From 0dc2d6317d4d6ebb07d48f07f86cd32df29c5515 Mon Sep 17 00:00:00 2001
From: edsu7 <22638361+edsu7@users.noreply.github.com>
Date: Fri, 10 Feb 2023 15:49:12 -0500
Subject: [PATCH 1/3] [wfpm v0.8.0] started a new version
 validate-seqtools@0.1.7 from validate-seqtools@0.1.6 which was released

---
 validate-seqtools/main.nf          | 2 +-
 validate-seqtools/pkg.json         | 2 +-
 validate-seqtools/tests/checker.nf | 2 +-
 3 files changed, 3 insertions(+), 3 deletions(-)

diff --git a/validate-seqtools/main.nf b/validate-seqtools/main.nf
index c06d013..8bad574 100755
--- a/validate-seqtools/main.nf
+++ b/validate-seqtools/main.nf
@@ -25,7 +25,7 @@
 /* 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 = '0.1.6'
+version = '0.1.7'
 
 container = [
     'ghcr.io': 'ghcr.io/icgc-argo/argo-data-submission.validate-seqtools'
diff --git a/validate-seqtools/pkg.json b/validate-seqtools/pkg.json
index 1b3c666..a75f6a7 100644
--- a/validate-seqtools/pkg.json
+++ b/validate-seqtools/pkg.json
@@ -1,6 +1,6 @@
 {
     "name": "validate-seqtools",
-    "version": "0.1.6",
+    "version": "0.1.7",
     "description": "Using Seq-tools, validates molecular",
     "main": "main.nf",
     "deprecated": false,
diff --git a/validate-seqtools/tests/checker.nf b/validate-seqtools/tests/checker.nf
index 67bea51..4853346 100755
--- a/validate-seqtools/tests/checker.nf
+++ b/validate-seqtools/tests/checker.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 = '0.1.6'
+version = '0.1.7'
 
 container = [
     'ghcr.io': 'ghcr.io/icgc-argo/argo-data-submission.validate-seqtools'

From dfe4bb413a09f20a598f78aad02c1107bc643db3 Mon Sep 17 00:00:00 2001
From: edsu7 <22638361+edsu7@users.noreply.github.com>
Date: Fri, 10 Feb 2023 15:59:32 -0500
Subject: [PATCH 2/3] fixed nextflow logic

---
 validate-seqtools/Dockerfile                      | 2 +-
 validate-seqtools/main.nf                         | 4 ++--
 validate-seqtools/tests/test-job-bam-w-skips.json | 2 +-
 3 files changed, 4 insertions(+), 4 deletions(-)

diff --git a/validate-seqtools/Dockerfile b/validate-seqtools/Dockerfile
index b8a0361..3b72eb9 100644
--- a/validate-seqtools/Dockerfile
+++ b/validate-seqtools/Dockerfile
@@ -11,7 +11,7 @@ RUN apt-get update && \
     apt-get install -y libz-dev pkg-config libtool m4 autotools-dev automake libncurses5-dev libbz2-dev liblzma-dev && \
     apt-get install -y git-all && \
     apt-get install -y jq && \
-    apt-get install -y locales
+    apt-get install -y locales pigz pbzip2
 
 # Set local
 
diff --git a/validate-seqtools/main.nf b/validate-seqtools/main.nf
index 8bad574..cf11e27 100755
--- a/validate-seqtools/main.nf
+++ b/validate-seqtools/main.nf
@@ -46,7 +46,7 @@ params.publish_dir = ""  // set to empty string will disable publishDir
 
 // tool specific parmas go here, add / change as needed
 params.json_file = ""
-params.skippable_tests = []
+params.skippable_tests = ""
 params.files = ""
 
 
@@ -73,7 +73,7 @@ process validateSeqtools {
     cp ${json_file} local_copy
     python3 /tools/main.py \
       -j local_copy \
-      -k ${skippable_tests.join(" ")} \
+      -k ${skippable_tests.replaceAll(","," ")} \
       -t ${params.cpus} \
       > seq-tools.log 2>&1
 
diff --git a/validate-seqtools/tests/test-job-bam-w-skips.json b/validate-seqtools/tests/test-job-bam-w-skips.json
index 2593150..73f131b 100644
--- a/validate-seqtools/tests/test-job-bam-w-skips.json
+++ b/validate-seqtools/tests/test-job-bam-w-skips.json
@@ -2,5 +2,5 @@
     "json_file": "input/anon_chr1_complete.json",
     "files": ["input/anon_chr1_complete.bam"],
     "expected_output": "expected/anon_chr1_rnaseq.validation_report.PASS-with-WARNING-and-SKIPPED-check.jsonl",
-    "skippable_tests" : ["c681","c683","c609"]
+    "skippable_tests" : "c681,c683,c609"
 }

From 5f82f85f764a509b6fc04782e4a9f0862cc3ecdc Mon Sep 17 00:00:00 2001
From: edsu7 <22638361+edsu7@users.noreply.github.com>
Date: Fri, 10 Feb 2023 16:06:17 -0500
Subject: [PATCH 3/3] update `checker.nf` for typo

---
 validate-seqtools/tests/checker.nf | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/validate-seqtools/tests/checker.nf b/validate-seqtools/tests/checker.nf
index 4853346..83a28a3 100755
--- a/validate-seqtools/tests/checker.nf
+++ b/validate-seqtools/tests/checker.nf
@@ -42,7 +42,7 @@ params.container_registry = ""
 params.container_version = ""
 params.container = ""
 
-params.skippable_tests=[]
+params.skippable_tests=""
 
 include { validateSeqtools } from '../main'