SRA NBCI fetch and preprossing script only works automatically for illumina sequences about ngs-preprocess HOT 7 CLOSED

nextflow     run fmalmeida/ngs-preprocess     -r dev     -latest     -profile docker     --sra_ids "./input/sra_ids.txt"     --lreads_min_length 750     --output "./preprocessed_data"
N E X T F L O W  ~  version 23.10.1
Pulling fmalmeida/ngs-preprocess ...
 checkout-out at 61b2aab4827693e8af4a8af7e0239d6a33752f81
Launching `https://github.com/fmalmeida/ngs-preprocess` [cheeky_koch] DSL2 - revision: 61b2aab482 [dev]

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  fmalmeida/ngs-preprocess v2.7.0
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Input/output options
  output           : ./preprocessed_data
  sra_ids          : ./input/sra_ids.txt

Long reads parameters
  lreads_min_length: 750

!! Only displaying parameters that differ from the pipeline defaults !!
------------------------------------------------------
If you use fmalmeida/ngs-preprocess for your analysis please cite:

* The pipeline
  https://doi.org/10.12688/f1000research.139488.1

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

* Software dependencies
  https://github.com/fmalmeida/ngs-preprocess#citation
------------------------------------------------------
executor >  local (11)
[53/e5251d] process > SRA_FETCH:GET_FASTQ (SRR9641620)    [100%] 3 of 3 ✔
[2f/ad6a32] process > SRA_FETCH:GET_METADATA (SRR9641620) [100%] 3 of 3 ✔
[-        ] process > NANOPORE:PORECHOP                   -
[-        ] process > NANOPORE:FILTER                     -
[-        ] process > NANOPORE:NANOPACK                   -
[-        ] process > PACBIO:BAM2FASTQ                    -
[54/07888c] process > PACBIO:NANOPACK (SRR9641620)        [100%] 2 of 2 ✔
[c1/959adc] process > PACBIO:FILTER (SRR9641620)          [100%] 2 of 2 ✔
[55/94a3b8] process > ILLUMINA:FASTP (SRR9641621)         [100%] 1 of 1 ✔

Pipeline completed at: 2024-05-13T14:52:32.747676151-04:00
Execution status: OK
Execution duration: 38m 53s
Thank you for using fmalmeida/ngs-preprocess pipeline!
Completed at: 13-May-2024 14:52:33
Duration    : 38m 53s
CPU hours   : 3.4
Succeeded   : 11

nextflow run fmalmeida/ngs-preprocess -profile docker --sra_ids "./input/sra_ids.txt" --lreads_min_length 750 --output "./preprocessed_data"
N E X T F L O W  ~  version 23.10.1
Project `fmalmeida/ngs-preprocess` is currently stickied on revision: v2.6 -- you need to explicitly specify a revision with the option `-r` in order to use it

nextflow run fmalmeida/ngs-preprocess -r master -latest -profile docker --sra_ids "./input/sra_ids.txt" --lreads_min_length 750 --output "./preprocessed_data"

 # Checking Quality
  nanoQC \
      -o NanoQC \
      SRR9641619_15.fastq SRR9641619_10.fastq SRR9641619_11.fastq SRR9641619_16.fastq SRR9641619_21.fastq SRR9641619_5.fastq SRR9641619_1.fastq SRR9641619_12.fastq SRR9641619_18.fastq SRR9641619_7.fastq SRR9641619_22.fastq SRR9641619_25.fastq SRR9641619_17.fastq SRR9641619_6.fastq SRR9641619_28.fastq SRR9641619_19.fastq SRR9641619_4.fastq SRR9641619_20.fastq SRR9641619_29.fastq SRR9641619_24.fastq SRR9641619_13.fastq SRR9641619_3.fastq SRR9641619_9.fastq SRR9641619_31.fastq SRR9641619_23.fastq SRR9641619_14.fastq SRR9641619_26.fastq SRR9641619_2.fastq SRR9641619_8.fastq SRR9641619_30.fastq SRR9641619_27.fastq ;
  
  # Generate Statistics Summary
  NanoStat \
      --fastq SRR9641619_15.fastq SRR9641619_10.fastq SRR9641619_11.fastq SRR9641619_16.fastq SRR9641619_21.fastq SRR9641619_5.fastq SRR9641619_1.fastq SRR9641619_12.fastq SRR9641619_18.fastq SRR9641619_7.fastq SRR9641619_22.fastq SRR9641619_25.fastq SRR9641619_17.fastq SRR9641619_6.fastq SRR9641619_28.fastq SRR9641619_19.fastq SRR9641619_4.fastq SRR9641619_20.fastq SRR9641619_29.fastq SRR9641619_24.fastq SRR9641619_13.fastq SRR9641619_3.fastq SRR9641619_9.fastq SRR9641619_31.fastq SRR9641619_23.fastq SRR9641619_14.fastq SRR9641619_26.fastq SRR9641619_2.fastq SRR9641619_8.fastq SRR9641619_30.fastq SRR9641619_27.fastq \
      -t 4 \
      -n SRR9641619.txt \
      --outdir NanoStats ;

Command exit status:
  2

Command output:
  WARNING: hex as part of --plots has been deprecated and will be ignored. To get the hex output, rerun with --legacy hex.

Command error:
  WARNING: hex as part of --plots has been deprecated and will be ignored. To get the hex output, rerun with --legacy hex.
  usage: nanoQC [-h] [-v] [-o OUTDIR] [--rna] [-l MINLEN] fastq
  nanoQC: error: unrecognized arguments: SRR9641619_10.fastq SRR9641619_11.fastq SRR9641619_16.fastq SRR9641619_21.fastq SRR9641619_5.fastq SRR9641619_1.fastq SRR9641619_12.fastq SRR9641619_18.fastq SRR9641619_7.fastq SRR9641619_22.fastq SRR9641619_25.fastq SRR9641619_17.fastq SRR9641619_6.fastq SRR9641619_28.fastq SRR9641619_19.fastq SRR9641619_4.fastq SRR9641619_20.fastq SRR9641619_29.fastq SRR9641619_24.fastq SRR9641619_13.fastq SRR9641619_3.fastq SRR9641619_9.fastq SRR9641619_31.fastq SRR9641619_23.fastq SRR9641619_14.fastq SRR9641619_26.fastq SRR9641619_2.fastq SRR9641619_8.fastq SRR9641619_30.fastq SRR9641619_27.fastq

nanoQC [-h] [-v] [-o OUTDIR] fastq

positional arguments:
  fastq                 Reads data in fastq.gz format.

optional arguments:
  -h, --help            show this help message and exit
  -v, --version         Print version and exit.
  -o, --outdir OUTDIR   Specify directory in which output has to be created.
  -l, --minlen int      Minimum length of reads to be included in the plots
                        This also controls the length plotted in the graphs
                        from the beginning and end of reads (length plotted = minlen / 2)