Correct the HISAT reference index to be a string instead of a file

[malachig]

Currently for the definitions/rnaseq.wdl we use reference_index as an input in our YAML.

In the WDL rnaseq pipeline it is defined as:

File reference_index

But it is not a file. This is a string that corresponds to the base name of the HISAT index files but does NOT correspond to a directory OR a specific file path.

From the HISAT manual:

-x
The basename of the index for the reference genome.

It only actually gets used here:

analysis-wdls/definitions/tools/hisat2_align.wdl

Line 56 in de14a42

-x ~{reference_index} \

I believe we can change this to String reference_index in the following locations and avoid the current workaround of creating an empty file with the base name.

analysis-wdls/definitions/rnaseq.wdl

Line 21 in de14a42

File reference_index

analysis-wdls/definitions/subworkflows/sequence_to_trimmed_fastq_and_hisat_alignments.wdl

Line 18 in de14a42

File reference_index

analysis-wdls/definitions/tools/hisat2_align.wdl

Line 5 in de14a42

File reference_index

analysis-wdls/definitions/tools/hisat2_align.wdl

Line 71 in de14a42

File reference_index