Adding nanopore functionality

[erinyoung]

Because of requests to input nanopore reads into this workflow, the artic pipeline has been added. This is a relatively new feature, and it would help if any errors and anomalies became issues so that they can resolved quickly.

[erinyoung]

Looks like I need to create my own artic container :

Command error:
  [M::mm_idx_stat::0.008*1.35] distinct minimizers: 5[587](https://github.com/UPHL-BioNGS/Cecret/actions/runs/6043198519/job/16399778645?pr=221#step:5:588) (99.93% are singletons); average occurrences: 1.004; average spacing: 5.332; total length: 29903
  [M::worker_pipeline::3.075*1.48] mapped 20706 sequences
  [M::main] Version: 2.24-r1122
  [M::main] CMD: minimap2 -a -x map-ont -t 2 schema/cecret/V1/cecret.reference.fasta SRR22452250_1_filtered.fastq.gz
  [M::main] Real time: 3.076 sec; CPU: 4.563 sec; Peak RSS: 0.039 GB
  Traceback (most recent call last):
    File "/usr/local/lib/python3.8/site-packages/medaka/medaka.py", line 35, in __call__
      model_fp = medaka.models.resolve_model(val)
    File "/usr/local/lib/python3.8/site-packages/medaka/models.py", line 87, in resolve_model
      raise RuntimeError(
  RuntimeError: The model file for r941_min_high_g360 is not installed and could not be installed to any of /usr/local/lib/python3.8/site-packages/medaka/data or /.medaka/data. If you cannot gain write permissions, download the model file manually from https://github.com/nanoporetech/medaka/raw/master/medaka/data/r941_min_high_g360_model.hdf5 and use the downloaded model as the --model option.
  
  During handling of the above exception, another exception occurred:
  
  Traceback (most recent call last):
    File "/usr/local/bin/medaka", line 11, in <module>
      sys.exit(main())
    File "/usr/local/lib/python3.8/site-packages/medaka/medaka.py", line 699, in main
      args = parser.parse_args()
    File "/usr/local/lib/python3.8/argparse.py", line 1768, in parse_args
      args, argv = self.parse_known_args(args, namespace)
    File "/usr/local/lib/python3.8/argparse.py", line 1800, in parse_known_args
      namespace, args = self._parse_known_args(args, namespace)
    File "/usr/local/lib/python3.8/argparse.py", line 1988, in _parse_known_args
      positionals_end_index = consume_positionals(start_index)
    File "/usr/local/lib/python3.8/argparse.py", line 1965, in consume_positionals
      take_action(action, args)
    File "/usr/local/lib/python3.8/argparse.py", line 1874, in take_action
      action(self, namespace, argument_values, option_string)
    File "/usr/local/lib/python3.8/argparse.py", line 1159, in __call__
      subnamespace, arg_strings = parser.parse_known_args(arg_strings, None)
    File "/usr/local/lib/python3.8/argparse.py", line 1800, in parse_known_args
      namespace, args = self._parse_known_args(args, namespace)
    File "/usr/local/lib/python3.8/argparse.py", line 2006, in _parse_known_args
      start_index = consume_optional(start_index)
    File "/usr/local/lib/python3.8/argparse.py", line 1946, in consume_optional
      take_action(action, args, option_string)
    File "/usr/local/lib/python3.8/argparse.py", line 1874, in take_action
      action(self, namespace, argument_values, option_string)
    File "/usr/local/lib/python3.8/site-packages/medaka/medaka.py", line 38, in __call__
      raise RuntimeError(msg.format(self.dest, str(e)))
  RuntimeError: Error validating model from '--model' argument: The model file for r941_min_high_g360 is not installed and could not be installed to any of /usr/local/lib/python3.8/site-packages/medaka/data or /.medaka/data. If you cannot gain write permissions, download the model file manually from https://github.com/nanoporetech/medaka/raw/master/medaka/data/r941_min_high_g360_model.hdf5 and use the downloaded model as the --model option..
  Running: minimap2 -a -x map-ont -t 2 schema/cecret/V1/cecret.reference.fasta SRR22452250_1_filtered.fastq.gz | samtools view -bS -F 4 - | samtools sort -o artic/SRR22452250_1.sorted.bam -
  Running: samtools index artic/SRR22452250_1.sorted.bam
  Running: align_trim --normalise 200 schema/cecret/V1/cecret.scheme.bed --start --remove-incorrect-pairs --report artic/SRR22452250_1.alignreport.txt < artic/SRR22452250_1.sorted.bam 2> artic/SRR22452250_1.alignreport.er | samtools sort -T artic/SRR22452250_1 - -o artic/SRR22452250_1.trimmed.rg.sorted.bam
  Running: align_trim --normalise 200 schema/cecret/V1/cecret.scheme.bed --remove-incorrect-pairs --report artic/SRR22452250_1.alignreport.txt < artic/SRR22452250_1.sorted.bam 2> artic/SRR22452250_1.alignreport.er | samtools sort -T artic/SRR22452250_1 - -o artic/SRR22452250_1.primertrimmed.rg.sorted.bam
  Running: samtools index artic/SRR22452250_1.trimmed.rg.sorted.bam
  Running: samtools index artic/SRR22452250_1.primertrimmed.rg.sorted.bam
  Running: medaka consensus --model r941_min_high_g360 --threads 2 --chunk_len 800 --chunk_ovlp 400 --RG 1 artic/SRR22452250_1.trimmed.rg.sorted.bam artic/SRR22452250_1.1.hdf
  Command failed:medaka consensus --model r941_min_high_g360 --threads 2 --chunk_len 800 --chunk_ovlp 400 --RG 1 artic/SRR22452250_1.trimmed.rg.sorted.bam artic/SRR22452250_1.1.hdf