home/eriny/.nextflow/assets/CDCgov/neissflow/assets/alleledb/ngmaster/pubmlst/ngmast/ngmast.txt

Institutional config options
  config_profile_description: null
  config_profile_url        : null

Generic options
  version                   : 2.0

!! Only displaying parameters that differ from the pipeline defaults !!
------------------------------------------------------
If you use neissflow/main.nf for your analysis please cite:

* The pipeline

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

* Software dependencies
  https://github.com/CDCgov/neissflow/main.nf/-/blob/main/CITATIONS.md
------------------------------------------------------
executor >  local (17)
[3a/4ece49] process > NFCORE_NEISSFLOW:NEISSFLOW:CHECK_FASTQS (2114122)                      [100%] 2 of 2 ✔
[df/b42c17] process > NFCORE_NEISSFLOW:NEISSFLOW:PREPROCESSING:FASTP (2114122)               [100%] 2 of 2 ✔
[49/ab0042] process > NFCORE_NEISSFLOW:NEISSFLOW:PREPROCESSING:PARSE_FASTP_REPORTS (2114122) [100%] 2 of 2 ✔
[4c/bfac7a] process > NFCORE_NEISSFLOW:NEISSFLOW:PREPROCESSING:COMBINE_FASTP_REPORTS         [100%] 1 of 1 ✔
[94/cf5c58] process > NFCORE_NEISSFLOW:NEISSFLOW:PREPROCESSING:FASTP_QC_CHECK                [100%] 1 of 1 ✔
[e1/67c7e2] process > NFCORE_NEISSFLOW:NEISSFLOW:SNIPPY (2114122)                            [100%] 2 of 2 ✔
[-        ] process > NFCORE_NEISSFLOW:NEISSFLOW:ASSEMBLY:ASSEMBLY_STATS                     -
[-        ] process > NFCORE_NEISSFLOW:NEISSFLOW:ASSEMBLY:QUAST                              -
[5d/1b895a] process > NFCORE_NEISSFLOW:NEISSFLOW:SPECIES_CHECK:MASH (2114122)                [100%] 2 of 2 ✔
[8a/24f714] process > NFCORE_NEISSFLOW:NEISSFLOW:SPECIES_CHECK:COMBINE_MASH_REPORTS          [100%] 1 of 1 ✔
[f7/20ada3] process > NFCORE_NEISSFLOW:NEISSFLOW:SPECIES_CHECK:STATS (2114122)               [100%] 2 of 2 ✔
[b2/4fbfea] process > NFCORE_NEISSFLOW:NEISSFLOW:SPECIES_CHECK:COVERAGE                      [100%] 1 of 1 ✔
[-        ] process > NFCORE_NEISSFLOW:NEISSFLOW:INITIAL_MERGE                               -
[-        ] process > NFCORE_NEISSFLOW:NEISSFLOW:QC_CHECK                                    -
[-        ] process > NFCORE_NEISSFLOW:NEISSFLOW:AMR_PROFILER:SNIPPY_AMR                     -
[-        ] process > NFCORE_NEISSFLOW:NEISSFLOW:AMR_PROFILER:DEPTH                          -
[-        ] process > NFCORE_NEISSFLOW:NEISSFLOW:AMR_PROFILER:VARIANT_ANALYSIS               -
[-        ] process > NFCORE_NEISSFLOW:NEISSFLOW:AMR_PROFILER:MLST                           -
[-        ] process > NFCORE_NEISSFLOW:NEISSFLOW:AMR_PROFILER:NGMASTER                       -
[-        ] process > NFCORE_NEISSFLOW:NEISSFLOW:AMR_PROFILER:BLASTN                         -
[-        ] process > NFCORE_NEISSFLOW:NEISSFLOW:AMR_PROFILER:MERGE_SINGLE_AMR               -
[-        ] process > NFCORE_NEISSFLOW:NEISSFLOW:AMR_PROFILER:MERGE_AMR                      -
[-        ] process > NFCORE_NEISSFLOW:NEISSFLOW:MERGE_REPORTS                               -
[-        ] process > NFCORE_NEISSFLOW:NEISSFLOW:PHYLOGENY:SNIPPY_CORE                       -
[-        ] process > NFCORE_NEISSFLOW:NEISSFLOW:PHYLOGENY:SNIPPY_CLEAN                      -
[-        ] process > NFCORE_NEISSFLOW:NEISSFLOW:PHYLOGENY:GUBBINS                           -
[-        ] process > NFCORE_NEISSFLOW:NEISSFLOW:PHYLOGENY:COUNT_MONO_NUC                    -
[-        ] process > NFCORE_NEISSFLOW:NEISSFLOW:PHYLOGENY:SNPDISTS                          -
[-        ] process > NFCORE_NEISSFLOW:NEISSFLOW:PHYLOGENY:OUTBREAK_DETECTION                -
[-        ] process > NFCORE_NEISSFLOW:NEISSFLOW:PHYLOGENY:CLUSTER_COLORING                  -
[-        ] process > NFCORE_NEISSFLOW:NEISSFLOW:PHYLOGENY:MAKE_PARTITION_GUIDE              -
[-        ] process > NFCORE_NEISSFLOW:NEISSFLOW:PHYLOGENY:RAXML                             -
[-        ] process > NFCORE_NEISSFLOW:NEISSFLOW:PHYLOGENY:REROOT                            -
[-        ] process > NFCORE_NEISSFLOW:NEISSFLOW:PHYLOGENY:PHYLOGENY_QC                      -
[-        ] process > NFCORE_NEISSFLOW:NEISSFLOW:PHYLOGENY:GOTREE_PNG                        -
[-        ] process > NFCORE_NEISSFLOW:NEISSFLOW:PHYLOGENY:REPORT                            -
[2d/bf066e] process > NFCORE_NEISSFLOW:NEISSFLOW:MULTIQC                                     [100%] 1 of 1 ✔
-[neissflow/main.nf] Pipeline completed successfully-
Completed at: 18-Nov-2025 12:18:15
Duration    : 1m 53s
CPU hours   : 0.5
Succeeded   : 17

