support for extension permutations / uncompressed data

[aswarren]

Description of feature

Command error:
INFO: Environment variable SINGULARITYENV_TMPDIR is set, but APPTAINERENV_TMPDIR is preferred
INFO: Environment variable SINGULARITYENV_NXF_DEBUG is set, but APPTAINERENV_NXF_DEBUG is preferred
INFO: gocryptfs not found, will not be able to use gocryptfs
WARNING: Skipping mount /sfs/applications/202406/software/standard/core/apptainer/1.2.2/var/apptainer/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container
[CRITICAL] The FASTQ file has an unrecognized extension: /samples/sample1.fastq
It should be one of: .fq.gz, .fastq.gz On line 2.