Compress intermediate files

[pdiakumis]

Need to bgzip + tabix a few of the intermediate VCFs to save a bit of space (noticed >20x diff in some cases):

• https://github.com/umccr/umccrise/blob/be0c0282d9044a6d802941b4c7e6e85c32c36114/umccrise/structural.smk#L205
• https://github.com/umccr/umccrise/blob/be0c0282d9044a6d802941b4c7e6e85c32c36114/umccrise/structural.smk#L229
• https://github.com/umccr/umccrise/blob/be0c0282d9044a6d802941b4c7e6e85c32c36114/umccrise/structural.smk#L400

Also need to compress/remove the FASTQs under work/<sbj>/oncoviruses/work:

total 12G
drwxr-sr-x 3 pd8253 gx8 4.0K May 31 19:19 detect_viral_reference
-rw-r--r-- 1 pd8253 gx8 2.5G May 31 19:19 step1_host_unmapped_or_mate_unmapped.namesorted.bam
-rw-r--r-- 1 pd8253 gx8 4.4G May 31 19:20 step2_host_unmapped_or_mate_unmapped.R1.fq
-rw-r--r-- 1 pd8253 gx8 4.4G May 31 19:20 step2_host_unmapped_or_mate_unmapped.R2.fq
-rw-r--r-- 1 pd8253 gx8    0 May 31 19:18 step2_host_unmapped_or_mate_unmapped.single.fq

[pdiakumis]

We might go back and remove all work folders if it cuts down costs considerably. Closing.