chore: clean repo

Dockerfile

@@ -1,4 +1,4 @@
-#Current version of post external release1 docker us-docker.pkg.dev/my-project/rrbs/rrbs:msamdars_11_14_2022
+#Current version of post external release1 docker us-docker.pkg.dev/motrpac-portal/rrbs/rrbs:msamdars_11_14_2022
 FROM python:3.8-slim-bullseye as compile-image
 
 # Install essentials, python3, python, libraries used for installing other packges, pip, pip3

config/backends/gcp/google.conf

@@ -16,7 +16,7 @@ engine {
   filesystems {
     gcs {
       auth = "application-default"
-      project = "my-project-dev"
+      project = "motrpac-portal-dev"
     }
   }
 }
@@ -28,10 +28,10 @@ backend {
       actor-factory = "cromwell.backend.impl.jes.JesBackendLifecycleActorFactory"
       config {
         // Google project
-        project = "my-project-dev"
+        project = "motrpac-portal-dev"
 
         // Base bucket for workflow executions
-        root = "gs://archanaraja/rrbs/test/pilot/"
+        root = "gs://my-bucket/rrbs/test/pilot/"
 
         // Polling for completion backs-off gradually for slower-running jobs.
         // This is the maximum polling interval (in seconds):
@@ -62,7 +62,7 @@ backend {
           gcs {
             // A reference to a potentially different auth for manipulating files via engine functions.
             auth = "application-default"
-            project = "my-project-dev"
+            project = "motrpac-portal-dev"
           }
         }
       }

config/backends/gcp/google_prod_PAPI.conf

@@ -16,7 +16,7 @@ engine {
   filesystems {
     gcs {
       auth = "application-default"
-      project = "my-project"
+      project = "motrpac-portal"
     }
   }
 }
@@ -28,7 +28,7 @@ backend {
       actor-factory = "cromwell.backend.google.pipelines.v2alpha1.PipelinesApiLifecycleActorFactory"
       config {
         // Google project
-        project = "my-project"
+        project = "motrpac-portal"
 
         // Base bucket for workflow executions
         root="gs://my-bucket/rrbs/pipeline_test/pilot/"
@@ -65,7 +65,7 @@ backend {
           gcs {
             // A reference to a potentially different auth for manipulating files via engine functions.
             auth = "application-default"
-            project = "my-project"
+            project = "motrpac-portal"
           }
         }
       }

docker_info.txt

@@ -1,18 +1,18 @@
 only the bismark version used was 0.20.1 , rest matches the MOP i believe we should use 0.22.1 , but needs clarification from Yongchao
 
-docker build . -t gcr.io/my-project-dev/motrpac_rrbs:araja_05_20_2019
-docker push gcr.io/my-project-dev/motrpac_rrbs:araja_05_20_2019
+docker build . -t gcr.io/motrpac-portal-dev/motrpac_rrbs:araja_05_20_2019
+docker push gcr.io/motrpac-portal-dev/motrpac_rrbs:araja_05_20_2019
 
 #Pushing the image to the production environment
 
-docker build . -t gcr.io/my-project/motrpac_rrbs:araja_05_20_2019
-docker push gcr.io/my-project/motrpac_rrbs:araja_05_20_2019
+docker build . -t gcr.io/motrpac-portal/motrpac_rrbs:araja_05_20_2019
+docker push gcr.io/motrpac-portal/motrpac_rrbs:araja_05_20_2019
 
 Fixed a typo in the Docker file
-Older docker image : gcr.io/my-project/motrpac_rrbs:araja_05_24_2019
+Older docker image : gcr.io/motrpac-portal/motrpac_rrbs:araja_05_24_2019
 
-#Previous well tested docker image : gcr.io/my-project/motrpac_rrbs:araja_06_17_2019 
+#Previous well tested docker image : gcr.io/motrpac-portal/motrpac_rrbs:araja_06_17_2019 
 