[kitkatm16]

Looks like you're missing one of these:

Input Type (required & PIPELINE WILL FAIL WITHOUT)
--only_fastq                   Use flag if only FASTQ input is provided (entire pipeline can run with just FASTQ input) [boolean]
--only_fasta                   Use flag if only FASTA contigs are provided (only snippy and the Phylogeny Subworkflow will run with this input) [boolean]
--fastq_w_fasta             Use flag if FASTQ and FASTA input are provided (entire pipeline can run with this input) [boolean]

I'm adding the all caps disclaimer in the updated docs since it seems like these get missed a lot

[erinyoung]

Thank you for your help with this (and I apologize for not getting the usage right)!

This is as far as I'm getting now

$ nextflow run CDCgov/neissflow -profile singularity --outdir neisslow --name UT-SH00354-251007 --input samplesheet.csv --pubmlst mlst_db --blastdb blastdb -resume --mash_db $(pwd)/RefSeqSketchesDefaults.msh -c test_config.config --only_fastq

 N E X T F L O W   ~  version 25.10.0

Launching `https://github.com/CDCgov/neissflow` [elegant_carson] DSL2 - revision: a9b8658a64 [main]



------------------------------------------------------
             _          __ _
  _ __   ___(_)___ ___ / _| | _____      __
 | '_ \ / _ \ / __/ __| |_| |/ _ \ \ /\ / /
 | | | |  __/ \__ \__ \  _| | (_) \ V  V /
 |_| |_|\___|_|___/___/_| |_|\___/ \_/\_/

  neissflow/main.nf v2.0.0-ga9b8658
------------------------------------------------------
Core Nextflow options
  revision                  : main
  runName                   : elegant_carson
  containerEngine           : singularity
  launchDir                 : /Volumes/NGS_2/pulsenet_and_arln/UT-SH00354-251007
  workDir                   : /Volumes/NGS_2/pulsenet_and_arln/UT-SH00354-251007/work
  projectDir                : /home/eriny/.nextflow/assets/CDCgov/neissflow
  userName                  : eriny
  profile                   : singularity
  configFiles               :

Input/output options
  input                     : samplesheet.csv
  outdir                    : neisslow
  name                      : UT-SH00354-251007

Input Type
  only_fastq                : true

Species ID parameters
  mash_db                   : /Volumes/NGS_2/pulsenet_and_arln/UT-SH00354-251007/RefSeqSketchesDefaults.msh
  FA19_ref                  : /home/eriny/.nextflow/assets/CDCgov/neissflow/assets/FA19.gb

Assembly Parameters
  FA19cg                    : /home/eriny/.nextflow/assets/CDCgov/neissflow/assets/FA19cg.fa

AMR Profiler parameters
  amr_ref                   : /home/eriny/.nextflow/assets/CDCgov/neissflow/assets/amr_genes.gbk
  loci                      : /home/eriny/.nextflow/assets/CDCgov/neissflow/assets/FA19_loci.tsv
  default_amr               : /home/eriny/.nextflow/assets/CDCgov/neissflow/assets/AMR_defaults.tsv
  columns                   : /home/eriny/.nextflow/assets/CDCgov/neissflow/assets/amr_columns.txt
  mtrR_mosaic_ref           : /home/eriny/.nextflow/assets/CDCgov/neissflow/assets/gene_refs/mosaic-mtrR.fasta
  a_blastdb                 : /home/eriny/.nextflow/assets/CDCgov/neissflow/assets/blastdb
  pubmlst                   : mlst_db
  blastdb                   : blastdb
  ngmasterdb                : /home/eriny/.nextflow/assets/CDCgov/neissflow/assets/alleledb/ngmaster/
  ngstar                    : /home/eriny/.nextflow/assets/CDCgov/neissflow/assets/alleledb/ngmaster/pubmlst/ngstar/ngstar.txt
  ngmast                    : /home/eriny/.nextflow/assets/CDCgov/neissflow/assets/alleledb/ngmaster/pubmlst/ngmast/ngmast.txt

