changed output names

docker/Dockerfile

@@ -171,9 +171,6 @@ RUN cd /home/imp/lib \
 && cd megahit \
 && make
 
-## KronaTools
-
-
 ######################
 # ship pipeline code #
 ######################

rules/Analysis/MGMT.rules

@@ -541,14 +541,16 @@ rule ANALYSIS_KRONA_PLOT_MG:
         "{U_OUT}/pwy2hierarchy.txt",
         "{AN_OUT}/MG.gene_depth.avg",
         "{AN_OUT}/MG.gene.len",
+    output:
         "{AN_OUT}/results/MG.gene_kegg_krona.txt",
         "{AN_OUT}/results/MG.gene_kegg_krona.html"
     shell:
         """
         echo "[x] PLOT KRONA `date +"%Y/%m/%d %H:%M:%S"`" >> {log}
-        python {SRCDIR}/genes.to.kronaTable.py -i {input[0]} -m {input[1]} -H {input[2]} -c {input[3]} -L {input[3]} -o {input[4]}
-        ktImportText -o {input[5]} {input[4]}"
+        python {SRCDIR}/genes.to.kronaTable.py -i {input[0]} -m {input[1]} -H {input[2]} -c {input[3]} -L {input[3]} -o {output[0]}
+        ktImportText -o {output[1]} {output[0]}"
         """
+
 rule ANALYSIS_KRONA_PLOT_MT:
     log:
         AN_LOG
@@ -560,11 +562,14 @@ rule ANALYSIS_KRONA_PLOT_MT:
         "{U_OUT}/pwy2hierarchy.txt",
         "{AN_OUT}/MT.gene_depth.avg",
         "{AN_OUT}/MT.gene.len",
+    output:
         "{AN_OUT}/results/MT.gene_kegg_krona.txt",
         "{AN_OUT}/results/MT.gene_kegg_krona.html"
     shell:
         """
         echo "[x] PLOT KRONA `date +"%Y/%m/%d %H:%M:%S"`" >> {log}
-        python {SRCDIR}/genes.to.kronaTable.py -i {input[0]} -m {input[1]} -H {input[2]} -c {input[3]} -L {input[3]} -o {input[4]}
-        ktImportText -o {input[5]} {input[4]}"
+        python {SRCDIR}/genes.to.kronaTable.py -i {input[0]} -m {input[1]} -H {input[2]} -c {input[3]} -L {input[3]} -o {output[0]}
+        ktImportText -o {output[1]} {output[0]}"
         """
+
+

rules/Analysis/master.rules

@@ -17,12 +17,12 @@ def analysis_output_files():
                  "MT.variants.isec.vcf.gz",
                  "MGMT.assembly.length.txt",
                  "MGMT.assembly.gc_content.txt",
-                 "MT.assembly.coverage_coverage.txt",
-                 "MT.assembly.coverage_depth.txt",
-                 "MT.assembly.coverage_flagstat.txt",
-                 "MG.assembly.coverage_coverage.txt",
-                 "MG.assembly.coverage_depth.txt",
-                 "MG.assembly.coverage_flagstat.txt",
+                 "MT.assembly.contig_coverage.txt",
+                 "MT.assembly.contig_depth.txt",
+                 "MT.assembly.contig_flagstat.txt",
+                 "MG.assembly.contig_coverage.txt",
+                 "MG.assembly.contig_depth.txt",
+                 "MG.assembly.contig_flagstat.txt",
                  "MGMT.vizbin.points",
                  "MGMT.vizbin.filtered.fa",
                  "MGMT.vizbin.with-contig-names.points"], dir=AN_OUT)