change WFs names

workflows/RnaSeqDemo/RnaSeqDemo.yaml

 {
 name: "RnaSeqDemo",
 docker_name: "RnaSeqDemo",
-description: "RnaSeq DE demo",
+description: "RnaSeq DE Demo",
 version: "0.0.1",
 author: "MBB",
 options: [
@@ -14,72 +14,43 @@ options: [
     },
 ],
 steps_in: [
-{ step_name: "FROGS_2", tool_name: "FROGS_preprocess", rule_name: "FROGS_preprocess_PE",
+{ step_name: "quality", tool_name: "trimmomatic", rule_name: "trimmomatic_SE",
     params: [
-        { input_name: read_dir, origin_command: raw_read_dir, origin_name: read_dir, origin_step: input},
+        { input_name: read, origin_command: raw_reads, origin_name: read, origin_step: input},
     ]
 },
-{ step_name: "FROGS_4", tool_name: "FROGS_cluster", rule_name: "FROGS_cluster",
+{ step_name: "quality_2", tool_name: "fastqc", rule_name: "fastqc_SE",
     params: [
-        { input_name: sequence_file, origin_command: FROGS_preprocess_PE, origin_name: sequence_file, origin_step: FROGS_2},
-        { input_name: count_file, origin_command: FROGS_preprocess_PE, origin_name: count_file, origin_step: FROGS_2},
+        { input_name: read, origin_command: trimmomatic_SE, origin_name: read, origin_step: quality},
     ]
 },
-{ step_name: "FROGS", tool_name: "FROGS_remove_chimera", rule_name: "FROGS_remove_chimera",
+{ step_name: "mapping", tool_name: "hisat2", rule_name: "hisat2_SE",
     params: [
-        { input_name: sequence_file, origin_command: FROGS_cluster, origin_name: cluster_seeds, origin_step: FROGS_4},
-        { input_name: abundance_biom, origin_command: FROGS_cluster, origin_name: abundance_file, origin_step: FROGS_4},
+        { input_name: read, origin_command: trimmomatic_SE, origin_name: read, origin_step: quality},
+        { input_name: index, origin_command: raw_hisat2_index, origin_name: hisat2_index, origin_step: input},
     ]
 },
-{ step_name: "FROGS_3", tool_name: "FROGS_filter_OTU", rule_name: "FROGS_filter_OTU",
+{ step_name: "quantification", tool_name: "htseq_count", rule_name: "htseq_count",
     params: [
-        { input_name: sequence_file, origin_command: FROGS_remove_chimera, origin_name: non_chimera_fasta, origin_step: FROGS},
-        { input_name: biom, origin_command: FROGS_remove_chimera, origin_name: abundance_file, origin_step: FROGS},
+        { input_name: bam, origin_command: hisat2_SE, origin_name: bam, origin_step: mapping},
+        { input_name: gff_file, origin_command: raw_gff3, origin_name: gff3, origin_step: input},
     ]
 },
-{ step_name: "FROGS_5", tool_name: "FROGS_affiliation", rule_name: "FROGS_affiliation",
+{ step_name: "differential_expression", tool_name: "deseq2", rule_name: "deseq2",
     params: [
-        { input_name: fasta, origin_command: FROGS_filter_OTU, origin_name: filtered_sequences, origin_step: FROGS_3},
-        { input_name: biom, origin_command: FROGS_filter_OTU, origin_name: abundance_file, origin_step: FROGS_3},
-    ]
-},
-{ step_name: "FROGS_6", tool_name: "FROGS_filter_affiliation", rule_name: "FROGS_filter_affiliation",
-    params: [
-        { input_name: fasta, origin_command: FROGS_filter_OTU, origin_name: filtered_sequences, origin_step: FROGS_3},
-        { input_name: biom, origin_command: FROGS_affiliation, origin_name: abundance_file, origin_step: FROGS_5},
-    ]
-},
-{ step_name: "FROGS_8", tool_name: "FROGS_biom_to_tsv", rule_name: "FROGS_biom_to_tsv",
-    params: [
-        { input_name: biom, origin_command: FROGS_filter_affiliation, origin_name: biom_filtered, origin_step: FROGS_6},
-    ]
-},
-{ step_name: "FROGS_7", tool_name: "FROGS_phyloseq_stats", rule_name: "FROGS_phyloseq_stats",
-    params: [
-        { input_name: biom_file, origin_command: FROGS_filter_affiliation, origin_name: biom_filtered, origin_step: FROGS_6},
-        { input_name: otu_sequence_file, origin_command: FROGS_filter_affiliation, origin_name: sequence_file, origin_step: FROGS_6},
+        { input_name: counts, origin_command: htseq_count, origin_name: stats, origin_step: quantification},
         { input_name: popmap_file, origin_command: raw_popmap, origin_name: popmap, origin_step: input},
     ]
 },
-{ step_name: "metabarcoding", tool_name: "lulu", rule_name: "lulu",
-    params: [
-        { input_name: abundance_file, origin_command: FROGS_biom_to_tsv, origin_name: lulu_abundance_file, origin_step: FROGS_8},
-        { input_name: sequence_file, origin_command: FROGS_filter_affiliation, origin_name: sequence_file, origin_step: FROGS_6},
-    ]
-},
 ],
 steps: [
-    { title: "FROGS_2", name: "FROGS_2", tools: [FROGS_preprocess], default: "FROGS_preprocess" },
-    { title: "FROGS_4", name: "FROGS_4", tools: [FROGS_cluster], default: "FROGS_cluster" },
-    { title: "FROGS", name: "FROGS", tools: [FROGS_remove_chimera], default: "FROGS_remove_chimera" },
-    { title: "FROGS_3", name: "FROGS_3", tools: [FROGS_filter_OTU], default: "FROGS_filter_OTU" },
-    { title: "FROGS_5", name: "FROGS_5", tools: [FROGS_affiliation], default: "FROGS_affiliation" },
-    { title: "FROGS_6", name: "FROGS_6", tools: [FROGS_filter_affiliation], default: "FROGS_filter_affiliation" },
-    { title: "FROGS_8", name: "FROGS_8", tools: [FROGS_biom_to_tsv], default: "FROGS_biom_to_tsv" },
-    { title: "FROGS_7", name: "FROGS_7", tools: [FROGS_phyloseq_stats], default: "FROGS_phyloseq_stats" },
-    { title: "metabarcoding", name: "metabarcoding", tools: [lulu], default: "lulu" },
+    { title: "quality", name: "quality", tools: [trimmomatic], default: "trimmomatic" },
+    { title: "quality_2", name: "quality_2", tools: [fastqc], default: "fastqc" },
+    { title: "mapping", name: "mapping", tools: [hisat2], default: "hisat2" },
+    { title: "quantification", name: "quantification", tools: [htseq_count], default: "htseq_count" },
+    { title: "differential_expression", name: "differential_expression", tools: [deseq2], default: "deseq2" },
 ],
-input: ["raw_read_dir","raw_popmap",],
+input: ["raw_reads","raw_hisat2_index","raw_gff3","raw_popmap",],
 params_equals: [
 
 ]