Add --recursive option to fastq_dir_to_samplesheet.py script

[cutleraging]

Description of the bug

Hello, thanks for your great work with this pipeline. I was trying to use the fastq_dir_to_samplesheet.py script to create the sampleSheet for me but it doesn't seem like it can a directory structure in which each folder contains the paired-end reads fora sample.

What my directory looks like

$ tree
.
├── S1
│   ├── MD5.txt
│   ├── S1_CKDL220024550-1A_HF35HDSX5_L1_1.fq.gz
│   └── S1_CKDL220024550-1A_HF35HDSX5_L1_2.fq.gz
├── S2
│   ├── MD5.txt
│   ├── S2_CKDL220024551-1A_HF35HDSX5_L1_1.fq.gz
│   └── S2_CKDL220024551-1A_HF35HDSX5_L1_2.fq.gz
├── S3
│   ├── MD5.txt
│   ├── S3_CKDL220024552-1A_HF35HDSX5_L1_1.fq.gz
│   └── S3_CKDL220024552-1A_HF35HDSX5_L1_2.fq.gz
├── S4
│   ├── MD5.txt
│   ├── S4_CKDL220024553-1A_HF35HDSX5_L1_1.fq.gz
│   └── S4_CKDL220024553-1A_HF35HDSX5_L1_2.fq.gz
├── S5
│   ├── MD5.txt
│   ├── S5_CKDL220024554-1A_HF35HDSX5_L1_1.fq.gz
│   └── S5_CKDL220024554-1A_HF35HDSX5_L1_2.fq.gz
└── S6
    ├── MD5.txt
    ├── S6_CKDL220024555-1A_HF35HDSX5_L1_1.fq.gz
    └── S6_CKDL220024555-1A_HF35HDSX5_L1_2.fq.gz

How I am running the script. I provide the top directory in which all the sub directories are contained

$ ./fastq_dir_to_samplesheet.py /01.RawData samplesheet.csv --strandedness reverse

WARNING: No FastQ files found so samplesheet has not been created!

Please check the values provided for the:
  - Path to the directory containing the FastQ files
  - '--read1_extension' parameter
  - '--read2_extension' parameter

I also saw on line 100 that recursive is set to False, but I tried changing it to true and still got nothing
return sorted(glob.glob(os.path.join(fastq_dir, f"*{extension}"), recursive=True))

Any help with this? Thanks!

Command used and terminal output

No response

Relevant files

No response

System information

No response

[cutleraging]

Update: I seemed to have made it recursive by changing line 100 to this
return sorted(glob.glob(os.path.join(fastq_dir, f"**/*{extension}"), recursive=True))
Cheers

[drpatelh]

Fixed in #908

Added boolean --recursive option to the script that is off by default.