add execution debug component

Author: rcannood

src/core/fetch_task_execution/config.vsh.yaml

@@ -0,0 +1,26 @@
+name: fetch_task_execution
+namespace: core
+arguments:
+  - type: string
+    name: --input
+    required: true
+    direction: input
+    example: s3://openproblems-nextflow/work/f6/8565066aee4771cc2790b92b4ac660
+    description: The S3 path to the task execution directory to fetch.
+  - type: string
+    name: --aws_profile
+    required: false
+    direction: input
+    description: The AWS profile to use for fetching the task execution directory.
+  - type: file
+    name: --output
+    required: true
+    direction: output
+    description: Output directory containing the fetched task execution files.
+resources:
+  - type: bash_script
+    path: script.sh
+engines:
+  - type: native
+runners:
+  - type: executable

src/core/fetch_task_execution/script.sh

@@ -0,0 +1,15 @@
+## VIASH START
+par_input=s3://openproblems-nextflow/work/f6/8565066aee4771cc2790b92b4ac660
+par_aws_profile=op
+par_output=debug
+## VIASH END
+
+aws s3 sync \
+  ${par_aws_profile:+--profile $par_aws_profile} \
+  "$par_input" "$par_output"
+
+cd "$par_output"
+
+sed -i 's#/home/ec2-user/miniconda/bin/aws#aws#g' .command.run
+
+AWS_DEFAULT_PROFILE=${par_aws_profile} bash .command.run nxf_stage