From d4e69b348fd737234a669405c5b4fb802050910f Mon Sep 17 00:00:00 2001
From: Thomas Yu <thomas.yu@sagebase.org>
Date: Thu, 9 Jan 2025 05:11:54 -0800
Subject: [PATCH 1/3] Add generate tmb module

---
 modules/generate_tmb.nf     | 26 ++++++++++++++++++++++++++
 scripts/tmb/README.md       | 28 ++++++++++++++++++++++++++++
 scripts/tmb/generate_tmb.sh |  8 ++++++++
 3 files changed, 62 insertions(+)
 create mode 100644 scripts/tmb/README.md
 create mode 100755 scripts/tmb/generate_tmb.sh

diff --git a/modules/generate_tmb.nf b/modules/generate_tmb.nf
index e69de29..936f40c 100644
--- a/modules/generate_tmb.nf
+++ b/modules/generate_tmb.nf
@@ -0,0 +1,26 @@
+
+params.release_folder_synid = 'syn62069187'
+
+process generate_tmb {
+    // container 'sagebionetworks/genie-tmb'
+    container 'test'
+    secret 'SYNAPSE_AUTH_TOKEN'
+
+    input:
+    val previous
+    // val release
+    val release_folder_synid
+    val production
+
+    output:
+    stdout
+
+    script:
+    """
+    /tmb/generate_tmb.sh $release_folder_synid
+    """
+}
+
+workflow {
+    generate_tmb('test', params.release_folder_synid, 'test')
+}
\ No newline at end of file
diff --git a/scripts/tmb/README.md b/scripts/tmb/README.md
new file mode 100644
index 0000000..ce73fbc
--- /dev/null
+++ b/scripts/tmb/README.md
@@ -0,0 +1,28 @@
+# Calculate TMB
+
+1. Follow readme here: https://github.com/cBioPortal/datahub-study-curation-tools/tree/master/tmb/calculate_tmb
+1. download the script
+
+    ```
+    wget https://raw.githubusercontent.com/cBioPortal/datahub-study-curation-tools/refs/heads/master/tmb/calculate_tmb/calc_nonsyn_tmb.py
+    ```
+
+1. Download a GENIE release (Example 17.6)
+
+    ```
+    synapse get -r --followLink syn64386356
+    ```
+
+1. Rename files as needed
+
+    ```
+    mv data_mutations_extended.txt data_mutations.txt
+    ```
+
+1. Run code (be sure to `pip install numpy`)
+
+    ```
+    python calc_nonsyn_tmb.py -i . -p .
+    ```
+
+1. View `tmb_output_data_clincal_sample.txt`
diff --git a/scripts/tmb/generate_tmb.sh b/scripts/tmb/generate_tmb.sh
new file mode 100755
index 0000000..a9041ec
--- /dev/null
+++ b/scripts/tmb/generate_tmb.sh
@@ -0,0 +1,8 @@
+#!/bin/bash
+
+release_folder_synapse_id=$1
+
+synapse get -r --followLink "$release_folder_synapse_id"
+mv data_mutations_extended.txt data_mutations.txt
+python calc_nonsyn_tmb.py -i . -p .
+synapse store tmb_output_data_clinical_sample.txt --parentId "$release_folder_synapse_id"

From 904ba039cfcd6ac8dff0e21136eb70cddd60491a Mon Sep 17 00:00:00 2001
From: Thomas Yu <thomas.yu@sagebase.org>
Date: Thu, 9 Jan 2025 05:17:55 -0800
Subject: [PATCH 2/3] Add dockerfiile

---
 scripts/tmb/Dockerfile | 10 ++++++++++
 1 file changed, 10 insertions(+)
 create mode 100644 scripts/tmb/Dockerfile

diff --git a/scripts/tmb/Dockerfile b/scripts/tmb/Dockerfile
new file mode 100644
index 0000000..b44f91d
--- /dev/null
+++ b/scripts/tmb/Dockerfile
@@ -0,0 +1,10 @@
+FROM ghcr.io/sage-bionetworks/synapsepythonclient:v4.6.1
+
+WORKDIR /tmb
+
+COPY requirements.txt requirements.txt
+COPY generate_tmb.sh generate_tmb.sh
+
+RUN pip install -r requirements.txt
+
+ADD https://raw.githubusercontent.com/cBioPortal/datahub-study-curation-tools/refs/heads/master/tmb/calculate_tmb/calc_nonsyn_tmb.py ./calc_nonsyn_tmb.py
\ No newline at end of file

From 1b19f146f7c5bfe946f60875fa075ae3efc62a7c Mon Sep 17 00:00:00 2001
From: Thomas Yu <thomas.yu@sagebase.org>
Date: Thu, 9 Jan 2025 05:19:06 -0800
Subject: [PATCH 3/3] edit readme

---
 scripts/tmb/README.md | 5 +++--
 1 file changed, 3 insertions(+), 2 deletions(-)

diff --git a/scripts/tmb/README.md b/scripts/tmb/README.md
index ce73fbc..b7601be 100644
--- a/scripts/tmb/README.md
+++ b/scripts/tmb/README.md
@@ -1,10 +1,11 @@
 # Calculate TMB
 
 1. Follow readme here: https://github.com/cBioPortal/datahub-study-curation-tools/tree/master/tmb/calculate_tmb
-1. download the script
+1. download the script and setup environment
 
     ```
     wget https://raw.githubusercontent.com/cBioPortal/datahub-study-curation-tools/refs/heads/master/tmb/calculate_tmb/calc_nonsyn_tmb.py
+    pip install -r requirements.txt
     ```
 
 1. Download a GENIE release (Example 17.6)
@@ -19,7 +20,7 @@
     mv data_mutations_extended.txt data_mutations.txt
     ```
 
-1. Run code (be sure to `pip install numpy`)
+1. Run code
 
     ```
     python calc_nonsyn_tmb.py -i . -p .