Remove explicit dependence on S3

[jashapiro]

As discussed in https://github.com/AlexsLemonade/ScPCA-admin/issues/298, the current metadata file that we use as the control list for this workflow, defined in params.run_metafile, assumes that certain files are on S3. When we make that explicit (allowing for files to be stored on other services or locally), we should adjust the workflow to use the urls as specified, not adding s3:// as we currently do, for example at

scpca-nf/modules/af-rna.nf

Lines 99 to 102 in bc587b5

	.map{meta -> tuple(meta,
	file("s3://${meta.s3_prefix}/*_R1_*.fastq.gz"),
	file("s3://${meta.s3_prefix}/*_R2_*.fastq.gz")
	)}

Note that if we changed the name of the s3_prefix field while accomplishing https://github.com/AlexsLemonade/ScPCA-admin/issues/298, this will also need to be updated.