links

rules/Analysis/prokka.rule

@@ -22,7 +22,7 @@ rule annotate:
             cd $(dirname $(which prokka))/.. && ln -s $PP db
             cd $CUR
         fi
-
+        rm -rf Analysis/annotation/
         prokka --force --outdir Analysis/annotation --cpus {THREADS} --metagenome {input[0]} >> Analysis/annotation.log 2>&1
 
         # Prokka gives a gff file with a long header and with all the contigs at the bottom.  The command below removes the

rules/Assembly/hybrid/megahit.hybrid.rules

@@ -30,7 +30,7 @@ rule megahit_hybrid_assembly_1:
         -t {THREADS} --cpu-only \
         -m "${{MAX_MEM}}" \
         --mem-flag 1
-        ln -fs $(echo {output[0]} | cut -f 2 -d /) {output[1]} && touch -h {output[1]}
+        ln -fs $(echo {output[0]} | cut -f 2,3 -d /) {output[1]} && touch -h {output[1]}
         """
 
 rule megahit_hybrid_assembly_2:
@@ -65,5 +65,5 @@ rule megahit_hybrid_assembly_2:
         -t {THREADS} --cpu-only \
         -m ${{MAX_MEM}} \
         --mem-flag 1
-        ln -fs $(echo {output[0]} | cut -f 2 -d /) {output[1]} && touch -h {output[1]}
+        ln -fs $(echo {output[0]} | cut -f 2,3 -d /) {output[1]} && touch -h {output[1]}
         """

rules/Preprocessing/filtering.rules

@@ -76,7 +76,7 @@ rule symlink_preprocessed_files:
         'Preprocessing/{type}.se.preprocessed.fq'
     shell:
         """
-        ln -s $(echo {input[0]} | cut -f 2 -d /) {output[0]} && touch -h {output[0]}
-        ln -s $(echo {input[1]} | cut -f 2 -d /) {output[1]} && touch -h {output[1]}
-        ln -s $(echo {input[2]} | cut -f 2 -d /) {output[2]} && touch -h {output[2]}
+        ln -fs $(echo {input[0]} | cut -f 2 -d /) {output[0]} && touch -h {output[0]}
+        ln -fs $(echo {input[1]} | cut -f 2 -d /) {output[1]} && touch -h {output[1]}
+        ln -fs $(echo {input[2]} | cut -f 2 -d /) {output[2]} && touch -h {output[2]}
         """

rules/Preprocessing/no-filtering.rules

@@ -27,7 +27,7 @@ rule no_filtering:
         'Preprocessing/{type}.se.preprocessed.fq'
     shell:
         """
-        ln -s {input[0]} {output[0]} && touch -h {output[0]}
-        ln -s {input[1]} {output[1]} && touch -h {output[1]}
-        ln -s {input[2]} {output[2]} && touch -h {output[2]}
+        ln -fs {input[0]} {output[0]} && touch -h {output[0]}
+        ln -fs {input[1]} {output[1]} && touch -h {output[1]}
+        ln -fs {input[2]} {output[2]} && touch -h {output[2]}
         """