Update Sniffles from 1.0.12 to 2.4

[fubar2]

• This PR does something else (explain below)

Update sniffles from 1.0.12 from 2020, to most recent 2.4 https://www.nature.com/articles/s41587-023-02024-y
Nearly all parameter names have changed over 4 years and dozens of new ones have been introduced.

This PR provides parameters to control the core use case (make a VCF with SV from a bam) at https://github.com/fritzsedlazeck/Sniffles?tab=readme-ov-file.

Could be sniffles2 as the author now calls it if we need a new tool after all this time? Keeping the tool id still allows the current old version to be run if anyone needs it - and one less new tool in the list.

Anyone know anyone using sniffles for long read SV detection?
New version has features for SV in populations - such as cancer patients, but would need a new .snf datatype, more tests/parameters and someone who really wants to work on it.

[bgruening]

@wm75 @npinter can you please have a look, or let us know if you prefer a separate v2 tool?

[fubar2]

@wm75 @npinter can you please have a look, or let us know if you prefer a separate v2 tool?

Weekly ping: @bgruening @wm75 @npinter - advice appreciated - do you prefer to make the tool menu a little longer, or keep this as a routinely updated sniffles and allow users to select and run the unchanged old version if they need?

One way or another, would really like to get this merged for VGP data please - tests look very interesting.

[fubar2]

The 4 year old IUC version of sniffles emits VCF that tabix refuses to index without a vcf sort:

[E::hts_idx_push] Unsorted positions on sequence #1: 163301 followed by 163203

DEBUG:jbrowse:bgzip -c /data/dnb10/galaxy_db/files/1/e/3/dataset_1e30b767-d1bd-43bd-b3b0-556d9f3d74f2.dat  > /data/jwd05e/main/073/596/73596814/outputs/dataset_9e76ca47-d642-4d54-bf6f-6366236275ca_files/sniffles_on_data_70_4
DEBUG:jbrowse:cd /data/jwd05e/main/073/596/73596814/outputs/dataset_9e76ca47-d642-4d54-bf6f-6366236275ca_files && tabix -f -p vcf /data/jwd05e/main/073/596/73596814/outputs/dataset_9e76ca47-d642-4d54-bf6f-6366236275ca_files/sniffles_on_data_70_4
[E::hts_idx_push] Unsorted positions on sequence #1: 163301 followed by 163203
tbx_index_build3 failed: /data/jwd05e/main/073/596/73596814/outputs/dataset_9e76ca47-d642-4d54-bf6f-6366236275ca_files/sniffles_on_data_70_4
Traceback (most recent call last):
  File "/opt/galaxy/shed_tools/toolshed.g2.bx.psu.edu/repos/fubar/jbrowse2/c4b77883c0a7/jbrowse2/jbrowse2.py", line 1712, in <module>
    for key in keys:
  File "/opt/galaxy/shed_tools/toolshed.g2.bx.psu.edu/repos/fubar/jbrowse2/c4b77883c0a7/jbrowse2/jbrowse2.py", line 1328, in process_annotations
    self.add_vcf(dataset_path, outputTrackConfig)
  File "/opt/galaxy/shed_tools/toolshed.g2.bx.psu.edu/repos/fubar/jbrowse2/c4b77883c0a7/jbrowse2/jbrowse2.py", line 975, in add_vcf
    self.subprocess_check_call(cmd)
  File "/opt/galaxy/shed_tools/toolshed.g2.bx.psu.edu/repos/fubar/jbrowse2/c4b77883c0a7/jbrowse2/jbrowse2.py", line 440, in subprocess_check_call
    subprocess.check_call(command, cwd=self.get_cwd(cwd))
  File "/usr/local/tools/_conda/envs/mulled-v1-9ce393a2a46dd43ab470c21687c5e351db9cceeeba55143258ad640cf9d99ac9/lib/python3.12/subprocess.py", line 413, in check_call
    raise CalledProcessError(retcode, cmd)
subprocess.CalledProcessError: Command '['tabix', '-f', '-p', 'vcf', '/data/jwd05e/main/073/596/73596814/outputs/dataset_9e76ca47-d642-4d54-bf6f-6366236275ca_files/sniffles_on_data_70_4']' returned non-zero exit status 1.

[mvdbeek]

Attention: deployment failure!

https://github.com/galaxyproject/tools-iuc/actions/runs/11020518027

[bebatut]

There seem to be issue with this tool. It is invalid on the ToolShed: https://toolshed.g2.bx.psu.edu/repository?repository_id=fd2e07886563dc35&changeset_revision=3f6f028f418f

sniffles.xml - This file requires an entry in the tool_data_table_conf.xml file. Upload a file named tool_data_table_conf.xml.sample to the repository that includes the required entry to correct this error.