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prepared for new NGS_Automated-4.2.0 release #132

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merged 4 commits into from
Apr 4, 2024
Merged

prepared for new NGS_Automated-4.2.0 release #132

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7e11485
prepared for new NGS_Automated-4.2.0 release
RoanKanninga Apr 4, 2024
952d63c
Merge branch 'master' of https://github.com/molgenis/ansible-pipelines
RoanKanninga Apr 4, 2024
6e6bde6
Update group_vars/wingedhelix_cluster/vars.yml
RoanKanninga Apr 4, 2024
ab2729a
Update group_vars/copperfist_cluster/vars.yml
RoanKanninga Apr 4, 2024
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51 changes: 43 additions & 8 deletions group_vars/betabarrel_cluster/vars.yml
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -18,7 +18,7 @@ lua_version: '5.1.4.9'
lmod_version: '8.6.2'
easybuild_version: '4.8.0'
eb_user: umcg-envsync
extra_easyconfigs_version: 24.03.1
extra_easyconfigs_version: 24.03.2
extra_easyconfigs_repository: 'take-it-easyconfigs'
# extra_easyconfigs_prefix: "{{ easybuild_software_dir }}/easyconfigs/{{ extra_easyconfigs_repository }}-{{ extra_easyconfigs_version }}/easybuild/easyconfigs/"
#
Expand Down Expand Up @@ -468,24 +468,34 @@ group_notification_targets:
analysis_phases: [copyBclDataToPrm]
notification_target: hpc-helpdesk_and_pr
machines: "{{ groups['chaperone'] }}"