 #Updated ubuntu version , fixed the qc script to round a metric , removed bismark as the source install had the wrong version of bismark methylation extractor
-Latest docker image : gcr.io/my-project/motrpac_rrbs:araja_07_09_2019
-Bismark docker : gcr.io/my-project/bismark:0.20.0
+Latest docker image : gcr.io/motrpac-portal/motrpac_rrbs:araja_07_09_2019
+Bismark docker : gcr.io/motrpac-portal/bismark:0.20.0

examples/input_json/rrbs_pipeline_inputs_GCloud.json

@@ -1,12 +1,12 @@
 {
     "rrbs_pipeline.r1": [
-        "gs://my-project-transfer-sinai/rrbs_rn_2019_06_03/fastq_raw/Rat_Muscle_R1.fastq.gz"
+        "gs://transfer-bucket/rrbs_rn_2019_06_03/fastq_raw/Rat_Muscle_R1.fastq.gz"
     ],
     "rrbs_pipeline.r2": [
-        "gs://my-project-transfer-sinai/rrbs_rn_2019_06_03/fastq_raw/Rat_Muscle_R2.fastq.gz"
+        "gs://transfer-bucket/rrbs_rn_2019_06_03/fastq_raw/Rat_Muscle_R2.fastq.gz"
     ],
     "rrbs_pipeline.i1": [
-        "gs://my-project-transfer-sinai/rrbs_rn_2019_06_03/fastq_raw/Rat_Muscle_I1.fastq.gz"
+        "gs://transfer-bucket/rrbs_rn_2019_06_03/fastq_raw/Rat_Muscle_I1.fastq.gz"
     ],
     "rrbs_pipeline.sample_prefix": [
         "Rat_Muscle"
@@ -69,8 +69,8 @@
     "rrbs_pipeline.trim_reg_adapt_disk": 150,
     "rrbs_pipeline.trim_reg_adapt_ncpu": 1,
     "rrbs_pipeline.trim_reg_adapt_ramGB": 40,
-    "rrbs_pipeline.docker": "gcr.io/my-project/motrpac_rrbs:araja_06_17_2019",
-    "rrbs_pipeline.bismark_docker": "gcr.io/my-project/bismark:0.20.0",
+    "rrbs_pipeline.docker": "gcr.io/motrpac-portal/motrpac_rrbs:araja_06_17_2019",
+    "rrbs_pipeline.bismark_docker": "gcr.io/motrpac-portal/bismark:0.20.0",
     "rrbs_pipeline.output_report_name": "Rat_Muscle_rrbs_rn_2019_06_03_report"
 }
 

examples/input_json/rrbs_pipeline_inputs_PILOT.json

@@ -1,12 +1,12 @@
 {
     "rrbs_pipeline.r1": [
-        "gs://my-project-transfer-sinai/rrbs_rn_2019_06_03/fastq_raw/Rat_Brown_fat_R1.fastq.gz"
+        "gs://transfer-bucket/rrbs_rn_2019_06_03/fastq_raw/Rat_Brown_fat_R1.fastq.gz"
     ],
     "rrbs_pipeline.r2": [
-        "gs://my-project-transfer-sinai/rrbs_rn_2019_06_03/fastq_raw/Rat_Brown_fat_R2.fastq.gz"
+        "gs://transfer-bucket/rrbs_rn_2019_06_03/fastq_raw/Rat_Brown_fat_R2.fastq.gz"
     ],
     "rrbs_pipeline.i1": [
-        "gs://my-project-transfer-sinai/rrbs_rn_2019_06_03/fastq_raw/Rat_Brown_fat_I1.fastq.gz"
+        "gs://transfer-bucket/rrbs_rn_2019_06_03/fastq_raw/Rat_Brown_fat_I1.fastq.gz"
     ],
     "rrbs_pipeline.sample_prefix": [
         "Rat_Brown_fat"
@@ -68,8 +68,8 @@
     "rrbs_pipeline.trim_reg_adapt_disk": 150,
     "rrbs_pipeline.trim_reg_adapt_ncpu": 1,
     "rrbs_pipeline.trim_reg_adapt_ramGB": 40,
-    "rrbs_pipeline.docker": "gcr.io/my-project/motrpac_rrbs:araja_06_17_2019",
-    "rrbs_pipeline.bismark_docker": "gcr.io/my-project/bismark:0.20.0",
+    "rrbs_pipeline.docker": "gcr.io/motrpac-portal/motrpac_rrbs:araja_06_17_2019",
+    "rrbs_pipeline.bismark_docker": "gcr.io/motrpac-portal/bismark:0.20.0",
     "rrbs_pipeline.output_report_name": "Rat_Brown_fat_rrbs_rn_2019_06_03_report"
 }
 

