changed icgc refs

ratschlab · Jul 29, 2021 · e94df44 · e94df44
1 parent 63eb0e1
commit e94df44
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Showing 3 changed files with 10 additions and 10 deletions.
diff --git a/genome-alignment-star/Dockerfile b/genome-alignment-star/Dockerfile
@@ -1,8 +1,8 @@
 FROM ratschlab/wf-base-miniconda4.8.3:v1.0.1
 
-LABEL org.opencontainers.image.source https://github.com/icgc-argo-rna-wg/icgc-argo-rna-seq-alignment
+LABEL org.opencontainers.image.source https://github.com/ratschlab/wftools-alignment-rna
 LABEL org.opencontainers.image.authors Andre Kahles ([email protected])
-LABEL org.opencontainers.image.title ICGC ARGO RNA-Seq alignment image
+LABEL org.opencontainers.image.title Raetschlab RNA-Seq alignment image - STAR
 
 ENV PATH="/opt/local:${PATH}"
 

diff --git a/genome-alignment-star/main.nf b/genome-alignment-star/main.nf
@@ -1,7 +1,7 @@
 #!/usr/bin/env nextflow
 
 /*
-  Copyright (c) 2021, icgc-argo-rna-wg
+  Copyright (c) 2021, ratschlab
 
   Permission is hereby granted, free of charge, to any person obtaining a copy
   of this software and associated documentation files (the "Software"), to deal
@@ -57,7 +57,7 @@ params.sample = ""
 params.sjdboverhang = 100
 params.pair_status = "paired"
 
-process icgcArgoRnaSeqAlignmentSTAR {
+process genomeAlignmentSTAR {
   container "${params.container ?: container[params.container_registry ?: default_container_registry]}:${params.container_version ?: version}"
   publishDir "${params.publish_dir}/${task.process.replaceAll(':', '_')}", mode: "copy", enabled: params.publish_dir
 
@@ -96,7 +96,7 @@ process icgcArgoRnaSeqAlignmentSTAR {
 // this provides an entry point for this main script, so it can be run directly without clone the repo
 // using this command: nextflow run <git_acc>/<repo>/<pkg_name>/<main_script>.nf -r <pkg_name>.v<pkg_version> --params-file xxx
 workflow {
-  icgcArgoRnaSeqAlignmentSTAR(
+  genomeAlignmentSTAR(
     file(params.index),
     file(params.gtf),
     params.input_files.collect({it -> file(it)}),

diff --git a/genome-alignment-star/tests/checker.nf b/genome-alignment-star/tests/checker.nf
@@ -1,7 +1,7 @@
 #!/usr/bin/env nextflow
 
 /*
-  Copyright (c) 2021, icgc-argo-rna-wg
+  Copyright (c) 2021, ratschlab
 
   Permission is hereby granted, free of charge, to any person obtaining a copy
   of this software and associated documentation files (the "Software"), to deal
@@ -56,7 +56,7 @@ params.sjdboverhang = 100
 params.pair_status = "paired"
 params.expected_output = "tests/expected/sample_01_Aligned.out.bam"
 
-include { icgcArgoRnaSeqAlignmentSTAR } from '../main' params(['cleanup': false, *:params])
+include { genomeAlignmentSTAR } from '../main' params(['cleanup': false, *:params])
 
 process diff_bam {
   container "${params.container ?: container[params.container_registry ?: default_container_registry]}:${params.container_version ?: version}"
@@ -106,7 +106,7 @@ workflow checker {
     expected_junctions
 
   main:
-    icgcArgoRnaSeqAlignmentSTAR(
+    genomeAlignmentSTAR(
         index,
         gtf,
         input_files,
@@ -117,12 +117,12 @@ workflow checker {
     )
 
     diff_bam(
-      icgcArgoRnaSeqAlignmentSTAR.out.bam,
+      genomeAlignmentSTAR.out.bam,
       expected_bam
     )
 
     diff_junctions(
-      icgcArgoRnaSeqAlignmentSTAR.out.junctions,
+      genomeAlignmentSTAR.out.junctions,
       expected_junctions
     )
 }