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Fixed linter issues and typo. #115

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Sep 8, 2023
Merged

Fixed linter issues and typo. #115

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2 changes: 1 addition & 1 deletion README.md
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Original file line number Diff line number Diff line change
Expand Up @@ -301,7 +301,7 @@ If an infra stack breaks down and we need to temporarily disable cronjobs to pre
minute: '*/10'
job: /bin/bash -c "{{ configure_env_in_cronjob }};
module load NGS_Automated/{{ group_module_versions['umcg-atd']['NGS_Automated'] }}-bare;
copyRawDataToPrm.sh -g umcg-atd -p NGS_Demultiplexing -s {{ groups['jumphost'] | first}}+{{ groups['user_interface'] | first }}"
copyRawDataToPrm.sh -g umcg-atd -p NGS_Demultiplexing -s {{ groups['jumphost'] | first }}+{{ groups['user_interface'] | first }}"
disabled: true
```
* Run the playbook to update the cronjobs.
4 changes: 2 additions & 2 deletions group_vars/betabarrel_cluster/vars.yml
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Original file line number Diff line number Diff line change
Expand Up @@ -20,7 +20,7 @@ easybuild_version: '4.8.0'
eb_user: umcg-envsync
extra_easyconfigs_version: 1.3
extra_easyconfigs_repository: 'take-it-easyconfigs'
#extra_easyconfigs_prefix: "{{ easybuild_software_dir }}/easyconfigs/{{ extra_easyconfigs_repository }}-{{ extra_easyconfigs_version }}/easybuild/easyconfigs/"
# extra_easyconfigs_prefix: "{{ easybuild_software_dir }}/easyconfigs/{{ extra_easyconfigs_repository }}-{{ extra_easyconfigs_version }}/easybuild/easyconfigs/"
#
# Group folder structures to construct on shared storage systems.
#
Expand Down Expand Up @@ -1133,7 +1133,7 @@ crontabs:
minute: '*/10'
job: /bin/bash -c "{{ configure_env_in_cronjob }};
module load NGS_Automated/{{ group_module_versions['umcg-patho']['NGS_Automated'] }}-bare;
copyBclDataToPrm.sh -g umcg-patho -s {{ groups['jumphost'] | first }}+{{ groups['user_interface'] | first }} -b prm35"
copyBclDataToPrm.sh -g umcg-patho -s {{ groups['jumphost'] | first }}+{{ groups['user_interface'] | first }} -p prm35"
#
# Sources, software and reference data to install/fetch.
#
Expand Down
30 changes: 15 additions & 15 deletions group_vars/copperfist_cluster/vars.yml
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Original file line number Diff line number Diff line change
Expand Up @@ -20,7 +20,7 @@ easybuild_version: '4.8.0'
eb_user: umcg-envsync
extra_easyconfigs_version: 1.3
extra_easyconfigs_repository: 'take-it-easyconfigs'
#extra_easyconfigs_prefix: "{{ easybuild_software_dir }}/easyconfigs/{{ extra_easyconfigs_repository }}-{{ extra_easyconfigs_version }}/easybuild/easyconfigs/"
# extra_easyconfigs_prefix: "{{ easybuild_software_dir }}/easyconfigs/{{ extra_easyconfigs_repository }}-{{ extra_easyconfigs_version }}/easybuild/easyconfigs/"
#
# Group folder structures to construct on shared storage systems.
#
Expand Down Expand Up @@ -532,22 +532,22 @@ crontabs:
minute: '*/10'
job: /bin/bash -c "{{ configure_env_in_cronjob }};
module load NGS_Automated/{{ group_module_versions['umcg-atd']['NGS_Automated'] }}-bare;
copyRawDataToPrm.sh -g umcg-atd -p NGS_Demultiplexing -s {{ groups['jumphost'] | first}}+{{ groups['user_interface'] | first }}"
copyRawDataToPrm.sh -g umcg-atd -p NGS_Demultiplexing -s {{ groups['jumphost'] | first }}+{{ groups['user_interface'] | first }}"
- name: NGS_Automated_copyRawDataToTmp # Unique ID required to update existing cronjob: do not modify.
