"Access to 'QC_2.out' is undefined" error

[rvijay-seqcoast]

Description of the bug

I am running into an issue when running hybrid assembly with ONT long reads and Illumina short reads. The error is at line 429 in readassembly.nf and states that 'QC_2.out' is undefined because 'QC_2' has not been invoked. I am assuming this error relates to the conditional logic at lines 409-424 in readassembly.nf.

Command used and terminal output

nextflow run https://github.com/emilytrybulec/argonaut \
         -name assembly_4994_1 \
         -params-file https://api.cloud.seqera.io/ephemeral/y9CYlh4OE0Wtcy26SiklzA.json \
         -with-tower \
         -r v.1.0.2 \
         -profile docker

Nextflow 24.04.2 is available - Please consider updating your version to it
N E X T F L O W  ~  version 23.10.1
Pulling emilytrybulec/argonaut ...
 downloaded from https://github.com/emilytrybulec/argonaut.git
Launching `https://github.com/emilytrybulec/argonaut` [assembly_4994_1] DSL2 - revision: 5becfa566c [v.1.0.2]
 _______________________________________________________
   __    __    __    __          __       ___
  |__|  |__|  | _   |  |  |\ |  |__| |  |  | 
  |  |  |  \  |__|  |__|  | \|  |  | |__|  |  
 _______________________________________________________
Core Nextflow options
  revision         : v.1.0.2
  runName          : assembly_4994_1
  containerEngine  : docker
  launchDir        : /
  workDir          : /seqcoast-aws/scratch/1rK7Rm6o5pNQfZ
  projectDir       : /.nextflow/assets/emilytrybulec/argonaut
  userName         : root
  profile          : docker
  configFiles      : /.nextflow/assets/emilytrybulec/argonaut/nextflow.config, /nextflow.config
Input options
  ONT_lr           : true
  PacBioHifi_lr    : false
  summary_txt_file : false
  shortread        : true
Short read QC options
  save_trimmed_fail: false
  save_merged      : false
Assembly options
  redundans        : false
Purge options
  purge            : true
Scaffolding options
  ragtag_scaffold  : false
Required params
  input            : s3://seqcoast-aws/seqcoast_team/seqera_test/argonaut_4994/4994_1/4994_1_ont_samplesheet.csv
  shortinput       : s3://seqcoast-aws/seqcoast_team/seqera_test/argonaut_4994/4994_1/4994_1_illumina_samplesheet.csv
  fastq            : s3://seqcoast-aws/seqcoast_team/seqera_test/argonaut_4994/4994_1/4994_1_long_combined.fastq.gz
  centrifuge_db    : s3://seqcoast-aws/seqcoast_team/reference-dbs/centrifuge/
  kraken_db        : s3://seqcoast-aws/seqcoast_team/reference-dbs/k2_standard_16gb_20240112.tar.gz
  rcf_db           : s3://seqcoast-aws/seqcoast_team/reference-dbs/recentrifuge/taxdump/
  busco_lineage    : fungi_odb10
  outdir           : s3://seqcoast-aws/seqcoast_team/seqera_test/argonaut_4994/4994_1/
Max job request options
  max_cpus         : 32
  max_memory       : 200.GB
!! Only displaying parameters that differ from the pipeline defaults !!
------------------------------------------------------
If you use nf-core/genomeassembly for your analysis please cite:
* The nf-core framework
  https://doi.org/10.1038/s41587-020-0439-x
* Software dependencies
  https://github.com/nf-core/genomeassembly/blob/master/CITATIONS.md
------------------------------------------------------
WARN: Found unexpected parameters:
* --blast_db: null
* --taxon_taxdump: null
* --taxon_taxid: null
* --pb_xml: null
* --samtools_sort: true
* --kraken_ill: true
* --kraken_pb: true
* --centrifuge_ont: true
- Ignore this warning: params.schema_ignore_params = "blast_db,taxon_taxdump,taxon_taxid,pb_xml,samtools_sort,kraken_ill,kraken_pb,centrifuge_ont" 
WARN: Access to undefined parameter `genomes` -- Initialise it to a default value eg. `params.genomes = some_value`
Uploading local `bin` scripts folder to s3://seqcoast-aws/scratch/1rK7Rm6o5pNQfZ/tmp/14/d07f03d27c4941adac215b7def6e5d/bin
assembling long reads with flye!
hybrid assembly with maSuRCA!
polishing assemblies with racon!
polishing assemblies with short reads using POLCA!
Access to 'QC_2.out' is undefined since the workflow 'QC_2' has not been invoked before accessing the output attribute
 -- Check script '.nextflow/assets/emilytrybulec/argonaut/./workflows/readassembly.nf' at line: 429 or see 'nf-1rK7Rm6o5pNQfZ.log' file for more details

Relevant files

No response

System information

Nextflow version: 23.10.1
Hardware: AWS
Executor: awsbatch
Container engine: Docker
OS: Linux
Version of argonaut: 1.0.2

[emilytrybulec]

Hi, thank you for bringing this to our attention- I believe the bug has been resolved. Please try resuming