scripts/README.md

@@ -51,6 +51,6 @@ python3 make_json_rrbs.py -g gs://my-bucket/rrbs/test/fastq_raw \
 -r rrbs-test \
 -a rat-rn6 \
 -n 1 \
--d us-docker.pkg.dev/my-project \
+-d us-docker.pkg.dev/motrpac-portal \
 -p my-project
 ```

scripts/make_json_rrbs.py

@@ -221,7 +221,7 @@ def make_json_dict(
         "--docker_repo",
         help="Docker repository prefix containing the images used in the workflow",
         type=str,
-        default="us-docker.pkg.dev/my-project/rrbs",
+        default="us-docker.pkg.dev/motrpac-portal/rrbs",
     )
     parser.add_argument(
         "-p",

scripts/run_docker.sh

@@ -1,4 +1,4 @@
-docker run -v `pwd`:`pwd` -w `pwd` -it gcr.io/my-project/motrpac_rrbs:araja_06_17_2019 bismark2summary *.bam
+docker run -v `pwd`:`pwd` -w `pwd` -it gcr.io/motrpac-portal/motrpac_rrbs:araja_06_17_2019 bismark2summary *.bam
 
-docker run -v `pwd`:`pwd` -w `pwd` -it gcr.io/my-project-dev/bismark:0.20.0 deduplicate_bismark -p --barcode --bam Rat_Muscle_R1_bismark_bt2_pe.bam Rat_Muscle_R1_bismark_bt2_pe.bam
+docker run -v `pwd`:`pwd` -w `pwd` -it gcr.io/motrpac-portal-dev/bismark:0.20.0 deduplicate_bismark -p --barcode --bam Rat_Muscle_R1_bismark_bt2_pe.bam Rat_Muscle_R1_bismark_bt2_pe.bam
 

wdl/align_trimmed/align_trimmed_inputs_GCloud.json

@@ -6,7 +6,7 @@
   "align_trimmed.alignTrimmed.bismark_multicore": "4",
   "align_trimmed.SID": "Muscle2",
   "align_trimmed.memory": "60",
-  "align_trimmed.docker": "gcr.io/my-project-dev/bismark:0.20.0",
+  "align_trimmed.docker": "gcr.io/motrpac-portal-dev/bismark:0.20.0",
   "align_trimmed.num_preempt": "0",
   "align_trimmed.disk": "100",
   "align_trimmed.ncpu": "16"

wdl/align_trimmed/align_trimmed_inputs_motrpac.json

@@ -6,7 +6,7 @@
   "align_trimmed.alignTrimmed.bismark_multicore": "4",
   "align_trimmed.SID": "Rat_Muscle",
   "align_trimmed.memory": "60",
-  "align_trimmed.docker": "gcr.io/my-project/bismark:0.20.0",
+  "align_trimmed.docker": "gcr.io/motrpac-portal/bismark:0.20.0",
   "align_trimmed.num_preempt": "0",
   "align_trimmed.disk": "200",
   "align_trimmed.ncpu": "16"

wdl/bowtie2_align/bowtie2_align_inputs.json

@@ -6,7 +6,7 @@
   "bowtie2_align_workflow.bowtie2_align.memory": "40",
   "bowtie2_align_workflow.bowtie2_align.num_preempt": "0",
   "bowtie2_align_workflow.bowtie2_align.fastqr2": "gs://my-bucket/rrbs/pipeline_test/rrbs_pipeline/7e9293eb-d5da-4bbd-92b8-5290adceb0b9/call-trimGalore/Rat_Muscle_attached_R2_val_2.fq.gz",
-  "bowtie2_align_workflow.bowtie2_align.docker": "gcr.io/my-project/motrpac_rrbs:araja_05_24_2019",
+  "bowtie2_align_workflow.bowtie2_align.docker": "gcr.io/motrpac-portal/motrpac_rrbs:araja_05_24_2019",
   "bowtie2_align_workflow.bowtie2_align.genome_dir_tar": "gs://my-bucket/references/rn/bowtie2_index/phix.tar.gz",
   "bowtie2_align_workflow.bowtie2_align.genome_dir": "phix"
 }

wdl/collect_qc_metrics/collect_qc_metrics_inputs_GCloud.json

@@ -5,7 +5,7 @@
   "collect_qc_metrics.collectQCMetrics.SID": "Rat_Muscle",
