fix(prepare_inputs): support relative paths

To ensure that output files for tests are identical regardless of the environment from which they are called, the script for preparing inputs now allows skipping of path expansion, essentially allowing the specification of relative file paths (e.g, relative to the location of the script).

Changes:

• add CLI argument --no-process-paths, which, together with setting --output-dir="", allows for the functionality described above
• update test tests/test_scripts_prepare_inputs_table/test.sh to add CLI arguments --no-process-paths and --output-dir=""
• update md5 hash sums for output files created by that test
• rename script to prepare_inputs.py (previousy labkey_to_snakemake.py (accounting for the use case where the input table is not derived from LabKey); also renamed the table with information to map LabKey to Snakemake table column identifiers accordingly

Fixes #120 (closed)

workflow/rules/single_end.snakefile.smk

@@ -237,7 +237,11 @@ rule quantification_salmon:
             "{sample}",
             "{sample}.salmon.se"),
         libType = lambda wildcards:
-                samples_table.loc[wildcards.sample, "libtype"]
+            samples_table.loc[wildcards.sample, "libtype"],
+        fraglen = lambda wildcards:
+            samples_table.loc[wildcards.sample, 'mean'],
+        fragsd = lambda wildcards:
+            samples_table.loc[wildcards.sample, 'sd']
 
     log:
         stderr = os.path.join(
@@ -262,6 +266,8 @@ rule quantification_salmon:
         --seqBias \
         --validateMappings \
         --threads {threads} \
+        --fldMean {params.fraglen} \
+        --fldSD {params.fragsd} \
         --writeUnmappedNames \
         --index {input.index} \
         --geneMap {input.gtf} \