Addition of samtools cat in the samtools_sort module broke compatibility with input SAM files

[pcrxn]

Have you checked the docs?

• nf-core website: troubleshooting
• nf-core modules documentation

Description of the bug

The addition of the samtools cat command within the execution stub of the samtools_sort module, by #5022, broke compatibility with using a SAM file as input for this module, since samtools cat only supports BAM and CRAM file types. This results in the following error:

Command error:
  INFO:    Converting SIF file to temporary sandbox...
  [main_cat] ERROR: input is not BAM or CRAM
  [W::hts_set_opt] Cannot change block size for this format
  samtools sort: failed to read header from "-"
  INFO:    Cleaning up image...

Command used and terminal output

No response

Relevant files

No response

System information

• Nextflow version: nextflow==23.10.1
• Hardware: Desktop
• Executor: Local
• Container engine and version: singularity==3.8.6
• OS and version: Linux Mint 21.2