   "collect_qc_metrics.collectQCMetrics.deduplication_report": "gs://sa-rrbs-pipeline/cromwell-execution/rrbs_pipeline/d725689f-9e58-47a7-a225-f4cc0ab1aef7/call-markDuplicatesSample/Rat_Muscle_attached_R1_val_1.fq_trimmed_bismark_bt2_pe.deduplication_report.txt",
   "collect_qc_metrics.collectQCMetrics.bismark_bt2_pe_report": "gs://sa-rrbs-pipeline/cromwell-execution/rrbs_pipeline/d725689f-9e58-47a7-a225-f4cc0ab1aef7/call-alignTrimmedSample/Rat_Muscle_attached_R1_val_1.fq_trimmed_bismark_bt2_PE_report.txt",
-  "collect_qc_metrics.collectQCMetrics.docker": "gcr.io/my-project-dev/motrpac_rrbs:SA_04_07_2019",
+  "collect_qc_metrics.collectQCMetrics.docker": "gcr.io/motrpac-portal-dev/motrpac_rrbs:SA_04_07_2019",
   "collect_qc_metrics.num_preempt": "0",
   "collect_qc_metrics.collectQCMetrics.species_bismark_summary_report": "gs://sa-rrbs-pipeline/cromwell-execution/rrbs_pipeline/d725689f-9e58-47a7-a225-f4cc0ab1aef7/call-alignTrimmedSample/bismark_summary_report.txt",
   "collect_qc_metrics.collectQCMetrics.multiQC_report": "gs://sa-rrbs-pipeline/cromwell-execution/rrbs_pipeline/d725689f-9e58-47a7-a225-f4cc0ab1aef7/call-multiQC/multiqc_report.tar.gz",

wdl/collect_qc_metrics/collect_qc_metrics_inputs_pilot.json

@@ -9,7 +9,7 @@
   "collect_qc_metrics.collectQCMetrics.bismark_bt2_pe_report": "gs://my-bucket/rrbs/pipeline_test/pilot/rrbs_pipeline/3ed27b39-6783-4126-8d8b-8ad8fb18a0fc/call-alignTrimmedSample/Rat_Muscle_attached_R1_val_1.fq_trimmed_bismark_bt2_PE_report.txt",
   "collect_qc_metrics.collectQCMetrics.mapping_report": "gs://my-bucket/rrbs/pipeline_test/pilot/rrbs_pipeline/3ed27b39-6783-4126-8d8b-8ad8fb18a0fc/call-chrinfo/Rat_Muscle_mapped_report.txt",
   "collect_qc_metrics.collectQCMetrics.trim_diversity_report": "gs://my-bucket/rrbs/pipeline_test/pilot/rrbs_pipeline/3ed27b39-6783-4126-8d8b-8ad8fb18a0fc/call-trimDiversityAdapt/trimDiversityAdapt.log",
-  "collect_qc_metrics.collectQCMetrics.docker": "gcr.io/my-project/motrpac_rrbs:araja_06_17_2019",
+  "collect_qc_metrics.collectQCMetrics.docker": "gcr.io/motrpac-portal/motrpac_rrbs:araja_06_17_2019",
   "collect_qc_metrics.num_preempt": "0",
   "collect_qc_metrics.collectQCMetrics.species_bismark_summary_report": "gs://my-bucket/rrbs/pipeline_test/pilot/rrbs_pipeline/3ed27b39-6783-4126-8d8b-8ad8fb18a0fc/call-alignTrimmedSample/bismark_summary_report.txt",
   "collect_qc_metrics.collectQCMetrics.multiQC_report": "gs://my-bucket/rrbs/pipeline_test/pilot/rrbs_pipeline/3ed27b39-6783-4126-8d8b-8ad8fb18a0fc/call-multiQC/multiqc_report.tar.gz",

wdl/compute_mapped/chr_info_inputs.json

@@ -1,8 +1,8 @@
 {
-  "mapped_workflow.samtools_mapped.input_bam": "gs://my-project-transfer-sinai/rrbs_rn_2019_06_03/bismark/Rat_Muscle_R1_bismark_bt2_pe.deduplicated.bam",
+  "mapped_workflow.samtools_mapped.input_bam": "gs://transfer-bucket/rrbs_rn_2019_06_03/bismark/Rat_Muscle_R1_bismark_bt2_pe.deduplicated.bam",
   "mapped_workflow.samtools_mapped.disk": "50",
   "mapped_workflow.samtools_mapped.memory": "20",
-  "mapped_workflow.samtools_mapped.docker": "gcr.io/my-project/motrpac_rrbs:araja_05_24_2019",
