Updated with batch patches. Submodule 2 works. Submodule 3 might have errors ran out of time

Author: aolveraNIH

AWS/Submodule_2_annotation_only.ipynb

@@ -293,11 +293,11 @@
    "outputs": [],
    "source": [
     "# replace batch bucket name in nextflow configuration file\n",
-    "! sed -i \"s/aws-batch-nigms-batch-bucket-/$BUCKET_NAME/g\" ../denovotranscript/nextflow.config\n",
+    "! sed -i \"s/aws-batch-nigms-batch-bucket-/$BUCKET_NAME/g\" /home/ec2-user/SageMaker/Transcriptome-Assembly-Refinement-and-Applications/denovotranscript/nextflow.config\n",
     "# replace job queue name in configuration file \n",
-    "! sed -i \"s/aws-batch-nigms-JobQueue/$AWS_QUEUE/g\" ../denovotranscipt/nextflow.config\n",
+    "! sed -i \"s/aws-batch-nigms-JobQueue/$AWS_QUEUE/g\" /home/ec2-user/SageMaker/Transcriptome-Assembly-Refinement-and-Applications/denovotranscipt/nextflow.config\n",
     "# replace the region placeholder with the region you are in \n",
-    "! sed -i \"s/aws-region/$AWS_REGION/g\" ../denovotranscipt/nextflow.config"
+    "! sed -i \"s/aws-region/$AWS_REGION/g\" /home/ec2-user/SageMaker/Transcriptome-Assembly-Refinement-and-Applications/denovotranscipt/nextflow.config"
    ]
   },
   {
@@ -330,8 +330,12 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "! nextflow run ../denovotranscript/main.nf --input ../denovotranscript/test_samplesheet_aws.csv -profile aws \\\n",
-    "--run_mode annotation_only --transcript_fasta s3://nigms-sandbox/nosi-inbremaine-storage/resources/trans/Oncorhynchus_mykiss_GGBN01.1.fa"
+    "! nextflow run /home/ec2-user/SageMaker/Transcriptome-Assembly-Refinement-and-Applications/denovotranscript/main.nf \\\n",
+    "    --input /home/ec2-user/SageMaker/Transcriptome-Assembly-Refinement-and-Applications/denovotranscript/test_samplesheet_aws.csv \\\n",
+    "    -profile docker,awsbatch \\\n",
+    "    -c /home/ec2-user/SageMaker/Transcriptome-Assembly-Refinement-and-Applications/denovotranscript/nextflow.config \\\n",
+    "    --run_mode annotation_only \\\n",
+    "    --transcript_fasta s3://nigms-sandbox/nosi-inbremaine-storage/resources/trans/Oncorhynchus_mykiss_GGBN01.1.fa --awsqueue $AWS_QUEUE --awsregion $AWS_REGION"
    ]
   },
   {

AWS/Submodule_3_basic_assembly.ipynb

@@ -300,7 +300,9 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "! nextflow run main.nf --input test_samplesheet.csv -profile aws --run_mode full"
+    "! nextflow run /home/ec2-user/SageMaker/Transcriptome-Assembly-Refinement-and-Applications/denovotranscript/main.nf \\\n",
+    "    --input /home/ec2-user/SageMaker/Transcriptome-Assembly-Refinement-and-Applications/denovotranscript/test_samplesheet_aws.csv \\\n",
+    "    -profile awsbatch --run_mode full --awsqueue $AWS_QUEUE --awsregion $AWS_REGION "
    ]
   },
   {

denovotranscript/nextflow.config

@@ -82,7 +82,7 @@ params {
     igenomes_ignore            = false
 
     // Boilerplate options
-    outdir                       = null
+    //outdir                       = null
     publish_dir_mode             = 'copy'
     email                        = null
     email_on_fail                = null
@@ -112,7 +112,7 @@ includeConfig 'conf/base.config'
 
 profiles {
 
-    aws {
+    awsbatch {
     process {
             executor = 'awsbatch'
             queue = params.awsqueue                           // Name of your Job queue