Add generate tmb module

modules/generate_tmb.nf

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+
+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')
+}

scripts/tmb/Dockerfile

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+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

scripts/tmb/README.md

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+# Calculate TMB
+
+1. Follow readme here: https://github.com/cBioPortal/datahub-study-curation-tools/tree/master/tmb/calculate_tmb
+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)
+
+    ```
+    synapse get -r --followLink syn64386356
+    ```
+
+1. Rename files as needed
+
+    ```
+    mv data_mutations_extended.txt data_mutations.txt
+    ```
+
+1. Run code
+
+    ```
+    python calc_nonsyn_tmb.py -i . -p .
+    ```
+
+1. View `tmb_output_data_clincal_sample.txt`

scripts/tmb/generate_tmb.sh

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+#!/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"