Remove star sequence concatenation from mature fasta file

OpenOmics · Sep 27, 2024 · d5476d9 · d5476d9
1 parent 3283295
commit d5476d9
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Showing 2 changed files with 10 additions and 18 deletions.
diff --git a/workflow/Snakefile b/workflow/Snakefile
@@ -127,11 +127,11 @@ rule all:
         # @imported from `rule mirdeep2_novel_p1_run` in rules/novel.smk
         # This rule is only run if `identify_novel_mirs` is set to True.
         provided(
-            [join(workpath, "novel", "pass1", "cohort_novel_mature_miRNA.tsv")],
+            [join(workpath, "novel", "pass1", "cohort_novel_mature_miRNA.fa")],
             identify_novel_mirs
         ),
         provided(
-            [join(workpath, "novel", "pass1", "cohort_novel_hairpin_miRNA.tsv")],
+            [join(workpath, "novel", "pass1", "cohort_novel_hairpin_miRNA.fa")],
             identify_novel_mirs
         ),
         # Second-pass rules for novel miR quantification,

diff --git a/workflow/rules/novel.smk b/workflow/rules/novel.smk
@@ -151,8 +151,8 @@ rule mirdeep2_novel_p1_run:
         arf       = join(workpath, "novel", "mapper", "cohort_mapped.arf"),
         collapsed = join(workpath, "novel", "mapper", "cohort_collapsed.fa"),
     output:
-        mature    = join(workpath, "novel", "pass1", "cohort_novel_mature_miRNA.tsv"),
-        hairpin   = join(workpath, "novel", "pass1", "cohort_novel_hairpin_miRNA.tsv"),
+        mature    = join(workpath, "novel", "pass1", "cohort_novel_mature_miRNA.fa"),
+        hairpin   = join(workpath, "novel", "pass1", "cohort_novel_hairpin_miRNA.fa"),
     log: 
         report    = join(workpath, "novel", "pass1", "mirdeep2.log")
     params:
@@ -211,18 +211,10 @@ rule mirdeep2_novel_p1_run:
             -print \\
             -quit
     )
-    star=$(
-        find "${{tmp}}/" \\
-            -type f \\
-            -iname "novel_star_*.fa" \\
-            -print \\
-            -quit
-    )
-    # Rename the identifier to contain the
-    # suffix _star to indicate if its a star
-    # sequence before merging the two files
-    sed -i '/^>.*/s/$/_star/' "${{star}}"
-    cat "${{mature}}" "${{star}}" > {output.mature}
+
+    # Create a symbolic link to the novel 
+    # mature sequences for quantification
+    ln -sf "${{mature}}" {output.mature}
     
     # Create a symbolic link to the novel 
     # hairpin sequences for quantification
@@ -257,8 +249,8 @@ rule mirdeep2_novel_p2_quantifier:
     input:
         arf       = join(workpath, "mirdeep2", "mapper", "{sample}_mapped.arf"),
         collapsed = join(workpath, "mirdeep2", "mapper", "{sample}_collapsed.fa"),
-        mature    = join(workpath, "novel", "pass1", "cohort_novel_mature_miRNA.tsv"),
-        hairpin   = join(workpath, "novel", "pass1", "cohort_novel_hairpin_miRNA.tsv"),
+        mature    = join(workpath, "novel", "pass1", "cohort_novel_mature_miRNA.fa"),
+        hairpin   = join(workpath, "novel", "pass1", "cohort_novel_hairpin_miRNA.fa"),
     output:
         mirna     = join(workpath, "novel", "counts", "{sample}_novel_miRNA_expressed.tsv"),
     params: