Fix BAM input

Remove "N_TRIES". Bump the Docker container image version.
Sentieon · Jan 30, 2018 · 558ecec · 558ecec
1 parent c73b42c
commit 558ecec
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Showing 4 changed files with 3 additions and 5 deletions.
diff --git a/examples/100x_wes.json b/examples/100x_wes.json
@@ -6,7 +6,6 @@
   "BQSR_SITES": "gs://sentieon-test/pipeline_test/reference/Mills_and_1000G_gold_standard.indels.b37.vcf.gz,gs://sentieon-test/pipeline_test/reference/1000G_phase1.indels.b37.vcf.gz,gs://sentieon-test/pipeline_test/reference/dbsnp_138.b37.vcf.gz",
   "DBSNP": "gs://sentieon-test/pipeline_test/reference/dbsnp_138.b37.vcf.gz",
   "PREEMPTIBLE_TRIES": "2",
-  "N_TRIES": "1",
   "STREAM_INPUT": "True",
   "ZONES": "us-central1-a,us-central1-b,us-central1-c,us-central1-f",
   "PROJECT_ID": "YOUR_PROJECT_HERE"

diff --git a/examples/30x_wgs.json b/examples/30x_wgs.json
@@ -6,7 +6,6 @@
   "BQSR_SITES": "gs://sentieon-test/pipeline_test/reference/Mills_and_1000G_gold_standard.indels.b37.vcf.gz,gs://sentieon-test/pipeline_test/reference/1000G_phase1.indels.b37.vcf.gz,gs://sentieon-test/pipeline_test/reference/dbsnp_138.b37.vcf.gz",
   "DBSNP": "gs://sentieon-test/pipeline_test/reference/dbsnp_138.b37.vcf.gz",
   "PREEMPTIBLE_TRIES": "2",
-  "N_TRIES": "1",
   "STREAM_INPUT": "True",
   "ZONES": "us-central1-a,us-central1-b,us-central1-c,us-central1-f",
   "PROJECT_ID": "YOUR_PROJECT_HERE"

diff --git a/pipeline_scripts/gc_germline.sh b/pipeline_scripts/gc_germline.sh
@@ -171,7 +171,7 @@ if [[ -n "$BAM" ]]; then
     fi
     local_bams=()
     for bam in ${bams[@]}; do
-        local_bams=$input_dir/$(basename $bam)
+        local_bam=$input_dir/$(basename $bam)
         transfer $bam $local_bam
         if $(test -e ${bam}.bai) || $(gsutil -q stat ${bam}.bai); then
             bai=${bam}.bai
@@ -183,7 +183,7 @@ if [[ -n "$BAM" ]]; then
         fi
         local_bai=$input_dir/$(basename $bai)
         transfer $bai $local_bai
-        local_bams+=($bam)
+        local_bams+=($local_bam)
     done
 else
     local_bams=()

diff --git a/runner/runner_default.json b/runner/runner_default.json
@@ -23,5 +23,5 @@
   "FQ2": null, 
   "DBSNP": null, 
   "FQ1": null, 
-  "DOCKER_IMAGE": "sentieon/sentieon-google-cloud:201711.01"
+  "DOCKER_IMAGE": "sentieon/sentieon-google-cloud:201711.01-1"
 }