Update snakemake

[AroneyS]

• test_short_read_recovery_fast
• test_short_read_recovery_queue_submission
• test_batch_recovery

[AroneyS]

Closes #237

[AroneyS]

@rhysnewell I get a lorikeet warning/error in test_batch_recovery. Do you think its related to this PR somehow?

Activating conda environment: ../../../../test/data/.conda/47d6b70ededa7a59c0365e7833f4e91a_
Activating conda environment: ../../../../test/data/.conda/47d6b70ededa7a59c0365e7833f4e91a_
[2025-01-17T02:12:56Z INFO  lorikeet] lorikeet version 0.8.2
[2025-01-17T02:12:56Z INFO  lorikeet_genome] Using min-read-aligned-percent 0%
[2025-01-17T02:12:56Z INFO  bird_tool_utils::clap_utils] Not using directory entry 'bins/final_bins/.snakemake_timestamp' as a genome FASTA file
[2025-01-17T02:12:56Z INFO  bird_tool_utils::external_command_checker] Found minimap2 version 2.28-r1209 
[2025-01-17T02:12:56Z INFO  bird_tool_utils::external_command_checker] Found samtools version 1.21 
[2025-01-17T02:12:56Z INFO  lorikeet_genome::utils::utils] Not pre-generating minimap2 index
[2025-01-17T02:12:56Z WARN  lorikeet_genome::utils::utils] Not using reference index...
[2025-01-17T02:12:56Z INFO  bird_tool_utils::external_command_checker] Found minimap2 version 2.28-r1209 
[2025-01-17T02:12:56Z INFO  bird_tool_utils::external_command_checker] Found samtools version 1.21 
[2025-01-17T02:12:56Z INFO  lorikeet_genome::utils::utils] Not pre-generating minimap2 index
[2025-01-17T02:12:56Z WARN  lorikeet_genome::utils::utils] Not using reference index...
[2025-01-17T02:12:56Z INFO  bird_tool_utils::external_command_checker] Found samtools version 1.21 
[2025-01-17T02:12:56Z INFO  lorikeet_genome::processing::lorikeet_engine] Processing long reads...
[2025-01-17T02:12:57Z INFO  lorikeet_genome::processing::lorikeet_engine] Processing short reads...
[2025-01-17T02:12:58Z INFO  bird_tool_utils::external_command_checker] Found samtools version 1.21 
[2025-01-17T02:12:58Z INFO  bird_tool_utils::external_command_checker] Found samtools version 1.21 
[2025-01-17T02:13:16Z WARN  lorikeet_genome::processing::lorikeet_engine] Python error PyErr { type: <class 'TypeError'>, value: TypeError("'NoneType' object is not subscriptable"), traceback: Some(<traceback object at 0x7f1ea47975c0>) }
[2025-01-17T02:13:16Z WARN  lorikeet_genome::processing::lorikeet_engine] Python error PyErr { type: <class 'TypeError'>, value: TypeError("'NoneType' object is not subscriptable"), traceback: Some(<traceback object at 0x7f1ea4797a80>) }
[2025-01-17T02:13:21Z INFO  lorikeet] Call complete.