Add a group_file inpput to edger and deseq2

tools/deseq2/deseq2.yaml

@@ -16,7 +16,8 @@
         command: ~,
         category: "differential_expression",
         output_dir: deseq2,
-        inputs: [{ name: counts, type: "tsv" }],
+        inputs: [{ name: counts, type: "tsv" }
+                 { name: group_file, type: "popmap", file: "", description: "Path to tsv file with samples conditions"}],
         outputs:
           [
             { name: de_table, type: "tsv", file: de_table.csv, description: "Tableau d'expression différentielle" },

tools/edger/edger.yaml

@@ -15,7 +15,9 @@
         command: ~,
         category: "differential_expression",
         output_dir: edger,
-        inputs: [{ name: counts, type: "tsv" }],
+        inputs: [{ name: counts, type: "tsv" },
+                 { name: group_file, type: "popmap", file: "", description: "Path to tsv file with samples conditions"},
+        ]
         outputs:
           [
             { name: de_table, type: "csv", file: de_table.csv, description: "Tableau d'expression différentielle" },

tools/hisat2/hisat2.rule.snakefile

@@ -18,7 +18,7 @@ if config["SeOrPe"] == "PE":
             maxins = config["<step_name>__hisat2_maxins_PE"],
             orientation = config["<step_name>__hisat2_orientation_PE"],
         shell:
-            "{params.command} "
+            "{params.command} --new-summary "
             "--threads {threads} "
             "-x {params.indexPrefix} "
             "-I {params.minins} "

tools/htseq_count/htseq_count.yaml

@@ -7,7 +7,7 @@
   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",
+  multiqc: "htseq",
   commands:
     [
       {