Change htseq-count name

tools/hisat2_index/hisat2_index.yaml

@@ -45,9 +45,9 @@
       "wget -O hisat2-2.2.1-linux-x86_64.zip https://cloud.biohpc.swmed.edu/index.php/s/oTtGWbWjaxsQ2Ho/download",
       "unzip hisat2-2.2.1-linux-x86_64.zip",
       "mv  hisat2-2.2.1 /opt/biotools/",
-      "rm -rf hisat2-2.2.1*"
-      "ENV PATH /opt/biotools/hisat2-2.2.1:$PATH "
-      "echo "export PATH=$PATH:/opt/biotools/hisat2-2.2.1" >> /etc/environment"
+      "rm -rf hisat2-2.2.1*",
+      "ENV PATH /opt/biotools/hisat2-2.2.1:$PATH ",
+      "echo \"export PATH=$PATH:/opt/biotools/hisat2-2.2.1\" >> /etc/environment"
     ],
   },
   citations:  {

tools/htseq-count/htseq-count.rule.snakefile → tools/htseq_count/htseq_count.rule.snakefile

@@ -7,7 +7,7 @@ rule <step_name>__htseq-count:
         config["results_dir"]+'/logs/' + config["<step_name>__htseq-count_output_dir"] + '/{sample}_htseq-count_log.txt'
     params:
         command = config["<step_name>__htseq-count_command"],
-        htseq-count_minaqual = config["htseq-count_minaqual"],
+        htseq_count_minaqual = config["htseq-count_minaqual"],
         htseq_stranded = config["htseq_stranded"],
         output_dir = config["results_dir"]+'/'+config["<step_name>__htseq-count_output_dir"]
     shell:

tools/htseq-count/htseq-count.yaml → tools/htseq_count/htseq_count.yaml

@@ -27,7 +27,7 @@
         options:
           [
             {
-              name: htseq-count_minaqual,
+              name: htseq_count_minaqual,
               prefix: -a,
               type: numeric,
               value: 10,