GH-282: move max retries out of wdls and into config (#151)

* remove max_retries from adapters * modify submit wdl to use default maxRetries except for confirm * remove max_retries inputs * Remove max_retries from stub submit wdl * Include confirm_submission in retried tasks The confirm_submission step has improved error handling and will no longer throw an error on retries, so it can be retried along with other tasks in the workflow. * Remove extra comma * Update pipeline-tools version
HumanCellAtlas · Aug 1, 2019 · f14403c · f14403c
1 parent e56129f
commit f14403c
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Showing 6 changed files with 8 additions and 26 deletions.
diff --git a/adapter_pipelines/Optimus/adapter.wdl b/adapter_pipelines/Optimus/adapter.wdl
@@ -136,10 +136,9 @@ workflow AdapterOptimus {
   String runtime_environment
   # By default, don't record http requests, unless we override in inputs json
   Boolean record_http = false
-  Int max_cromwell_retries = 0
   Boolean add_md5s = false
 
-  String pipeline_tools_version = "v0.56.1"
+  String pipeline_tools_version = "v0.56.2"
 
   call GetInputs as prep {
     input:

diff --git a/adapter_pipelines/cellranger/adapter.wdl b/adapter_pipelines/cellranger/adapter.wdl
@@ -146,10 +146,9 @@ workflow Adapter10xCount {
   String runtime_environment
   # By default, don't record http requests, unless we override in inputs json
   Boolean record_http = false
-  Int max_cromwell_retries = 0
   Boolean add_md5s = false
 
-  String pipeline_tools_version = "v0.56.1"
+  String pipeline_tools_version = "v0.56.2"
 
   call GetInputs {
     input:
@@ -181,8 +180,7 @@ workflow Adapter10xCount {
       fastqs = rename_fastqs.outputs,
       reference_name = GetInputs.reference_name,
       transcriptome_tar_gz = GetInputs.transcriptome_tar_gz,
-      expect_cells = GetInputs.expect_cells,
-      max_retries = max_cromwell_retries
+      expect_cells = GetInputs.expect_cells
   }
 
   call InputsForSubmit {
@@ -254,7 +252,6 @@ workflow Adapter10xCount {
       pipeline_tools_version = pipeline_tools_version,
       add_md5s = add_md5s,
       pipeline_version = analysis.pipeline_version,
-      max_retries = max_cromwell_retries,
       # The sorted bam is the largest output. Other outputs will increase space by ~50%.
       # Factor of 2 and addition of 50 GB gives some buffer.
       disk_space = ceil(size(analysis.sorted_bam, "GB") * 2 + 50)

diff --git a/adapter_pipelines/ss2_single_end/adapter.wdl b/adapter_pipelines/ss2_single_end/adapter.wdl
@@ -67,10 +67,9 @@ workflow AdapterSmartSeq2SingleCellUnpaired {
   String runtime_environment
   # By default, don't record http requests, unless we override in inputs json
   Boolean record_http = false
-  Int max_cromwell_retries = 0
   Boolean add_md5s = false
 
-  String pipeline_tools_version = "v0.56.1"
+  String pipeline_tools_version = "v0.56.2"
 
   call GetInputs as prep {
     input:
@@ -98,8 +97,7 @@ workflow AdapterSmartSeq2SingleCellUnpaired {
       stranded = prep.inputs.stranded,
       sample_name = prep.inputs.sample_id,
       output_name = prep.inputs.sample_id,
-      fastq = prep.inputs.fastq,
-      max_retries = max_cromwell_retries
+      fastq = prep.inputs.fastq
   }
 
   call submit_wdl.submit {
@@ -187,7 +185,6 @@ workflow AdapterSmartSeq2SingleCellUnpaired {
       record_http = record_http,
       pipeline_tools_version = pipeline_tools_version,
       add_md5s = add_md5s,
-      max_retries = max_cromwell_retries,
       pipeline_version = analysis.pipeline_version,
       # The bam files are by far the largest outputs. The extra 5 GB should easily cover everything else.
       disk_space = ceil(size(analysis.aligned_bam, "GB") + size(analysis.aligned_transcriptome_bam, "GB") + 5)

diff --git a/adapter_pipelines/ss2_single_sample/adapter.wdl b/adapter_pipelines/ss2_single_sample/adapter.wdl
@@ -67,10 +67,9 @@ workflow AdapterSmartSeq2SingleCell{
   String runtime_environment
   # By default, don't record http requests, unless we override in inputs json
   Boolean record_http = false
-  Int max_cromwell_retries = 0
   Boolean add_md5s = false
 
