Canonicalize all file arguments to the report script.

When given relative file names the report script may not be able to
find files, so we use readlink to canonicalize all file names.  In the
common case this is not needed, because we use absolute file names
throughout.  For remote execution we may opt to delay canonicalization
to avoid retaining references to local directories.

snakefile.py

@@ -639,19 +639,19 @@ def hisat2_file_arguments(args):
   resources:
     mem_mb = config['execution']['rules']['report1']['memory']
   shell:
-    """{RSCRIPT_EXEC} {params.reportR}       \
-    --logo={input.logo}                      \
-    --prefix='{wildcards.analysis}'          \
-    --reportFile={params.reportRmd}          \
-    --countDataFile={input.counts}           \
-    --colDataFile={input.coldata}            \
-    --gtfFile={input.gtf}                    \
-    --caseSampleGroups='{params.case}'       \
-    --controlSampleGroups='{params.control}' \
-    --covariates='{params.covariates}'       \
-    --workdir={params.outdir}                \
-    --organism='{ORGANISM}'                  \
-    --description='{params.description}'     \
+    """{RSCRIPT_EXEC} $(readlink --canonicalize {params.reportR}) \
+    --logo=$(readlink --canonicalize {input.logo})                \
+    --prefix='{wildcards.analysis}'                               \
+    --reportFile=$(readlink --canonicalize {params.reportRmd})    \
+    --countDataFile=$(readlink --canonicalize {input.counts})     \
+    --colDataFile=$(readlink --canonicalize {input.coldata})      \
+    --gtfFile=$(readlink --canonicalize {input.gtf})              \
+    --caseSampleGroups='{params.case}'                            \
+    --controlSampleGroups='{params.control}'                      \
+    --covariates='{params.covariates}'                            \
+    --workdir=$(readlink --canonicalize {params.outdir})          \
+    --organism='{ORGANISM}'                                       \
+    --description='{params.description}'                          \
     --selfContained='{params.selfContained}' >> {log} 2>&1"""
 
 rule deseq_collate_report1:
@@ -692,20 +692,21 @@ def hisat2_file_arguments(args):
     os.path.join(OUTPUT_DIR, "report", "salmon", '{analysis}.salmon.transcripts.deseq_results.tsv')
   resources:
     mem_mb = config['execution']['rules']['report2']['memory']
-  shell: """{RSCRIPT_EXEC} {params.reportR}          \
-  --logo={input.logo}                                \
-  --prefix='{wildcards.analysis}.salmon.transcripts' \
-  --reportFile={params.reportRmd}                    \
-  --countDataFile={input.counts}                     \
-  --colDataFile={input.coldata}                      \
-  --gtfFile={input.gtf}                              \
-  --caseSampleGroups='{params.case}'                 \
-  --controlSampleGroups='{params.control}'           \
-  --covariates='{params.covariates}'                 \
-  --workdir={params.outdir}                          \
-  --organism='{ORGANISM}'                            \
-  --description='{params.description}'               \
-  --selfContained='{params.selfContained}' >> {log} 2>&1"""
+  shell:
+    """{RSCRIPT_EXEC} $(readlink --canonicalize {params.reportR}) \
+    --logo=$(readlink --canonicalize {input.logo})                \
+    --prefix='{wildcards.analysis}.salmon.transcripts'            \
+    --reportFile=$(readlink --canonicalize {params.reportRmd})    \
+    --countDataFile=$(readlink --canonicalize {input.counts})     \
+    --colDataFile=$(readlink --canonicalize {input.coldata})      \
+    --gtfFile=$(readlink --canonicalize {input.gtf})              \
+    --caseSampleGroups='{params.case}'                            \
+    --controlSampleGroups='{params.control}'                      \
+    --covariates='{params.covariates}'                            \
+    --workdir=$(readlink --canonicalize {params.outdir})          \
+    --organism='{ORGANISM}'                                       \
+    --description='{params.description}'                          \
+    --selfContained='{params.selfContained}' >> {log} 2>&1"""
 
 rule deseq_collate_report2:
   input:
@@ -745,20 +746,21 @@ def hisat2_file_arguments(args):
     os.path.join(OUTPUT_DIR, "report", "salmon", '{analysis}.salmon.genes.deseq_results.tsv')
   resources:
     mem_mb = config['execution']['rules']['report3']['memory']
-  shell: """{RSCRIPT_EXEC} {params.reportR}    \
-  --logo={input.logo}                          \
-  --prefix='{wildcards.analysis}.salmon.genes' \
-  --reportFile={params.reportRmd}              \
-  --countDataFile={input.counts}               \
-  --colDataFile={input.coldata}                \
-  --gtfFile={input.gtf}                        \
-  --caseSampleGroups='{params.case}'           \
-  --controlSampleGroups='{params.control}'     \
-  --covariates='{params.covariates}'           \
-  --workdir={params.outdir}                    \
-  --organism='{ORGANISM}'                      \
-  --description='{params.description}'         \
-  --selfContained='{params.selfContained}' >> {log} 2>&1"""
+  shell:
+    """{RSCRIPT_EXEC} $(readlink --canonicalize {params.reportR}) \
+    --logo=$(readlink --canonicalize {input.logo})                \
+    --prefix='{wildcards.analysis}.salmon.genes'                  \
+    --reportFile=$(readlink --canonicalize {params.reportRmd})    \
+    --countDataFile=$(readlink --canonicalize {input.counts})     \
+    --colDataFile=$(readlink --canonicalize {input.coldata})      \
+    --gtfFile=$(readlink --canonicalize {input.gtf})              \
+    --caseSampleGroups='{params.case}'                            \
+    --controlSampleGroups='{params.control}'                      \
+    --covariates='{params.covariates}'                            \
+    --workdir=$(readlink --canonicalize {params.outdir})          \
+    --organism='{ORGANISM}'                                       \
+    --description='{params.description}'                          \
+    --selfContained='{params.selfContained}' >> {log} 2>&1"""
 
 rule deseq_collate_report3:
   input: