Rename workflow to add short-reads

Author: bebatut

workflows/read_preprocessing/read-qc-trimming/.dockstore.yml renamed to workflows/read_preprocessing/short-reads-qc-trimming/.dockstore.yml

@@ -3,9 +3,9 @@ workflows:
 - name: main
   subclass: Galaxy
   publish: true
-  primaryDescriptorPath: /raw-reads-quality-control-and-trimming.ga
+  primaryDescriptorPath: /short-reads-quality-control-and-trimming.ga
   testParameterFiles:
-  - /raw-reads-quality-control-and-trimming-tests.yml
+  - /short-reads-quality-control-and-trimming-tests.yml
   authors:
   - name: "B\xE9r\xE9nice Batut"
     orcid: 0000-0001-9852-1987

workflows/read_preprocessing/read-qc-trimming/CHANGELOG.md renamed to workflows/read_preprocessing/short-reads-qc-trimming/CHANGELOG.md

@@ -1,8 +1,8 @@
-# Raw reads quality control and trimming
+# Short-reads quality control and trimming
 
 Before starting any analysis, it is always a good idea to assess the quality of the input data and to discard poor-quality base content by trimming and filtering reads.
 
-This workflow takes paired-end Illumina fastq(.gz) files and executes the following steps:
+This workflow takes paired-end Illumina (**short-reads**) fastq(.gz) files and executes the following steps:
 1. Quality control and trimming using **fastp**
 2. Aggregation of the quality control reports using **MultiQC**
 

workflows/read_preprocessing/read-qc-trimming/README.md renamed to workflows/read_preprocessing/short-reads-qc-trimming/README.md

@@ -17,8 +17,8 @@
     "format-version": "0.1",
     "license": "MIT",
     "release": "0.1",
-    "name": "Raw reads quality control and trimming",
-    "readme": "Before starting any analysis, it is always a good idea to assess the quality of the input data and to discard poor-quality base content by trimming and filtering reads.\n\nThis workflow takes paired-end Illumina fastq(.gz) files and executes the following steps:\n1. Quality control and trimming using **fastp**\n2. Aggregation of the quality control reports using **MultiQC**\n",
+    "name": "Short-reads quality control and trimming",
+    "readme": "Before starting any analysis, it is always a good idea to assess the quality of the input data and to discard poor-quality base content by trimming and filtering reads.\n\nThis workflow takes paired-end Illumina (**short-reads**) fastq(.gz) files and executes the following steps:\n1. Quality control and trimming using **fastp**\n2. Aggregation of the quality control reports using **MultiQC**\n",
     "report": {
         "markdown": "\n# Workflow Execution Report\n\n## Workflow Inputs\n```galaxy\ninvocation_inputs()\n```\n\n## Workflow Outputs\n```galaxy\ninvocation_outputs()\n```\n\n## Workflow\n```galaxy\nworkflow_display()\n```\n"
     },