fix: append all split FASTA files to the list for TRF execution

[weichisyu]

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Description

The size of the output FASTQ file is different when the -t argument is greater then 1.
I found that it might be caused by line 124 in kneaddata/trf_parallel.py
Since file_handle_write is always not None after the file is opened(line 124), only the first temporary file is appended to the tempfile_written_list and datfile_to_write_list(line 115~116). As a result, the trf command actually executes only one parallel temporary file.

Related Issue

Screenshots (if appropriate):

[sagun98]

Hi @weichisyu ,
Thank you for reaching out to the bioBakery Lab and pointing out the “TRF parallel run” issue + fix. I have added your email and username in the Contribution section of Kneaddata User’s Manual Here: https://github.com/biobakery/kneaddata/blob/master/readme.md#contributions. Please let me know if you would like to change any of your information listed here. Thank you again.

[weichisyu]

Hi @sagun98,
Thank you for reviewing and accepting my PR! I appreciate it.
The information looks correct, and no changes are needed at this time.