Merge pull request #23 from icgc-argo/[email protected].…

…0-1.3.0 [release]
icgc-argo · Feb 15, 2021 · 901d1c3 · 901d1c3
2 parents 20351de + 33ae99b
commit 901d1c3
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Showing 5 changed files with 12 additions and 9 deletions.
diff --git a/demo-dna-seq-processing-wf/main.nf b/demo-dna-seq-processing-wf/main.nf
@@ -24,7 +24,7 @@
 
 nextflow.enable.dsl = 2
 name = 'dna-seq-processing'
-version = '1.6.0-1.2.0'
+version = '1.7.0-1.3.0'
 
 
 params.ref_genome_fa = ""
@@ -36,6 +36,7 @@ params.cpus = 1
 params.mem = 1
 params.tempdir = "NO_DIR"
 params.publish_dir = ""
+params.container_registry = ""
 
 params.bwaMemAligner = [:]
 params.bamMergeSortMarkdup = [:]
@@ -44,13 +45,15 @@ bwaMemAligner_params = [
     'cpus': params.cpus,
     'mem': params.mem,
     'publish_dir': params.publish_dir,
+    'container_registry': params.container_registry,
     *:(params.bwaMemAligner ?: [:])
 ]
 
 bamMergeSortMarkdup_params = [
     'cpus': params.cpus,
     'mem': params.mem,
     'publish_dir': params.publish_dir,
+    'container_registry': params.container_registry,
     'output_format': 'cram',
     'markdup': true,
     'lossy': false,

diff --git a/demo-dna-seq-processing-wf/pkg.json b/demo-dna-seq-processing-wf/pkg.json
@@ -1,10 +1,10 @@
 {
     "name": "demo-dna-seq-alignment-wf",
-    "version": "1.6.0-1.2.0",
+    "version": "1.7.0-1.3.0",
     "description": "DNA Seq Alignment Workflow with QC Metrics Collection",
     "main": "main.nf",
     "scripts": {
-        "test": "pushd tests && ./run_tests.sh; popd"
+        "test": "wfpm test"
     },
     "deprecated": false,
     "keywords": [
@@ -20,9 +20,9 @@
         "url": "https://github.com/icgc-argo/demo-wfpkgs.git"
     },
     "dependencies": [
-        "github.com/icgc-argo/demo-wfpkgs/demo-aligned-seq-qc@1.0.0",
-        "github.com/icgc-argo/demo-wfpkgs/demo-dna-seq-alignment@1.5.5",
-        "github.com/icgc-argo/demo-wfpkgs/demo-utils@1.0.0"
+        "github.com/icgc-argo/demo-wfpkgs/demo-aligned-seq-qc@1.1.0",
+        "github.com/icgc-argo/demo-wfpkgs/demo-dna-seq-alignment@1.7.0",
+        "github.com/icgc-argo/demo-wfpkgs/demo-utils@1.2.0"
     ],
     "devDependencies": [],
     "contributors": [

diff --git a/demo-dna-seq-processing-wf/tests/checker.nf b/demo-dna-seq-processing-wf/tests/checker.nf
@@ -31,6 +31,7 @@ params.ref_genome_fa = "reference/tiny-grch38-chr11-530001-537000.fa.gz"
 params.metadata = "NO_FILE"
 params.tempdir = "NO_DIR"
 params.publish_dir = "outdir"
+params.container_registry = "ghcr.io"
 
 include { DnaSeqProcess } from '../main.nf' params(params)
 

diff --git a/demo-dna-seq-processing-wf/tests/test-1lane_bam.nf.json b/demo-dna-seq-processing-wf/tests/test-1lane_bam.nf.json
@@ -3,5 +3,5 @@
     "ref_genome_fa": "reference/tiny-grch38-chr11-530001-537000.fa",
     "metadata": "input/0ae2c59b-2976-485c-a2c5-9b2976085cbf.fq.sequencing_experiment.song-analysis.json",
     "tempdir": "/tmp",
-    "container_registry": "quay.io"
+    "container_registry": "ghcr.io"
 }
diff --git a/demo-dna-seq-processing-wf/tests/test-2lane_bam.nf.json b/demo-dna-seq-processing-wf/tests/test-2lane_bam.nf.json
@@ -6,6 +6,5 @@
     "aligned_lane_prefix": "grch38-aligned",
     "metadata": "input/0ae2c59b-2976-485c-a2c5-9b2976085cbf.bam-1.sequencing_experiment.song-analysis.json",
     "tempdir": "/tmp/",
-    "cpus": 2,
-    "container_registry": "quay.io"
+    "cpus": 2
 }