Institutional config options
  config_profile_description: null
  config_profile_url        : null

Generic options
  version                   : 2.0

!! Only displaying parameters that differ from the pipeline defaults !!
------------------------------------------------------
If you use neissflow/main.nf for your analysis please cite:

* The pipeline

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

* Software dependencies
  https://github.com/CDCgov/neissflow/main.nf/-/blob/main/CITATIONS.md
------------------------------------------------------
executor >  local (8)
[3a/4ece49] process > NFCORE_NEISSFLOW:NEISSFLOW:CHECK_FASTQS (2114122)                      [100%] 2 of 2, cached: 2 ✔
[98/2589ac] process > NFCORE_NEISSFLOW:NEISSFLOW:PREPROCESSING:FASTP (2114118)               [100%] 2 of 2, cached: 2 ✔
[49/ab0042] process > NFCORE_NEISSFLOW:NEISSFLOW:PREPROCESSING:PARSE_FASTP_REPORTS (2114122) [100%] 2 of 2, cached: 2 ✔
[4c/bfac7a] process > NFCORE_NEISSFLOW:NEISSFLOW:PREPROCESSING:COMBINE_FASTP_REPORTS         [100%] 1 of 1, cached: 1 ✔
[94/cf5c58] process > NFCORE_NEISSFLOW:NEISSFLOW:PREPROCESSING:FASTP_QC_CHECK                [100%] 1 of 1, cached: 1 ✔
[53/ce7784] process > NFCORE_NEISSFLOW:NEISSFLOW:SNIPPY (2114118)                            [100%] 2 of 2, cached: 2 ✔
[16/423309] process > NFCORE_NEISSFLOW:NEISSFLOW:ASSEMBLY:SHOVILL (2114122)                  [100%] 2 of 2 ✔
[c9/75a52a] process > NFCORE_NEISSFLOW:NEISSFLOW:ASSEMBLY:ASSEMBLY_STATS                     [100%] 1 of 1 ✔
[13/3ee125] process > NFCORE_NEISSFLOW:NEISSFLOW:ASSEMBLY:QUAST (2114122)                    [100%] 2 of 2 ✔
[5d/1b895a] process > NFCORE_NEISSFLOW:NEISSFLOW:SPECIES_CHECK:MASH (2114122)                [100%] 2 of 2, cached: 2 ✔
[8a/24f714] process > NFCORE_NEISSFLOW:NEISSFLOW:SPECIES_CHECK:COMBINE_MASH_REPORTS          [100%] 1 of 1, cached: 1 ✔
[f7/20ada3] process > NFCORE_NEISSFLOW:NEISSFLOW:SPECIES_CHECK:STATS (2114122)               [100%] 2 of 2, cached: 2 ✔
[b2/4fbfea] process > NFCORE_NEISSFLOW:NEISSFLOW:SPECIES_CHECK:COVERAGE                      [100%] 1 of 1, cached: 1 ✔
[00/df5664] process > NFCORE_NEISSFLOW:NEISSFLOW:INITIAL_MERGE                               [100%] 1 of 1 ✔
[ee/26fca8] process > NFCORE_NEISSFLOW:NEISSFLOW:QC_CHECK                                    [100%] 1 of 1 ✔
[-        ] process > NFCORE_NEISSFLOW:NEISSFLOW:AMR_PROFILER:SNIPPY_AMR                     -
[-        ] process > NFCORE_NEISSFLOW:NEISSFLOW:AMR_PROFILER:DEPTH                          -
[-        ] process > NFCORE_NEISSFLOW:NEISSFLOW:AMR_PROFILER:VARIANT_ANALYSIS               -
[-        ] process > NFCORE_NEISSFLOW:NEISSFLOW:AMR_PROFILER:MLST                           -
[-        ] process > NFCORE_NEISSFLOW:NEISSFLOW:AMR_PROFILER:NGMASTER                       -
[-        ] process > NFCORE_NEISSFLOW:NEISSFLOW:AMR_PROFILER:BLASTN                         -
[-        ] process > NFCORE_NEISSFLOW:NEISSFLOW:AMR_PROFILER:MERGE_SINGLE_AMR               -
[-        ] process > NFCORE_NEISSFLOW:NEISSFLOW:AMR_PROFILER:MERGE_AMR                      -
[-        ] process > NFCORE_NEISSFLOW:NEISSFLOW:MERGE_REPORTS                               -
[-        ] process > NFCORE_NEISSFLOW:NEISSFLOW:PHYLOGENY:SNIPPY_CORE                       -
[-        ] process > NFCORE_NEISSFLOW:NEISSFLOW:PHYLOGENY:SNIPPY_CLEAN                      -
[-        ] process > NFCORE_NEISSFLOW:NEISSFLOW:PHYLOGENY:GUBBINS                           -
[-        ] process > NFCORE_NEISSFLOW:NEISSFLOW:PHYLOGENY:COUNT_MONO_NUC                    -
[-        ] process > NFCORE_NEISSFLOW:NEISSFLOW:PHYLOGENY:SNPDISTS                          -
[-        ] process > NFCORE_NEISSFLOW:NEISSFLOW:PHYLOGENY:OUTBREAK_DETECTION                -
[-        ] process > NFCORE_NEISSFLOW:NEISSFLOW:PHYLOGENY:CLUSTER_COLORING                  -
[-        ] process > NFCORE_NEISSFLOW:NEISSFLOW:PHYLOGENY:MAKE_PARTITION_GUIDE              -
[-        ] process > NFCORE_NEISSFLOW:NEISSFLOW:PHYLOGENY:RAXML                             -
[-        ] process > NFCORE_NEISSFLOW:NEISSFLOW:PHYLOGENY:REROOT                            -
[-        ] process > NFCORE_NEISSFLOW:NEISSFLOW:PHYLOGENY:PHYLOGENY_QC                      -
[-        ] process > NFCORE_NEISSFLOW:NEISSFLOW:PHYLOGENY:GOTREE_PNG                        -
[-        ] process > NFCORE_NEISSFLOW:NEISSFLOW:PHYLOGENY:REPORT                            -
[87/a8ce35] process > NFCORE_NEISSFLOW:NEISSFLOW:MULTIQC                                     [100%] 1 of 1 ✔
-[neissflow/main.nf] Pipeline completed successfully-
Completed at: 18-Nov-2025 13:15:33
Duration    : 1m 37s
CPU hours   : 1.0 (49.1% cached)
Succeeded   : 8
Cached      : 16

