diff --git a/ansible/roles/combine/tasks/nextflow-dedup-file-type.yaml b/ansible/roles/combine/tasks/nextflow-dedup-file-type.yaml index df9f302..90d2d46 100644 --- a/ansible/roles/combine/tasks/nextflow-dedup-file-type.yaml +++ b/ansible/roles/combine/tasks/nextflow-dedup-file-type.yaml @@ -97,6 +97,11 @@ when: - not combined_file.stat.exists +- name: Ensure nextflow_poll_period_minutes is not zero + set_fact: + nextflow_poll_period_minutes: 1 + when: nextflow_poll_period_minutes | int == 0 + - name: Display nextflow command timeout (Deduplicate) debug: msg: nextflow_timeout_minutes={{ nextflow_timeout_minutes }} nextflow_poll_period_minutes={{ nextflow_poll_period_minutes }} diff --git a/ansible/roles/combine/tasks/nextflow-merge-file-type.yaml b/ansible/roles/combine/tasks/nextflow-merge-file-type.yaml index ae25056..86a2aad 100644 --- a/ansible/roles/combine/tasks/nextflow-merge-file-type.yaml +++ b/ansible/roles/combine/tasks/nextflow-merge-file-type.yaml @@ -97,6 +97,11 @@ when: - not combined_file.stat.exists +- name: Ensure nextflow_poll_period_minutes is not zero + set_fact: + nextflow_poll_period_minutes: 1 + when: nextflow_poll_period_minutes | int == 0 + - name: Display nextflow command timeout (Merge) debug: msg: nextflow_timeout_minutes={{ nextflow_timeout_minutes }} nextflow_poll_period_minutes={{ nextflow_poll_period_minutes }} diff --git a/ansible/roles/fragment/tasks/fragmentation.yaml b/ansible/roles/fragment/tasks/fragmentation.yaml index 102465d..15a18fa 100644 --- a/ansible/roles/fragment/tasks/fragmentation.yaml +++ b/ansible/roles/fragment/tasks/fragmentation.yaml @@ -73,6 +73,11 @@ nextflow_poll_period_minutes: "{{ (nextflow_timeout_minutes | int / 100) | int }}" when: deployment=="production" +- name: Ensure nextflow_poll_period_minutes is not zero + set_fact: + nextflow_poll_period_minutes: 1 + when: nextflow_poll_period_minutes | int == 0 + - name: Log line to report blockinfile: marker: "" diff --git a/ansible/roles/inchi/tasks/gen-isomol-inchi-database.yaml b/ansible/roles/inchi/tasks/gen-isomol-inchi-database.yaml index a6d52b4..56e4537 100644 --- a/ansible/roles/inchi/tasks/gen-isomol-inchi-database.yaml +++ b/ansible/roles/inchi/tasks/gen-isomol-inchi-database.yaml @@ -72,6 +72,11 @@ nextflow_poll_period_minutes: "{{ (nextflow_timeout_minutes | int / 100) | int }}" when: deployment=="production" +- name: Ensure nextflow_poll_period_minutes is not zero + set_fact: + nextflow_poll_period_minutes: 1 + when: nextflow_poll_period_minutes | int == 0 + # Move the nextflow workflow and config into place (from templates) # so they move from "/{{ deployment }}" to "{{ reppath }}/nextflow"... diff --git a/ansible/roles/inchi/tasks/gen-nonisomol-inchi-database.yaml b/ansible/roles/inchi/tasks/gen-nonisomol-inchi-database.yaml index fc80cfe..750edd9 100644 --- a/ansible/roles/inchi/tasks/gen-nonisomol-inchi-database.yaml +++ b/ansible/roles/inchi/tasks/gen-nonisomol-inchi-database.yaml @@ -60,6 +60,11 @@ nextflow_poll_period_minutes: "{{ (nextflow_timeout_minutes | int / 100) | int }}" when: deployment=="production" +- name: Ensure nextflow_poll_period_minutes is not zero + set_fact: + nextflow_poll_period_minutes: 1 + when: nextflow_poll_period_minutes | int == 0 + # Move the nextflow workflow and config into place (from templates) # so they move from "/{{ deployment }}" to "{{ reppath }}/nextflow"... @@ -92,7 +97,7 @@ debug: var: nextflow_cmd -- name: Display nextflow command timeout (Fragmentation) +- name: Display nextflow command timeout (Generate Non-Isomol Inchi) debug: msg: nextflow_timeout_minutes={{ nextflow_timeout_minutes }} nextflow_poll_period_minutes={{ nextflow_poll_period_minutes }} diff --git a/ansible/roles/standardise/tasks/standardise-file.yaml b/ansible/roles/standardise/tasks/standardise-file.yaml index d3c1726..58a5623 100644 --- a/ansible/roles/standardise/tasks/standardise-file.yaml +++ b/ansible/roles/standardise/tasks/standardise-file.yaml @@ -84,6 +84,11 @@ nextflow_poll_period_minutes: "{{ (nextflow_timeout_minutes | int / 100) | int }}" when: deployment == "production" + - name: Ensure nextflow_poll_period_minutes is not zero + set_fact: + nextflow_poll_period_minutes: 1 + when: nextflow_poll_period_minutes | int == 0 + - name: Log line to report blockinfile: marker: ""