user: umcg-atd-dm
machines: "{{ groups['chaperone'] | default([]) }}"
minute: '*/10'
job: /bin/bash -c "{{ configure_env_in_cronjob }};
module load NGS_Automated/{{ group_module_versions['umcg-atd']['NGS_Automated'] }}-bare;
copyRawDataToTmp.sh -g umcg-atd -p NGS_DNA -s {{ groups['jumphost'] | first}}+{{ groups['user_interface'] | first }}"
copyRawDataToTmp.sh -g umcg-atd -p NGS_DNA -s {{ groups['jumphost'] | first }}+{{ groups['user_interface'] | first }}"
- name: NGS_Automated_copyRawDataToPrm_genomescan # Unique ID required to update existing cronjob: do not modify.
user: umcg-atd-dm
machines: "{{ groups['chaperone'] | default([]) }}"
minute: '*/10'
job: /bin/bash -c "{{ configure_env_in_cronjob }};
module load NGS_Automated/{{ group_module_versions['umcg-atd']['NGS_Automated'] }}-bare;
copyRawDataToPrm.sh -a -g umcg-atd -s {{ groups['jumphost'] | first}}+{{ groups['user_interface'] | first }} -r /groups/umcg-gst/tmp06 -f run01.processGsRawData.finished -p DRAGEN;
copySamplesheetsForBatchToPrm.sh -g umcg-atd -s {{ groups['jumphost'] | first}}+{{ groups['user_interface'] | first }} -r /groups/umcg-gst/tmp06"
copyRawDataToPrm.sh -a -g umcg-atd -s {{ groups['jumphost'] | first }}+{{ groups['user_interface'] | first }} -r /groups/umcg-gst/tmp06 -f run01.processGsRawData.finished -p DRAGEN;
copySamplesheetsForBatchToPrm.sh -g umcg-atd -s {{ groups['jumphost'] | first }}+{{ groups['user_interface'] | first }} -r /groups/umcg-gst/tmp06"
- name: NGS_Automated_copyProjectDataToPrm # Unique ID required to update existing cronjob: do not modify.
user: umcg-atd-dm
machines: "{{ groups['chaperone'] | default([]) }}"
Expand Down Expand Up @@ -723,22 +723,22 @@ crontabs:
minute: '*/10'
job: /bin/bash -c "{{ configure_env_in_cronjob }};
module load NGS_Automated/{{ group_module_versions['umcg-gd']['NGS_Automated'] }}-bare;
copyRawDataToPrm.sh -g umcg-gd -p NGS_Demultiplexing -s {{ groups['jumphost'] | first}}+{{ groups['user_interface'] | first }}"
copyRawDataToPrm.sh -g umcg-gd -p NGS_Demultiplexing -s {{ groups['jumphost'] | first }}+{{ groups['user_interface'] | first }}"
- name: NGS_Automated_copyRawDataToTmp # Unique ID required to update existing cronjob: do not modify.
user: umcg-gd-dm
machines: "{{ groups['chaperone'] | default([]) }}"
minute: '*/10'
job: /bin/bash -c "{{ configure_env_in_cronjob }};
module load NGS_Automated/{{ group_module_versions['umcg-gd']['NGS_Automated'] }}-bare;
copyRawDataToTmp.sh -g umcg-gd -p NGS_DNA -s {{ groups['jumphost'] | first}}+{{ groups['user_interface'] | first }}"
copyRawDataToTmp.sh -g umcg-gd -p NGS_DNA -s {{ groups['jumphost'] | first }}+{{ groups['user_interface'] | first }}"
- name: NGS_Automated_copyRawDataToPrm_genomescan # Unique ID required to update existing cronjob: do not modify.
