Fixed bugs in denovotranscript.nf and nextflow.config files. Fixed some of the commands in submodule 2

Author: aolveraNIH

GoogleCloud/Submodule_2_annotation_only.ipynb

@@ -123,6 +123,17 @@
     ">`gsutil` is a tool allows you to interact with Google storage buckes through the command line."
    ]
   },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "b6c7eca2",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "# Create the bucket in your notebook first \n",
+    "!mkdir ./resources"
+   ]
+  },
   {
    "cell_type": "code",
    "execution_count": null,
@@ -148,7 +159,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "! grep -c \">\" ./resources/trans/Oncorhynchus_mykiss_GGBN01.1.fa"
+    "!grep -c \">\" /home/jupyter/resources/trans/Oncorhynchus_mykiss_GGBN01.1.fa"
    ]
   },
   {
@@ -304,7 +315,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "! cat ./onlyAnnRun/output/RUN_INFO.txt"
+    "! cat ./<Your-Output-Directory-annotation-only>/output/RUN_INFO.txt"
    ]
   },
   {

denovotranscript/nextflow.config

@@ -113,7 +113,7 @@ profiles {
     wave.enabled = true
     aws.region = 'us-east-1'                                             // YOUR AWS REGION
 
-    workDir = 's3://<YOUR-BUCKET-NAME>/<Your-Work-Directory>/''          // Path of your working directory
+    workDir = 's3://<YOUR-BUCKET-NAME>/<Your-Work-Directory>/'          // Path of your working directory
     params.outdir = 's3://<YOUR-BUCKET-NAME>/<Your-Output-Directory>/'   // Path of your output directory
 
 

denovotranscript/workflows/denovotranscript.nf

@@ -121,6 +121,7 @@ workflow DENOVOTRANSCRIPT {
         ch_multiqc_files = ch_multiqc_files.mix(FASTQC_FINAL.out.zip.collect{it[1]})
         ch_versions = ch_versions.mix(FASTQC_FINAL.out.versions)
     }
+    }
 
     if (!params.qc_only) {
 
@@ -337,7 +338,7 @@ workflow DENOVOTRANSCRIPT {
         }
 
     }
-}
+
     //
     // Collate and save software versions
     //