Support uncompressed FASTQ file formats (.fastq, .fq)

[Copilot]

The samplesheet validator rejected uncompressed FASTQ files from SRA downloads, requiring .fastq.gz or .fq.gz extensions only.

Changes

• Validation logic (bin/check_samplesheet.py): Extended file extension check to accept .fastq, .fq, .fastq.gz, and .fq.gz
• Documentation (docs/guide/usage.md): Documented supported file formats in samplesheet specification

# Before
if not fastq.endswith(".fastq.gz") and not fastq.endswith(".fq.gz"):
    print_error("FastQ file does not have extension '.fastq.gz' or '.fq.gz'!")

# After  
if not (
    fastq.endswith(".fastq.gz")
    or fastq.endswith(".fq.gz")
    or fastq.endswith(".fastq")
    or fastq.endswith(".fq")
):
    print_error("FastQ file does not have extension '.fastq.gz', '.fq.gz', '.fastq', or '.fq'!")

Backward compatible - all existing samplesheets with compressed files continue to work.

Original prompt

---

This section details on the original issue you should resolve

<issue_title>Pipeline fails at samplesheet check if files are not fastq.gz or fq.gz</issue_title>
<issue_description>### Description of the bug

Files downloaded from SRA archive were imported as unpacked .fastq files. CHAMPAGNE failed at samplesheet check. Log indicates failure at

CHAMPAGNE/bin/check_samplesheet.py

Line 109 in 0031bfd

if not fastq.endswith(".fastq.gz") and not fastq.endswith(".fq.gz"):

Appears to require both file as fastq.gz format and matching format name in samplesheet.csv

Command used and terminal output

champagne run --output . --input samplesheet.csv

Relevant files

No response

System information

No response</issue_description>

<agent_instructions>Modify the pipeline to accept input files in .fastq format, rather than requiring they be gzipped.</agent_instructions>

Comments on the Issue (you are @copilot in this section)

• Fixes Pipeline fails at samplesheet check if files are not fastq.gz or fq.gz #301

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