It seems like these samples passed QC, so I must be missing another flag. I'm hoping to run this workflow like the GC program would expect me to. I've attached the passed_qc1.tsv file here.

neissflow_passed_qc1.tsv

[kitkatm16]

This would be expected behavior if your samples passed QC check 1, but failed QC check 2. Can you check the neissflow_passed_qc2.tsv file? It can be found in neissflow_out/QC_CHECK/

[kitkatm16]

If you want to test the entire pipeline with samples that are guaranteed to pass both, I recommend using the test set that's included with the repo

[erinyoung]

It does look they failed assembly QC.

I chose these two because they already passed QC on CDC's side, are you using more stringent metrics?

[kitkatm16]

neissflow uses the QC metrics decided upon by CDC's STD Laboratory Reference and Research Branch. The QC criteria can be found in the README

[kitkatm16]

These QC metrics are more recent so if those samples are older they may have previously passed

[erinyoung]

I reran the test profile, and ran into this error:

I thought I already created an issue for this, but I must be mis-remembering. The test profile has a filename issue.

$ nextflow run CDCgov/neissflow -profile singularity,test --outdir neissflow --name test --pubmlst mlst_db --blastdb blastdb -resume --mash_db $(pwd)/RefSeqSketchesDefaults.msh -c test_config.config --only_fastq

 N E X T F L O W   ~  version 25.10.0

The specified configuration file does not exist: /Volumes/NGS_2/Bioinformatics/eriny/testing_neissflow/test_config.config -- check the name or choose another file

[kitkatm16]

In order for the test profile to work you'll need to change the path to the input samplesheet in the test.config. Another quirk of Nextflow is that ${projectDir} doesn't actually work outside of nextflow.config, and I only included this as a placeholder. In order to get this to work, swap ${projectDir} out for the actual path to the repo.

The error you're showing there seems to actually be unrelated, and it seems like test_config.config that you're passing in with -c test_config.config is not file.

I thought I had included these instructions in the docs, but I can't seem to find it so that would be a good thing for me to add!

[erinyoung]

There's a few workarounds for that, the nf-core standard is to set a path as a param.

Here's some examples
Viralrecon : https://github.com/nf-core/viralrecon/blob/master/conf/test.config
TaxProfiler: https://github.com/nf-core/taxprofiler/blob/master/conf/test.config

[kitkatm16]

Thank you for showing me! I'll see if I can get that to work in this case