+  "mapped_workflow.samtools_mapped.docker": "gcr.io/motrpac-portal/motrpac_rrbs:araja_05_24_2019",
   "mapped_workflow.samtools_mapped.num_preempt": "0",
   "mapped_workflow.samtools_mapped.ncpu": "8",
   "mapped_workflow.samtools_mapped.SID": "Rat_Muscle"

wdl/index_genomes/IndexGenomes_inputs_GCloud.json

@@ -3,7 +3,7 @@
   "Bismark_Index_Generation.indexGenome.refAnnotation": "gs://my-bucket/references/rn/v96/sorted/Rattus_norvegicus.Rnor_6.0.96.gtf",
   "Bismark_Index_Generation.indexGenome.genome_dir": "rat",
   "Bismark_Index_Generation.memory": "64",
-  "Bismark_Index_Generation.docker": "gcr.io/my-project/motrpac_rrbs:araja_05_20_2019",
+  "Bismark_Index_Generation.docker": "gcr.io/motrpac-portal/motrpac_rrbs:araja_05_20_2019",
   "Bismark_Index_Generation.disk": "150",
   "Bismark_Index_Generation.ncpu": "8",
   "Bismark_Index_Generation.num_preempt": "0"

wdl/index_genomes/IndexGenomes_inputs_lambda_GCloud.json

@@ -2,7 +2,7 @@
   "Bismark_Index_Generation.indexGenome.refGenome": "gs://my-bucket/rrbs/genomes/lambda/lambda.fasta",
   "Bismark_Index_Generation.indexGenome.genome_dir": "lambda",
   "Bismark_Index_Generation.memory": "64",
-  "Bismark_Index_Generation.docker": "gcr.io/my-project/motrpac_rrbs:araja_05_20_2019",
+  "Bismark_Index_Generation.docker": "gcr.io/motrpac-portal/motrpac_rrbs:araja_05_20_2019",
   "Bismark_Index_Generation.disk": "150",
   "Bismark_Index_Generation.ncpu": "10",
   "Bismark_Index_Generation.num_preempt": "0"

wdl/index_genomes/google.conf

@@ -16,7 +16,7 @@ engine {
   filesystems {
     gcs {
       auth = "application-default"
-      project = "my-project-dev"
+      project = "motrpac-portal-dev"
     }
   }
 }
@@ -28,7 +28,7 @@ backend {
       actor-factory = "cromwell.backend.impl.jes.JesBackendLifecycleActorFactory"
       config {
         // Google project
-        project = "my-project-dev"
+        project = "motrpac-portal-dev"
 
         // Base bucket for workflow executions
         root = "gs://sa-rrbs-pipeline/cromwell-execution"
@@ -62,7 +62,7 @@ backend {
           gcs {
             // A reference to a potentially different auth for manipulating files via engine functions.
             auth = "application-default"
-            project = "my-project-dev"
+            project = "motrpac-portal-dev"
           }
         }
       }

wdl/mark_duplicates/mark_duplicates_inputs_GCloud.json

@@ -3,7 +3,7 @@
   "mark_duplicates.disk": "50",
   "mark_duplicates.num_preempt": "0",
   "mark_duplicates.ncpu": "1",
-  "mark_duplicates.docker": "gcr.io/my-project/bismark:0.20.0",
+  "mark_duplicates.docker": "gcr.io/motrpac-portal/bismark:0.20.0",
   "mark_duplicates.markDuplicates.SID": "Rat_Muscle",
   "mark_duplicates.markDuplicates.bismark_reads": "gs://my-bucket/rrbs/pipeline_test/pilot/mark_duplicates/090a4c20-ca61-4586-b60a-51dd41cb97eb/call-markDuplicates/mark_udup/Rat_Muscle_attached_R1_val_1.fq_trimmed_bismark_bt2_pe.bam"
 }

wdl/mark_duplicates/mark_duplicates_inputs_Local.json

