Merge branch 'main' of https://github.com/ICGC-ARGO-Structural-Variation-CN-WG/wfpm-demo into sequenza-wf@0.2.0

Author: desiree.schnidrig1

seqz-main/Dockerfile

@@ -7,9 +7,10 @@ RUN apt-get update \
     && git clone https://github.com/aroneklund/copynumber.git \
     && /opt/conda/bin/R CMD INSTALL copynumber
 
-COPY *.R /scripts/
+ENV PATH="/tools:${PATH}"
 
-USER sequenza
-WORKDIR /home/sequenza
+COPY runSequenza.R /tools/
+
+ENTRYPOINT ["/usr/bin/env"]
 
 CMD ["/bin/bash"]

seqz-main/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 = '0.2.0'  // package version
+version = '0.3.0'
 
 container = [
     'ghcr.io': 'ghcr.io/icgc-argo-structural-variation-cn-wg/wfpm-demo.seqz-main'
@@ -51,7 +51,6 @@ params.publish_dir = "output_dir/"  // set to empty string will disable publishD
 // tool specific parmas go here, add / change as needed
 params.seqz = ""
 params.genome = 'hg38'
-params.runscript      = "${baseDir}/scripts/runSequenza.R"
 params.output_pattern = "*_*" // output file name pattern are *.pdf|*.txt|*.RData
 
 
@@ -64,7 +63,6 @@ process seqzMain {
 
   input:  // input, make update as needed
     path seqz
-    path runscript
 
   output:  // output, make update as needed
     path "${params.output_pattern}", emit: results
@@ -74,7 +72,7 @@ process seqzMain {
     // add and initialize variables here as needed
 
     """
-    Rscript !{runscript} --seqz !{seqz} --genome !{params.genome}
+    Rscript /tools/runSequenza.R --seqz !{seqz} --genome !{params.genome}
     """
 }
 
@@ -83,7 +81,6 @@ process seqzMain {
 // using this command: nextflow run <git_acc>/<repo>/<pkg_name>/<main_script>.nf -r <pkg_name>.v<pkg_version> --params-file xxx
 workflow {
   seqzMain(
-    file(params.seqz),
-    file(params.runscript)
+    file(params.seqz)
   )
 }

seqz-main/pkg.json

@@ -1,6 +1,6 @@
 {
     "name": "seqz-main",
-    "version": "0.2.0",
+    "version": "0.3.0",
     "description": "run sequenza (the input for this package - *.seqz.gz - can be generated with the seqz-preprocess package)",
     "main": "main.nf",
     "deprecated": false,

seqz-main/scripts/runSequenza.R seqz-main/runSequenza.Rseqz-main/scripts/runSequenza.R renamed to seqz-main/runSequenza.R

@@ -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 = '0.2.0'  // package version
+version = '0.3.0'
 
 container = [
     'ghcr.io': 'ghcr.io/icgc-argo-structural-variation-cn-wg/wfpm-demo.seqz-main'
@@ -49,7 +49,6 @@ params.container = ""
 
 // tool specific parmas go here, add / change as needed
 params.seqz = ""
-params.runscript = ""
 params.expected_output = ""
 
 include { seqzMain } from '../main'
@@ -76,13 +75,11 @@ process file_smart_diff {
 workflow checker {
   take:
     seqz
-    runscript
     expected_output
 
   main:
     seqzMain(
-      seqz,
-      runscript
+      seqz
     )
 
     file_smart_diff(
@@ -95,7 +92,6 @@ workflow checker {
 workflow {
   checker(
     file(params.seqz),
-    file(params.runscript),
     file(params.expected_output)
   )
 }