Add htseq-count

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

+rule <step_name>__htseq-count:
+    input:
+        **<step_name>__htseq-count_inputs()
+    output:
+        stats = config["results_dir"]+'/' + config["<step_name>__htseq-count_output_dir"] + '/{sample}.txt',
+    log:
+        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_stranded = config["htseq_stranded"],
+        output_dir = config["results_dir"]+'/'+config["<step_name>__htseq-count_output_dir"]
+    shell:
+        "{params.command} -f bam -a  {params.htseq-count_minaqual}  -s {params.htseq_stranded} -r {params.htseq_orientation} {input.bam} {input.gff_file} 2> {log} > {output.stats}"

tools/htseq-count/htseq-count.yaml

+{
+  id: htseq-count,
+  name: Htseq-count,
+  article: doi:10.1093/bioinformatics/btu638,
+  website: "https://htseq.readthedocs.io",
+  git: "https://github.com/htseq/htseq",
+  description: "A tool to quantify gene expression in RNA-Seq and similar experiments.",
+  version: "release_0.13.5",
+  documentation: "https://htseq.readthedocs.io",
+  multiqc: "htseq-count",
+  commands:
+    [
+      {
+        name: htseq-count,
+
+        command: htseq-count,
+        category: "quantification",
+        output_dir: htseq-count,
+        inputs: [
+          { name: bam, type: "bams" },
+          {name: gff_file, type: "gff3"}
+        ],
+        outputs:
+          [
+            { name: stats, type: "txt", file: "{sample}_htseq-count.txt", description: "a table with counts for each feature" }
+          ],
+        options:
+          [
+            {
+              name: htseq-count_minaqual,
+              prefix: -a,
+              type: numeric,
+              value: 10,
+              min: 1,
+              max: 80,
+              step: 1,
+              label: "skip all reads with alignment quality lower than the given minimum value",
+            },
+            {
+              name: htseq_stranded,
+              type: radio,
+              choices:
+                [
+                  Not stranded: "no",
+                  Stranded: "yes",
+                  Reverse Stranded: "reverse",
+                ],
+              value: "no",
+              label: "whether the data is from a strand-specific assay.",
+            },
+            {
+              name: htseq_orientation,
+              type: radio,
+              choices:
+                [
+                  Position: "position",
+                  Name: "name"
+                ],
+              value: "position",
+              label: "the way that alignment have been sorted (either by read name or by alignment position).",
+            },
+          ],
+      },
+    ],
+  install: { 
+    htseq: [
+      "pip3 install "HTSeq==0.13.5"
+    ]
+  },
+  citations:  {
+    htseq: [
+      "Simon Anders, Paul Theodor Pyl, Wolfgang Huber. HTSeq - A Python framework to work with high-throughput sequencing data Bioinformatics (2014)."
+    ]
+  }
+}