user: umcg-gd-dm
machines: "{{ groups['chaperone'] | default([]) }}"
minute: '*/10'
job: /bin/bash -c "{{ configure_env_in_cronjob }};
module load NGS_Automated/{{ group_module_versions['umcg-gd']['NGS_Automated'] }}-bare;
copyRawDataToPrm.sh -a -g umcg-gd -s {{ groups['jumphost'] | first}}+{{ groups['user_interface'] | first }} -r /groups/umcg-gst/tmp06 -f run01.processGsRawData.finished -p DRAGEN;
copySamplesheetsForBatchToPrm.sh -g umcg-gd -s {{ groups['jumphost'] | first}}+{{ groups['user_interface'] | first }} -r /groups/umcg-gst/tmp06"
copyRawDataToPrm.sh -a -g umcg-gd -s {{ groups['jumphost'] | first }}+{{ groups['user_interface'] | first }} -r /groups/umcg-gst/tmp06 -f run01.processGsRawData.finished -p DRAGEN;
copySamplesheetsForBatchToPrm.sh -g umcg-gd -s {{ groups['jumphost'] | first }}+{{ groups['user_interface'] | first }} -r /groups/umcg-gst/tmp06"
- name: NGS_Automated_copyProjectDataToPrm # Unique ID required to update existing cronjob: do not modify.
user: umcg-gd-dm
machines: "{{ groups['chaperone'] | default([]) }}"
Expand Down Expand Up @@ -873,14 +873,14 @@ crontabs:
minute: '*/10'
job: /bin/bash -c "{{ configure_env_in_cronjob }};
module load NGS_Automated/{{ group_module_versions['umcg-gsad']['NGS_Automated'] }}-bare;
copyRawDataToTmp.sh -g umcg-gsad -p GAP -s {{ groups['jumphost'] | first}}+{{ groups['user_interface'] | first }}"
copyRawDataToTmp.sh -g umcg-gsad -p GAP -s {{ groups['jumphost'] | first }}+{{ groups['user_interface'] | first }}"
- name: NGS_Automated_copyRawDataToPrm # Unique ID required to update existing cronjob: do not modify.
user: umcg-gsad-dm
machines: "{{ groups['chaperone'] | default([]) }}"
minute: '*/10'
job: /bin/bash -c "{{ configure_env_in_cronjob }};
module load NGS_Automated/{{ group_module_versions['umcg-gsad']['NGS_Automated'] }}-bare;
copyRawDataToPrm.sh -g umcg-gsad -s {{ groups['jumphost'] | first}}+{{ groups['user_interface'] | first }} -p AGCT"
copyRawDataToPrm.sh -g umcg-gsad -s {{ groups['jumphost'] | first }}+{{ groups['user_interface'] | first }} -p AGCT"
- name: NGS_Automated_startPipeline # Unique ID required to update existing cronjob: do not modify.
user: umcg-gsad-ateambot
machines: "{{ groups['user_interface'] | default([]) }}"
Expand Down Expand Up @@ -946,14 +946,14 @@ crontabs:
minute: '*/10'
job: /bin/bash -c "{{ configure_env_in_cronjob }};
module load NGS_Automated/{{ group_module_versions['umcg-gap']['NGS_Automated'] }}-bare;
copyRawDataToTmp.sh -g umcg-gap -p GAP -s {{ groups['jumphost'] | first}}+{{ groups['user_interface'] | first }}"
copyRawDataToTmp.sh -g umcg-gap -p GAP -s {{ groups['jumphost'] | first }}+{{ groups['user_interface'] | first }}"
- name: NGS_Automated_copyRawDataToPrm # Unique ID required to update existing cronjob: do not modify.
user: umcg-gap-dm
machines: "{{ groups['chaperone'] | default([]) }}"
minute: '*/10'
job: /bin/bash -c "{{ configure_env_in_cronjob }};
module load NGS_Automated/{{ group_module_versions['umcg-gap']['NGS_Automated'] }}-bare;
copyRawDataToPrm.sh -g umcg-gap -s {{ groups['jumphost'] | first}}+{{ groups['user_interface'] | first }} -p AGCT"
copyRawDataToPrm.sh -g umcg-gap -s {{ groups['jumphost'] | first }}+{{ groups['user_interface'] | first }} -p AGCT"
- name: NGS_Automated_startPipeline # Unique ID required to update existing cronjob: do not modify.