@@ -3,7 +3,7 @@
   "mark_duplicates.disk": "30",
   "mark_duplicates.num_preempt": "25",
   "mark_duplicates.ncpu": "5",
-  "mark_duplicates.docker": "gcr.io/my-project-dev/motrpac_rrbs:SA_04_07_2019",
+  "mark_duplicates.docker": "gcr.io/motrpac-portal-dev/motrpac_rrbs:SA_04_07_2019",
   "mark_duplicates.markDuplicates.SID": "Muscle2_1000ksub",
   "mark_duplicates.markDuplicates.bismarkReads": "/Users/akre96/Documents/github/rrbs_bismark/sampleData/Muscle2_1000ksub_attached_R1_val_1.fq_trimmed_bismark_bt2_pe.bam"
 }

wdl/mark_umi_dup/mark_udup_inputs_GCloud.json

@@ -3,7 +3,7 @@
   "mark_duplicates.disk": "50",
   "mark_duplicates.num_preempt": "0",
   "mark_duplicates.ncpu": "1",
-  "mark_duplicates.docker": "gcr.io/my-project/motrpac_rrbs:araja_06_17_2019",
+  "mark_duplicates.docker": "gcr.io/motrpac-portal/motrpac_rrbs:araja_06_17_2019",
   "mark_duplicates.markDuplicates.SID": "Rat_Muscle",
   "mark_duplicates.markDuplicates.bismark_reads": "gs://my-bucket/rrbs/pipeline_test/pilot/align_trimmed/d978a9a6-9332-4642-8740-af808efc8736/call-alignTrimmed/Rat_Muscle_attached_R1_val_1.fq_trimmed_bismark_bt2_pe.bam"
 }

wdl/quantify_methylation/quantify_methylation_inputs_GCloud.json

@@ -1,7 +1,7 @@
 {
   "quantify_methylation.quantifyMethylation.bismark_deduplicated_reads": "gs://my-bucket/rrbs/pipeline_test/pilot/mark_duplicates/bf54d50f-1815-4d09-aab7-24cd37cec91c/call-markDuplicates/dedup/Rat_Muscle_attached_R1_val_1.fq_trimmed_bismark_bt2_pe.deduplicated.bam",
   "quantify_methylation.memory": "60",
-  "quantify_methylation.docker": "gcr.io/my-project/bismark:0.20.0",
+  "quantify_methylation.docker": "gcr.io/motrpac-portal/bismark:0.20.0",
   "quantify_methylation.SID": "Rat_Muscle",
   "quantify_methylation.num_preempt": "25",
   "quantify_methylation.disk": "100",

wdl/trim_reads/inputs/attachUMI_inputs_Local.json

@@ -3,7 +3,7 @@
   "attach_umi.disk": "10",
   "attach_umi.memory": "10",
   "attach_umi.num_preempt": "5",
-  "attach_umi.docker": "gcr.io/my-project-dev/motrpac_rrbs:SA_04_07_2019",
+  "attach_umi.docker": "gcr.io/motrpac-portal-dev/motrpac_rrbs:SA_04_07_2019",
   "attach_umi.attachUMI.SID": "Muscle2_100ksub",
   "attach_umi.attachUMI.r1": "/Users/akre96/Documents/github/rrbs_bismark/sampleData/Muscle2_100ksub_R1.fastq.gz",
   "attach_umi.attachUMI.r2": "/Users/akre96/Documents/github/rrbs_bismark/sampleData/Muscle2_100ksub_R2.fastq.gz",

wdl/trim_reads/inputs/fastQC_inputs_Local.json

@@ -3,7 +3,7 @@
   "fastqc_report.disk": "10",
   "fastqc_report.memory": "10",
   "fastqc_report.num_preempt": "5",
-  "fastqc_report.docker": "gcr.io/my-project-dev/motrpac_rrbs:SA_04_07_2019",
+  "fastqc_report.docker": "gcr.io/motrpac-portal-dev/motrpac_rrbs:SA_04_07_2019",
   "fastqc_report.fastQC.r1": "/Users/akre96/Documents/github/rrbs_bismark/sampleData/Muscle2_100ksub_R1.fastq.gz",
   "fastqc_report.fastQC.r2": "/Users/akre96/Documents/github/rrbs_bismark/sampleData/Muscle2_100ksub_R2.fastq.gz"
 }

wdl/trim_reads/inputs/multiQC_inputs_GCloud.json

@@ -3,7 +3,7 @@
