Revert "[GEN-2152] Allow user-defined maf center list in maf processing step …" (#39)

This reverts commit 96d1d02.

Author: danlu1

README.md

@@ -82,22 +82,9 @@ Note that all the docker parameters have set default docker containers based on
     ```
 
 * Processes **mutation** files on test pipeline
-1. To execute the MAF process for all centers, you can either specify the `maf_centers` as "ALL" or leave it blank. 
-    ```
-    nextflow run main.nf -profile aws_test --process_type maf_process --create_new_maf_db -with-docker ghcr.io/sage-bionetworks/genie:main
-    ```
-    Or
-    ```
-    nextflow run main.nf -profile aws_test --process_type maf_process --maf_centers ALL --create_new_maf_db -with-docker ghcr.io/sage-bionetworks/genie:main
-    ```
-2. To execute the MAF process for a single center, you can specify the `maf_centers` parameter using the name of that center.
-    ```
-    nextflow run main.nf -profile aws_test --process_type maf_process --maf_centers TEST --create_new_maf_db -with-docker ghcr.io/sage-bionetworks/genie:main
-    ```
 
-3. To execute the MAF process for multiple centers, you can specify the `maf_centers` as a comma-separated list of center names and **append** results to the MAF table.
     ```
-    nextflow run main.nf -profile aws_test --process_type maf_process --maf_centers TEST,SAGE --create_new_maf_db false -with-docker ghcr.io/sage-bionetworks/genie:main
+    nextflow run main.nf -profile aws_test --process_type maf_process --create_new_maf_db -with-docker ghcr.io/sage-bionetworks/genie:main
     ```
 
 * Runs **processing** and **consortium** release (including data guide creation) on test pipeline

main.nf

@@ -14,7 +14,6 @@ include { reset_processing } from './modules/reset_processing'
 include { validate_data } from './modules/validate_data'
 include { process_main } from './modules/process_main'
 include { process_maf } from './modules/process_maf'
-include { process_maf as process_maf_remaining_centers} from './modules/process_maf'
 
 // SET PARAMETERS
 
@@ -30,10 +29,6 @@ params.center = "ALL"
 params.create_new_maf_db = false
 // release name (pass in TEST.public to test the public release scripts)
 params.release = "TEST.consortium"
-// List all centers to be processed for maf_process
-params.maf_centers = "ALL"
-// List of centers to be processed converted from params.maf_centers
-maf_center_list = params.maf_centers?.split(",").toList()
 
 // Validate input parameters
 WorkflowMain.initialise(workflow, params, log)
@@ -95,7 +90,6 @@ if (major_release == "TEST") {
   center_map_synid = "syn11601248"
   is_prod = false
   is_staging = false
-  
 } else if (major_release == "STAGING"){
   project_id = "syn22033066"
   center_map_synid = "syn22089188"
@@ -110,49 +104,6 @@ else {
   is_staging = false
 }
 
-// Extract center list for MAF processing
-if (major_release == "TEST"){
-  all_centers = ["SAGE", "TEST", "GOLD"]
-} else {
-  all_centers = ["JHU","DFCI","GRCC","NKI","MSK","UHN","VICC","MDA","WAKE","YALE","UCSF","CRUK","CHOP","VHIO","SCI","PROV","COLU","UCHI","DUKE","UMIAMI"]
-}
-if (params.maf_centers == "ALL") {
-  maf_center_list = all_centers
-}
-
-def process_maf_helper(maf_centers, ch_project_id, maf_center_list, create_new_maf_db) {
-    /**
-  * Processes MAF files for a given center list.
-  *
-  * @param maf_centers          Parameter containing the centers to be processed, can be "ALL" or a comma-separated list
-  * @param ch_project_id        Channel with project ID
-  * @param maf_center_list          List of centers to be processed converted from params.maf_centers
-  * @param create_new_maf_db    Boolean flag to create new DB
-  * @return                     A collect output of the MAF process
-  */
-
-  // Create a channel from the list of centers
-  ch_maf_centers = Channel.fromList(maf_center_list)
-  // placeholder for previous output
-  previous = "default"
-  // If maf_centers is "ALL", we will process all centers in the maf_center_list
-  if (maf_centers == "ALL") {
-    // Create a channel to indicate whether it's the first center or not
-    ch_maf_centers = ch_maf_centers.branch { v ->
-        first: v == maf_center_list[0]
-        remaining: v != maf_center_list[0]
-    }
-    // Process the first center with createNewMafDb as true
-    process_maf_first_center = process_maf(previous, ch_project_id, ch_maf_centers.first, true).collect()
-    // Process the rest with createNewMafDb as false
-    return process_maf_remaining_centers(process_maf_first_center, ch_project_id, ch_maf_centers.remaining, false).collect()
-
-  } else {
-    // Process centers as the specified maf center list
-    return process_maf(previous, ch_project_id, ch_maf_centers, create_new_maf_db).collect()
-  }
-}
-
 workflow {
   ch_release = Channel.value(params.release)
   ch_project_id = Channel.value(project_id)
@@ -169,14 +120,13 @@ workflow {
     validate_data(ch_project_id, ch_center)
     // validate_data.out.view()
   } else if (params.process_type == "maf_process") {
-    // Call the function
-    process_maf_helper(params.maf_centers, ch_project_id, maf_center_list, params.create_new_maf_db)
+    process_maf(ch_project_id, ch_center, params.create_new_maf_db)
     // process_maf.out.view()
   } else if (params.process_type == "main_process") {
     process_main("default", ch_project_id, ch_center)
   } else if (params.process_type == "consortium_release") {
-    process_maf_col = process_maf_helper(params.maf_centers, ch_project_id, maf_center_list, params.create_new_maf_db)
-    process_main(process_maf_col, ch_project_id, ch_center)
+    process_maf(ch_project_id, ch_center, params.create_new_maf_db)
+    process_main(process_maf.out, ch_project_id, ch_center)
     create_consortium_release(process_main.out, ch_release, ch_is_prod, ch_seq_date, ch_is_staging)
     create_data_guide(create_consortium_release.out, ch_release, ch_project_id)
     if (!is_staging) {

modules/process_maf.nf

@@ -4,13 +4,10 @@ process process_maf {
     secret 'SYNAPSE_AUTH_TOKEN'
 
     input:
-    val previous
     val proj_id
     val center
     val create_new_maf_db
 
-    tag "processing_${center}"
-
     output:
     stdout
 

nextflow_schema.json

@@ -31,11 +31,6 @@
                     "description": "Pick a center to process or validate. Defaults to ALL which means all centers. This value should be ALL if you pick consortium release or public release.",
                     "default": "ALL"
                 },
-                "maf_centers": {
-                    "type": "string",
-                    "description": "The list of centers to be processed in the MAF processing. Defaults to ALL which means all centers.",
-                    "default": "ALL"
-                },
                 "create_new_maf_db": {
                     "type": "boolean",
                     "description": "Create a new maf Synapse Table. Toggle this for every consortium release."