user: umcg-gap-ateambot
machines: "{{ groups['user_interface'] | default([]) }}"
Expand Down Expand Up @@ -1109,7 +1109,7 @@ crontabs:
minute: '*/10'
job: /bin/bash -c "{{ configure_env_in_cronjob }};
module load NGS_Automated/{{ group_module_versions['umcg-labgnkbh']['NGS_Automated'] }}-bare;
copyRawDataToPrm.sh -a -g umcg-labgnkbh -p NGS_Demultiplexing -m prm46 -s {{ groups['jumphost'] | first}}+{{ groups['user_interface'] | first }}"
copyRawDataToPrm.sh -a -g umcg-labgnkbh -p NGS_Demultiplexing -m prm46 -s {{ groups['jumphost'] | first }}+{{ groups['user_interface'] | first }}"
######################################################################################################################
# umcg-patho group
######################################################################################################################
Expand All @@ -1133,7 +1133,7 @@ crontabs:
minute: '*/10'
job: /bin/bash -c "{{ configure_env_in_cronjob }};
module load NGS_Automated/{{ group_module_versions['umcg-patho']['NGS_Automated'] }}-bare;
copyBclDataToPrm.sh -g umcg-patho -s {{ groups['jumphost'] | first}}+{{ groups['user_interface'] | first }} -b prm36"
copyBclDataToPrm.sh -g umcg-patho -s {{ groups['jumphost'] | first }}+{{ groups['user_interface'] | first }} -p prm36"
#
# Sources, software and reference data to install/fetch.
#
Expand Down
30 changes: 15 additions & 15 deletions group_vars/wingedhelix_cluster/vars.yml
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Original file line number Diff line number Diff line change
Expand Up @@ -19,7 +19,7 @@ lmod_version: '8.6.2'
easybuild_version: '4.8.0'
extra_easyconfigs_version: 1.3
extra_easyconfigs_repository: 'take-it-easyconfigs'
#extra_easyconfigs_prefix: "{{ easybuild_software_dir }}/easyconfigs/{{ extra_easyconfigs_repository }}-{{ extra_easyconfigs_version }}/easybuild/easyconfigs/"
# extra_easyconfigs_prefix: "{{ easybuild_software_dir }}/easyconfigs/{{ extra_easyconfigs_repository }}-{{ extra_easyconfigs_version }}/easybuild/easyconfigs/"
#
# Group folder structures to construct on shared storage systems.
#
Expand Down Expand Up @@ -531,22 +531,22 @@ crontabs:
minute: '*/10'
job: /bin/bash -c "{{ configure_env_in_cronjob }};
module load NGS_Automated/{{ group_module_versions['umcg-atd']['NGS_Automated'] }}-bare;
copyRawDataToPrm.sh -g umcg-atd -p NGS_Demultiplexing -s {{ groups['jumphost'] | first}}+{{ groups['user_interface'] | first }}"
copyRawDataToPrm.sh -g umcg-atd -p NGS_Demultiplexing -s {{ groups['jumphost'] | first }}+{{ groups['user_interface'] | first }}"
- name: NGS_Automated_copyRawDataToTmp # Unique ID required to update existing cronjob: do not modify.
user: umcg-atd-dm
machines: "{{ groups['chaperone'] | default([]) }}"
minute: '*/10'
job: /bin/bash -c "{{ configure_env_in_cronjob }};
module load NGS_Automated/{{ group_module_versions['umcg-atd']['NGS_Automated'] }}-bare;
copyRawDataToTmp.sh -g umcg-atd -p NGS_DNA -s {{ groups['jumphost'] | first}}+{{ groups['user_interface'] | first }}"
copyRawDataToTmp.sh -g umcg-atd -p NGS_DNA -s {{ groups['jumphost'] | first }}+{{ groups['user_interface'] | first }}"
- name: NGS_Automated_copyRawDataToPrm_genomescan # Unique ID required to update existing cronjob: do not modify.