   "multiqc_report.disk": "10",
   "multiqc_report.memory": "10",
   "multiqc_report.num_preempt": "5",
-  "multiqc_report.docker": "gcr.io/my-project-dev/motrpac_rrbs:SA_03_08_2019",
-  "multiqc_report.multiQC.fastQCReports": ["gs://archanaraja/rnaseq/test/pilot/cromwell-execution/rnaseq_pipeline/e0fc6dfe-e30b-4005-bab9-e378d3d5ab1b/call-preTrimFastQC/fastqc_report.tar.gz","gs://archanaraja/rnaseq/test/pilot/cromwell-execution/fastqc_report/19205ac5-c669-40bc-9381-a1309260f4af/call-fastQC/fastqc_report_post_trim.tar.gz"]
+  "multiqc_report.docker": "gcr.io/motrpac-portal-dev/motrpac_rrbs:SA_03_08_2019",
+  "multiqc_report.multiQC.fastQCReports": ["gs://my-bucket/rnaseq/test/pilot/cromwell-execution/rnaseq_pipeline/e0fc6dfe-e30b-4005-bab9-e378d3d5ab1b/call-preTrimFastQC/fastqc_report.tar.gz","gs://my-bucket/rnaseq/test/pilot/cromwell-execution/fastqc_report/19205ac5-c669-40bc-9381-a1309260f4af/call-fastQC/fastqc_report_post_trim.tar.gz"]
 }
 

wdl/trim_reads/inputs/multiQC_inputs_Local.json

@@ -3,7 +3,7 @@
   "multiqc_report.disk": "10",
   "multiqc_report.memory": "10",
   "multiqc_report.num_preempt": "5",
-  "multiqc_report.docker": "gcr.io/my-project-dev/motrpac_rrbs:SA_04_07_2019",
+  "multiqc_report.docker": "gcr.io/motrpac-portal-dev/motrpac_rrbs:SA_04_07_2019",
   "multiqc_report.multiQC.fastQCReports": ["/Users/akre96/Documents/github/rrbs_bismark/sampleData/pre_fastqc_report.tar.gz","/Users/akre96/Documents/github/rrbs_bismark/sampleData/post_fastqc_report.tar.gz"]
 }
 

wdl/trim_reads/inputs/trimDiversityAdapt_inputs_GCloud.json

@@ -3,7 +3,7 @@
   "trim_diversity_adapters.disk": "10",
   "trim_diversity_adapters.num_preempt": "25",
   "trim_diversity_adapters.ncpu": "5",
-  "trim_diversity_adapters.docker": "gcr.io/my-project-dev/motrpac_rrbs:SA_04_07_2019",
+  "trim_diversity_adapters.docker": "gcr.io/motrpac-portal-dev/motrpac_rrbs:SA_04_07_2019",
   "trim_diversity_adapters.trimDiversityAdapt.script": "gs://sa-rrbs-pipeline/packages/NuMetRRBS/trimRRBSdiversityAdaptCustomers.py",
   "trim_diversity_adapters.trimDiversityAdapt.r1_trimmed": "gs://sa-rrbs-pipeline/task-outputs/trimGalore/Muscle2_R1_val_1.fq.gz",
   "trim_diversity_adapters.trimDiversityAdapt.r2_trimmed": "gs://sa-rrbs-pipeline/task-outputs/trimGalore/Muscle2_R2_val_2.fq.gz"

wdl/trim_reads/inputs/trimDiversityAdapt_inputs_Local.json

@@ -3,7 +3,7 @@
   "trim_diversity_adapters.disk": "10",
   "trim_diversity_adapters.num_preempt": "25",
   "trim_diversity_adapters.ncpu": "5",
-  "trim_diversity_adapters.docker": "gcr.io/my-project-dev/motrpac_rrbs:SA_04_07_2019",
+  "trim_diversity_adapters.docker": "gcr.io/motrpac-portal-dev/motrpac_rrbs:SA_04_07_2019",
   "trim_diversity_adapters.SID": "Muscle2_sub",
   "trim_diversity_adapters.trimDiversityAdapt.r1_trimmed": "/Users/akre96/Documents/github/rrbs_bismark/sampleData/Muscle2_sub_R1_val_1.fq.gz",
   "trim_diversity_adapters.trimDiversityAdapt.r2_trimmed": "/Users/akre96/Documents/github/rrbs_bismark/sampleData/Muscle2_sub_R2_val_2.fq.gz"