Merge branch 'rebased_denovo_nf-core' into AWS-GCP

Merging rebased denovo nf-core branch to AWS-GCP branch

Author: aolveraNIH

GoogleCloud/Submodule_2_annotation_only.ipynb

@@ -6,7 +6,7 @@
    "metadata": {},
    "source": [
     "# MDIBL Transcriptome Assembly Learning Module\n",
-    "# Notebook 2: Using \"denovoscript\" to Performing an \"Annotation Only\" Run"
+    "# Notebook 2: Using \"denovoscript\" to Perform an \"Annotation Only\" Run"
    ]
   },
   {
@@ -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"
    ]
   },
   {
@@ -267,7 +278,7 @@
    "outputs": [],
    "source": [
     "! mkdir -p <Your-Output-Directory-annotation-only>\n",
-    "! gsutil cp -r s3://<YOUR-BUCKET-NAME>/<Your-Output-Directory-annotation-only>/ ./<Your-Output-Directory-annotation-only>"
+    "! gsutil -m cp -r gs://<YOUR-BUCKET-NAME>/<Your-Output-Directory-annotation-only>/ <Your-Output-Directory-annotation-only>"
    ]
   },
   {
@@ -277,24 +288,15 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "! ls -l ./<Your-Output-Directory-annotation-only>"
-   ]
-  },
-  {
-   "cell_type": "markdown",
-   "id": "a96e29ed",
-   "metadata": {},
-   "source": [
-    "----\n",
-    "# Andrea, please update this part"
+    "! ls -l <Your-Output-Directory-annotation-only>"
    ]
   },
   {
    "cell_type": "markdown",
    "id": "f3255502-270c-4ebb-9f72-141c4fab5c0f",
    "metadata": {},
    "source": [
-    "Let's take a look at the `RUN_INFO.txt` file to see what the parameters and programs associated with our analysis were."
+    "Let's take a look at the `params.json` file to see what the parameters and programs associated with our analysis were. This json file will have the date you ran the pipeline as well a pipeline identifier. Update the code below to look at the `params.json` file."
    ]
   },
   {
@@ -304,15 +306,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "! cat ./onlyAnnRun/output/RUN_INFO.txt"
-   ]
-  },
-  {
-   "cell_type": "markdown",
-   "id": "9c86c829",
-   "metadata": {},
-   "source": [
-    "---"
+    "! cat ./<Your-Output-Directory-annotation-only>/pipeline_info/params_<Date-identifier>.json"
    ]
   },
   {
@@ -331,7 +325,7 @@
     ">\n",
     ">Container systems ([Docker](https://www.docker.com/) and [Singularity](https://sylabs.io/singularity/) are the two most well-known examples) address this by installing and encapsulating the program and all of its necessary supporting components in an image. Each program is then executed in the context of its container image, which is activated just long enough to run its program.\n",
     ">\n",
-    ">Because of the way that we have run the TransPi workflow in the previous, our system will already have several container images installed. We can now work directly with these images."
+    ">Because of the way that we have run the denovotranscript workflow previously, our system will already have several container images installed. We can now work directly with these images."
    ]
   },
   {
@@ -420,6 +414,17 @@
     "! echo $THREADS"
    ]
   },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "ac8e5dc6",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "# make the output folder \n",
+    "!mkdir -p ./buscoOutput"
+   ]
+  },
   {
    "cell_type": "code",
    "execution_count": null,
@@ -428,9 +433,9 @@
    "outputs": [],
    "source": [
     "! docker run -it --rm --volume /home:/home quay.io/biocontainers/busco:5.4.3--pyhdfd78af_0 busco \\\n",
-    "-i /home/ec2-user/SageMaker/Transcriptome-Assembly-Refinement-and-Applications/GoogleCloud/resources/trans/Oncorhynchus_mykiss_GGBN01.1.fa \\\n",
+    "-i /home/jupyter/resources/trans/Oncorhynchus_mykiss_GGBN01.1.fa \\\n",
     "-l vertebrata_odb10 -o GGBN01_busco_vertebrata \\\n",
-    "--out_path /home/ec2-user/SageMaker/Transcriptome-Assembly-Refinement-and-Applications/GoogleCloud/buscoOutput -m tran -c $THREADS"
+    "--out_path ./buscoOutput -m tran -c $THREADS"
    ]
   },
   {
@@ -535,9 +540,9 @@
    "outputs": [],
    "source": [
     "! docker run -it --rm --volume /home:/home quay.io/biocontainers/busco:5.4.3--pyhdfd78af_0 busco \\\n",
-    "    -i /home/ec2-user/SageMaker/Transcriptome-Assembly-Refinement-and-Applications/GoogleCloud/resources/trans/Pseudacris_regilla_GAEI01.1.fa \\\n",
+    "    -i /home/jupyter/resources/trans/Pseudacris_regilla_GAEI01.1.fa \\\n",
     "    -l vertebrata_odb10 -o GAEI01_busco_vertebrata \\\n",
-    "    --out_path /home/ec2-user/SageMaker/Transcriptome-Assembly-Refinement-and-Applications/GoogleCloud/buscoOutpu -m tran -c $THREADS"
+    "    --out_path ./buscoOutput -m tran -c $THREADS"
    ]
   },
   {