Merge branch 'main' of https://github.com/icgc-argo-workflows/icgc-argo-mutational-signatures into matrixgenerator@0.1.0

Author: alvinwt

.github/workflows/build-test-release.yml

@@ -95,6 +95,7 @@ jobs:
 
     - name: Install Nextflow
       run: |
+        export NXF_VER=21.10.6
         wget --tries=10 -qO- https://get.nextflow.io | bash
         sudo chmod 755 nextflow
         sudo mv nextflow /usr/local/bin/

nextflow.config

@@ -1,7 +1,7 @@
 manifest {
     homePage = 'https://github.com/icgc-argo-workflows/icgc-argo-mutational-signatures'
     description = 'ICGC ARGO Mutational Signatures Workflow Packages'
-    nextflowVersion = '>=20.10'
+    nextflowVersion = '21.10'
 }
 
 docker {

signaturetoolslib/Dockerfile

@@ -20,7 +20,7 @@ RUN wget https://cdn.rstudio.com/r/${OS_IDENTIFIER}/pkgs/R-${R_VERSION}-1-1.x86_
  yum clean all
 
 
-RUN R -e "install.packages("remotes", dependencies=TRUE,repos='http://cran.rstudio.com/')"
+RUN R -e "install.packages('remotes', dependencies=TRUE,repos='http://cran.rstudio.com/')"
 
 
 ## Installing packages from Bioconductor

signaturetoolslib/SignatureToolsLib.R

@@ -1,12 +1,8 @@
 #!/usr/bin/Rscript
 
-# Library
 library(signature.tools.lib)
 library("optparse")
 
-#####INPUT
-
-###
 option_list = list(
   make_option(c("-i", "--input_file"), type="character", default=NULL,
               help="Matrix of counts", metavar="character"),
@@ -23,38 +19,36 @@ if (is.null(opt$input_file) | is.null(opt$output_dir) ){
   stop("Missing some input arguments... Exiting...", call.=FALSE)
 }
 
-### Set seed 
+## Set seed used to match expected output
 set.seed(164)
 
-##### Input variables
+## Input variables
 DIR_RES <- opt$output_dir
 INPUT_MAT <- opt$input_file
 
-# Import variables
+## Import matrix of counts
 mut_mat_ICGC <- read.table(INPUT_MAT, row.names = 1, header=TRUE)
 
-## Function for extracting signatures
-extractSignatures <- function(input_matrix, sig_matrix) {
+## Function for signature attribution
+assignSignatures <- function(input_matrix, sig_matrix) {
 
+## use Fit function, FitMS is still undergoing testing 
   subs_fit_res <- signature.tools.lib::Fit(catalogues = input_matrix,
                                            exposureFilterType = "giniScaledThreshold",
                                            signatures = sig_matrix,
                                            useBootstrap = TRUE,
                                            nboot = 100,
                                            nparallel = 6 )
-  # Save 
-  #snv_exp <- subs_fit_res$E_median_filtered
-  # Return
   return(subs_fit_res)
 }
 
-
-# Extract the signatures
-sign_res <- extractSignatures(mut_mat_ICGC, COSMIC30_subs_signatures)
+## Assign the signatures
+## Currently testing with COSMIC 30 signatures (To update)
+sign_res <- assignSignatures(mut_mat_ICGC, COSMIC30_subs_signatures)
 
 ### Save output as JSON
-fitToJSON(sign_res,
-          paste0(DIR_RES, "/export_signatures.json") )
+signature.tools.lib::fitToJSON(sign_res,
+          paste0(DIR_RES, "/export_assignments.json") )
 
 
-                       
+                       

signaturetoolslib/main.nf

@@ -29,7 +29,7 @@
 /* this block is auto-generated based on info from pkg.json where   */
 /* changes can be made if needed, do NOT modify this block manually */
 nextflow.enable.dsl = 2
-version = '0.1.0'  // package version
+version = '0.1.1'
 
 container = [
     'ghcr.io': 'ghcr.io/icgc-argo-workflows/icgc-argo-mutational-signatures.signaturetoolslib'
@@ -63,7 +63,7 @@ process signaturetoolslib {
     path input_file
 
   output:  // output, make update as needed
-    path "${params.output_dir}/export_signatures.json", emit: output_file
+    path "${params.output_dir}/export_assignments.json", emit: output_file
 
   script:
     // add and initialize variables here as needed

signaturetoolslib/pkg.json

@@ -1,6 +1,6 @@
 {
     "name": "signaturetoolslib",
-    "version": "0.1.0",
+    "version": "0.1.1",
     "description": "Mutational signature tool",
     "main": "main.nf",
     "deprecated": false,

signaturetoolslib/tests/checker.nf

@@ -34,7 +34,7 @@
 /* this block is auto-generated based on info from pkg.json where   */
 /* changes can be made if needed, do NOT modify this block manually */
 nextflow.enable.dsl = 2
-version = '0.1.0'  // package version
+version = '0.1.1'
 
 container = [
     'ghcr.io': 'ghcr.io/icgc-argo-workflows/icgc-argo-mutational-signatures.signaturetoolslib'

…slib/tests/expected/test_signatures.json …lib/tests/expected/test_assignments.jsonsignaturetoolslib/tests/expected/test_signatures.json renamed to signaturetoolslib/tests/expected/test_assignments.json signaturetoolslib/tests/expected/test_signatures.json renamed to signaturetoolslib/tests/expected/test_assignments.json

@@ -1,5 +1,5 @@
 {
-	"fitAlgorithm": Fit,
+	"fitAlgorithm": "Fit",
 	"nsamples": 10,
 	"nsignatures": 30,
 	"nchannels": 96,

signaturetoolslib/tests/test-job-1.json

@@ -1,7 +1,7 @@
 {
     "input_file": "input/Synthetic.eso.mutation.counts-10-samples.tsv",
-    "expected_output": "expected/test_signatures.json",
+    "expected_output": "expected/test_assignments.json",
     "output_dir": "outdir_dir",
     "cpus": 2,
     "mem": 6
-}
+}