Fixes #96: update salmon index output description

BIMSBbioinfo · Jun 7, 2021 · c8e93f2 · c8e93f2
1 parent af27e21
commit c8e93f2
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Showing 2 changed files with 3 additions and 3 deletions.
diff --git a/snakefile.py b/snakefile.py
@@ -189,7 +189,7 @@ def lookup(column, predicate, fields=[]):
     'salmon_index' : {
         'description': "Create SALMON index file.",
         'files':
-          [os.path.join(OUTPUT_DIR, 'salmon_index', "sa.bin")]
+          [os.path.join(OUTPUT_DIR, 'salmon_index', "pos.bin")]
     },
     'salmon_quant' : {
         'description': "Calculate read counts per transcript using SALMON.",
@@ -381,7 +381,7 @@ def hisat2_file_arguments(args):
   input:
       CDNA_FASTA
   output:
-      salmon_index_file = os.path.join(OUTPUT_DIR, 'salmon_index', "sa.bin")
+      salmon_index_file = os.path.join(OUTPUT_DIR, 'salmon_index', "pos.bin")
   resources:
       mem_mb = 5000
   params:

diff --git a/tests/test_salmon/test_salmon_index.sh.in b/tests/test_salmon/test_salmon_index.sh.in
@@ -26,7 +26,7 @@ head -n 2 ${samplesheet} > ${tmp_samplesheet}
 ${builddir}/pigx-rnaseq -s ${tmp_settings} --target salmon_index ${tmp_samplesheet}
 
 rm ${tmp_settings} ${tmp_samplesheet}
-if ! test -f ${testfolder}/salmon_index/sa.bin
+if ! test -f ${testfolder}/salmon_index/pos.bin
 then
   echo "ERROR: failed the SALMON indexing test"
   exit 1