user: umcg-atd-dm
machines: "{{ groups['chaperone'] | default([]) }}"
minute: '*/10'
job: /bin/bash -c "{{ configure_env_in_cronjob }};
module load NGS_Automated/{{ group_module_versions['umcg-atd']['NGS_Automated'] }}-bare;
copyRawDataToPrm.sh -a -g umcg-atd -s {{ groups['jumphost'] | first}}+{{ groups['user_interface'] | first }} -r /groups/umcg-gst/tmp07 -f run01.processGsRawData.finished -p DRAGEN;
copySamplesheetsForBatchToPrm.sh -g umcg-atd -s {{ groups['jumphost'] | first}}+{{ groups['user_interface'] | first }} -r /groups/umcg-gst/tmp07"
copyRawDataToPrm.sh -a -g umcg-atd -s {{ groups['jumphost'] | first }}+{{ groups['user_interface'] | first }} -r /groups/umcg-gst/tmp07 -f run01.processGsRawData.finished -p DRAGEN;
copySamplesheetsForBatchToPrm.sh -g umcg-atd -s {{ groups['jumphost'] | first }}+{{ groups['user_interface'] | first }} -r /groups/umcg-gst/tmp07"
- name: NGS_Automated_copyProjectDataToPrm # Unique ID required to update existing cronjob: do not modify.
user: umcg-atd-dm
machines: "{{ groups['chaperone'] | default([]) }}"
Expand Down Expand Up @@ -722,22 +722,22 @@ crontabs:
minute: '*/10'
job: /bin/bash -c "{{ configure_env_in_cronjob }};
module load NGS_Automated/{{ group_module_versions['umcg-gd']['NGS_Automated'] }}-bare;
copyRawDataToPrm.sh -g umcg-gd -p NGS_Demultiplexing -s {{ groups['jumphost'] | first}}+{{ groups['user_interface'] | first }}"
copyRawDataToPrm.sh -g umcg-gd -p NGS_Demultiplexing -s {{ groups['jumphost'] | first }}+{{ groups['user_interface'] | first }}"
- name: NGS_Automated_copyRawDataToTmp # Unique ID required to update existing cronjob: do not modify.
user: umcg-gd-dm
machines: "{{ groups['chaperone'] | default([]) }}"
minute: '*/10'
job: /bin/bash -c "{{ configure_env_in_cronjob }};
module load NGS_Automated/{{ group_module_versions['umcg-gd']['NGS_Automated'] }}-bare;
copyRawDataToTmp.sh -g umcg-gd -p NGS_DNA -s {{ groups['jumphost'] | first}}+{{ groups['user_interface'] | first }}"
copyRawDataToTmp.sh -g umcg-gd -p NGS_DNA -s {{ groups['jumphost'] | first }}+{{ groups['user_interface'] | first }}"
- name: NGS_Automated_copyRawDataToPrm_genomescan # Unique ID required to update existing cronjob: do not modify.
user: umcg-gd-dm
machines: "{{ groups['chaperone'] | default([]) }}"
minute: '*/10'
job: /bin/bash -c "{{ configure_env_in_cronjob }};
module load NGS_Automated/{{ group_module_versions['umcg-gd']['NGS_Automated'] }}-bare;
copyRawDataToPrm.sh -a -g umcg-gd -s {{ groups['jumphost'] | first}}+{{ groups['user_interface'] | first }} -r /groups/umcg-gst/tmp07 -f run01.processGsRawData.finished -p DRAGEN;
copySamplesheetsForBatchToPrm.sh -g umcg-gd -s {{ groups['jumphost'] | first}}+{{ groups['user_interface'] | first }} -r /groups/umcg-gst/tmp07"
copyRawDataToPrm.sh -a -g umcg-gd -s {{ groups['jumphost'] | first }}+{{ groups['user_interface'] | first }} -r /groups/umcg-gst/tmp07 -f run01.processGsRawData.finished -p DRAGEN;
copySamplesheetsForBatchToPrm.sh -g umcg-gd -s {{ groups['jumphost'] | first }}+{{ groups['user_interface'] | first }} -r /groups/umcg-gst/tmp07"
- name: NGS_Automated_copyProjectDataToPrm # Unique ID required to update existing cronjob: do not modify.
user: umcg-gd-dm
machines: "{{ groups['chaperone'] | default([]) }}"
Expand Down Expand Up @@ -872,14 +872,14 @@ crontabs:
minute: '*/10'
job: /bin/bash -c "{{ configure_env_in_cronjob }};
module load NGS_Automated/{{ group_module_versions['umcg-gsad']['NGS_Automated'] }}-bare;
copyRawDataToTmp.sh -g umcg-gsad -p GAP -s {{ groups['jumphost'] | first}}+{{ groups['user_interface'] | first }}"
copyRawDataToTmp.sh -g umcg-gsad -p GAP -s {{ groups['jumphost'] | first }}+{{ groups['user_interface'] | first }}"
- name: NGS_Automated_copyRawDataToPrm # Unique ID required to update existing cronjob: do not modify.