-  String pipeline_tools_version = "v0.56.1"
+  String pipeline_tools_version = "v0.56.2"
 
   call GetInputs as prep {
     input:
@@ -99,8 +98,7 @@ workflow AdapterSmartSeq2SingleCell{
       sample_name = prep.inputs.sample_id,
       output_name = prep.inputs.sample_id,
       fastq1 = prep.inputs.fastq_1,
-      fastq2 = prep.inputs.fastq_2,
-      max_retries = max_cromwell_retries
+      fastq2 = prep.inputs.fastq_2
   }
 
   call submit_wdl.submit {
@@ -193,7 +191,6 @@ workflow AdapterSmartSeq2SingleCell{
       record_http = record_http,
       pipeline_tools_version = pipeline_tools_version,
       add_md5s = add_md5s,
-      max_retries = max_cromwell_retries,
       pipeline_version = analysis.pipeline_version,
       # The bam files are by far the largest outputs. The extra 5 GB should easily cover everything else.
       disk_space = ceil(size(analysis.aligned_bam, "GB") + size(analysis.aligned_transcriptome_bam, "GB") + 5)

diff --git a/adapter_pipelines/submit.wdl b/adapter_pipelines/submit.wdl
@@ -9,7 +9,6 @@ task get_metadata {
   Int? individual_request_timeout
   Boolean record_http
   String pipeline_tools_version
-  Int max_retries = 0
 
   command <<<
     export RECORD_HTTP_REQUESTS="${record_http}"
@@ -29,7 +28,6 @@ task get_metadata {
   >>>
   runtime {
     docker: "quay.io/humancellatlas/secondary-analysis-pipeline-tools:" + pipeline_tools_version
-    maxRetries: max_retries
   }
   output {
     File metadata = "metadata.json"
@@ -137,7 +135,6 @@ task stage_files {
   String rb = "}"
   Boolean record_http
   String pipeline_tools_version
-  Int max_retries = 0
   Int disk_space
 
   command <<<
@@ -184,7 +181,6 @@ task stage_files {
   runtime {
     docker: "quay.io/humancellatlas/secondary-analysis-pipeline-tools:" + pipeline_tools_version
     disks: "local-disk ${disk_space} HDD"
-    maxRetries: max_retries
   }
   output {
     Array[File] http_requests = glob("request_*.txt")
@@ -260,7 +256,6 @@ workflow submit {
   Boolean record_http = false
   String pipeline_tools_version
   Boolean add_md5s
-  Int max_retries = 0
   # Version of the pipeline, should be included in the pipeline file
   String pipeline_version
   # Disk space to allocate for stage_files task
@@ -278,8 +273,7 @@ workflow submit {
       individual_request_timeout = individual_request_timeout,
       retry_multiplier = retry_multiplier,
       retry_max_interval = retry_max_interval,
-      pipeline_tools_version = pipeline_tools_version,
-      max_retries = max_retries
+      pipeline_tools_version = pipeline_tools_version
   }
 
   call create_submission {
@@ -320,7 +314,6 @@ workflow submit {
       retry_max_interval = retry_max_interval,
       record_http = record_http,
       pipeline_tools_version = pipeline_tools_version,
-      max_retries = max_retries,
       disk_space = disk_space
   }
 

diff --git a/adapter_pipelines/submit_stub/submit.wdl b/adapter_pipelines/submit_stub/submit.wdl
@@ -31,7 +31,6 @@ workflow submit {
   Boolean record_http = false
   String pipeline_tools_version
   Boolean add_md5s
-  Int max_retries = 0
   # Version of the pipeline, should be included in the pipeline file
   String pipeline_version
   # Disk space to allocate for stage_files task