user: umcg-gsad-dm
machines: "{{ groups['chaperone'] | default([]) }}"
minute: '*/10'
job: /bin/bash -c "{{ configure_env_in_cronjob }};
module load NGS_Automated/{{ group_module_versions['umcg-gsad']['NGS_Automated'] }}-bare;
copyRawDataToPrm.sh -g umcg-gsad -s {{ groups['jumphost'] | first}}+{{ groups['user_interface'] | first }} -p AGCT"
copyRawDataToPrm.sh -g umcg-gsad -s {{ groups['jumphost'] | first }}+{{ groups['user_interface'] | first }} -p AGCT"
- name: NGS_Automated_startPipeline # Unique ID required to update existing cronjob: do not modify.
user: umcg-gsad-ateambot
machines: "{{ groups['user_interface'] | default([]) }}"
Expand Down Expand Up @@ -945,14 +945,14 @@ crontabs:
minute: '*/10'
job: /bin/bash -c "{{ configure_env_in_cronjob }};
module load NGS_Automated/{{ group_module_versions['umcg-gap']['NGS_Automated'] }}-bare;
copyRawDataToTmp.sh -g umcg-gap -p GAP -s {{ groups['jumphost'] | first}}+{{ groups['user_interface'] | first }}"
copyRawDataToTmp.sh -g umcg-gap -p GAP -s {{ groups['jumphost'] | first }}+{{ groups['user_interface'] | first }}"
- name: NGS_Automated_copyRawDataToPrm # Unique ID required to update existing cronjob: do not modify.
user: umcg-gap-dm
machines: "{{ groups['chaperone'] | default([]) }}"
minute: '*/10'
job: /bin/bash -c "{{ configure_env_in_cronjob }};
module load NGS_Automated/{{ group_module_versions['umcg-gap']['NGS_Automated'] }}-bare;
copyRawDataToPrm.sh -g umcg-gap -s {{ groups['jumphost'] | first}}+{{ groups['user_interface'] | first }} -p AGCT"
copyRawDataToPrm.sh -g umcg-gap -s {{ groups['jumphost'] | first }}+{{ groups['user_interface'] | first }} -p AGCT"
- name: NGS_Automated_startPipeline # Unique ID required to update existing cronjob: do not modify.
user: umcg-gap-ateambot
machines: "{{ groups['user_interface'] | default([]) }}"
Expand Down Expand Up @@ -1114,7 +1114,7 @@ crontabs:
disabled: true
job: /bin/bash -c "{{ configure_env_in_cronjob }};
module load NGS_Automated/{{ group_module_versions['umcg-labgnkbh']['NGS_Automated'] }}-bare;
copyRawDataToPrm.sh -a -g umcg-labgnkbh -p NGS_Demultiplexing -m prm47 -s {{ groups['jumphost'] | first}}+{{ groups['user_interface'] | first }}"
copyRawDataToPrm.sh -a -g umcg-labgnkbh -p NGS_Demultiplexing -m prm47 -s {{ groups['jumphost'] | first }}+{{ groups['user_interface'] | first }}"
######################################################################################################################
# umcg-patho group
######################################################################################################################
Expand All @@ -1141,7 +1141,7 @@ crontabs:
disabled: true
job: /bin/bash -c "{{ configure_env_in_cronjob }};
module load NGS_Automated/{{ group_module_versions['umcg-patho']['NGS_Automated'] }}-bare;
copyBclDataToPrm.sh -g umcg-patho -s {{ groups['jumphost'] | first}}+{{ groups['user_interface'] | first }} -b prm37"
copyBclDataToPrm.sh -g umcg-patho -s {{ groups['jumphost'] | first }}+{{ groups['user_interface'] | first }} -p prm37"
#
# Sources, software and reference data to install/fetch.
#
Expand Down