######################################################################################################################
# umcg-lab group
######################################################################################################################
- group: umcg-lab
lfs: tmp05
user: umcg-lab-ateambot
type: notification_webhooks
analysis_phases: [moveSequencingData]
notification_target: hpc-helpdesk
machines: "{{ groups['user_interface'] }}"
#
# Cronjobs for functional accounts.
#
group_module_versions:
umcg-gd:
NGS_Automated: 4.1.0
NGS_Automated: 4.2.0
NGS_DNA: 4.2.2
ConcordanceCheck: 2.2.1
ngs-utils: 24.02.2
NGS_Demultiplexing: 2.5.4
umcg-gap:
NGS_Automated: 4.1.0
NGS_Automated: 4.2.0
GAP: 2.7.0
AGCT: 1.3.0
ngs-utils: 24.02.2
umcg-genomescan:
NGS_Automated: 4.1.0
NGS_Automated: 4.2.0
nf_ngs_dna: 1.0.0
NGS_DNA: 4.2.2
ngs-utils: 24.02.2
umcg-atd:
Expand All @@ -495,20 +505,21 @@ group_module_versions:
ngs-utils: 24.02.2
NGS_Demultiplexing: 2.5.4
umcg-gsad:
NGS_Automated: 4.1.0
NGS_Automated: 4.2.0
GAP: 2.7.0
AGCT: 1.3.0
ngs-utils: 24.02.2
umcg-gst:
NGS_Automated: 4.2.0
nf_ngs_dna: 1.0.0
NGS_DNA: 4.2.2
ngs-utils: 24.02.2
umcg-labgnkbh:
NGS_Automated: 4.1.0
NGS_Automated: 4.2.0
ngs-utils: 24.02.2
NGS_Demultiplexing: 2.5.4
umcg-patho:
NGS_Automated: 4.1.0
NGS_Automated: 4.2.0
ngs-utils: 24.02.2
# umcg-pr:
# NGS_Automated: 4.1.0
Expand Down Expand Up @@ -1109,6 +1120,13 @@ crontabs:
job: /bin/bash -c "{{ configure_env_in_cronjob }};
module load NGS_Automated/{{ group_module_versions['umcg-gst']['NGS_Automated'] }}-NGS_DNA-{{ group_module_versions['umcg-gst']['NGS_DNA'] }};
startDragenPipeline.sh -g umcg-gst"
- name: NGS_Automated_startNextflowDragenPipeline # Unique ID required to update existing cronjob: do not modify.
user: umcg-gst-ateambot
machines: "{{ groups['user_interface'] | default([]) }}"
minute: '*/10'
job: /bin/bash -c "{{ configure_env_in_cronjob }};
module load NGS_Automated/{{ group_module_versions['umcg-gst']['NGS_Automated'] }}-nf_ngs_dna-{{ group_module_versions['umcg-gst']['nf_ngs_dna'] }};
startNextflowDragenPipeline.sh -g umcg-gst"
- name: NGS_Automated_calculateProjectMd5s # Unique ID required to update existing cronjob: do not modify.
user: umcg-gst-ateambot
machines: "{{ groups['user_interface'] | default([]) }}"
Expand Down Expand Up @@ -1154,6 +1172,13 @@ crontabs:
job: /bin/bash -c "{{ configure_env_in_cronjob }};
module load NGS_Automated/{{ group_module_versions['umcg-genomescan']['NGS_Automated'] }}-NGS_DNA-{{ group_module_versions['umcg-genomescan']['NGS_DNA'] }};
startDragenPipeline.sh -g umcg-genomescan"
- name: NGS_Automated_startNextflowDragenPipeline # Unique ID required to update existing cronjob: do not modify.
user: umcg-genomescan-ateambot
machines: "{{ groups['user_interface'] | default([]) }}"
minute: '*/10'
job: /bin/bash -c "{{ configure_env_in_cronjob }};
module load NGS_Automated/{{ group_module_versions['umcg-genomescan']['NGS_Automated'] }}-nf_ngs_dna-{{ group_module_versions['umcg-genomescan']['nf_ngs_dna'] }};
startNextflowDragenPipeline.sh -g umcg-genomescan"
- name: NGS_Automated_calculateProjectMd5s # Unique ID required to update existing cronjob: do not modify.
user: umcg-genomescan-ateambot
machines: "{{ groups['user_interface'] | default([]) }}"
Expand Down Expand Up @@ -1247,6 +1272,16 @@ crontabs:
# job: /bin/bash -c "{{ configure_env_in_cronjob }};
# module load NGS_Automated/{{ group_module_versions['umcg-pr']['NGS_Automated'] }}-bare;
# copyBclDataToPrm.sh -g umcg-pr -s {{ groups['jumphost'] | first }}+{{ groups['user_interface'] | first }} -p prm55"
######################################################################################################################
# umcg-lab group
######################################################################################################################
- name: NGS_Automated_moveSequencingData # Unique ID required to update existing cronjob: do not modify.
user: umcg-lab-ateambot
machines: "{{ groups['user_interface'] | default([]) }}"
minute: '*/10'
job: /bin/bash -c "{{ configure_env_in_cronjob }};
module load NGS_Automated/{{ group_module_versions['umcg-lab']['NGS_Automated'] }}-bare;
moveSequencingData.sh -t tmp05"

#
# Sources, software and reference data to install/fetch.
Expand Down
51 changes: 43 additions & 8 deletions group_vars/copperfist_cluster/vars.yml
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -18,7 +18,7 @@ lua_version: '5.1.4.9'
lmod_version: '8.6.2'
easybuild_version: '4.8.0'
eb_user: umcg-envsync
extra_easyconfigs_version: 24.03.1
extra_easyconfigs_version: 24.03.2
extra_easyconfigs_repository: 'take-it-easyconfigs'
# extra_easyconfigs_prefix: "{{ easybuild_software_dir }}/easyconfigs/{{ extra_easyconfigs_repository }}-{{ extra_easyconfigs_version }}/easybuild/easyconfigs/"
#
Expand Down Expand Up @@ -468,24 +468,34 @@ group_notification_targets:
analysis_phases: [copyBclDataToPrm]
notification_target: hpc-helpdesk_and_pr
machines: "{{ groups['chaperone'] }}"

######################################################################################################################
# umcg-lab group
######################################################################################################################
- group: umcg-lab
lfs: tmp06
user: umcg-lab-ateambot
type: notification_webhooks
analysis_phases: [moveSequencingData]
notification_target: hpc-helpdesk
machines: "{{ groups['user_interface'] }}"
#
# Cronjobs for functional accounts.
#
group_module_versions:
umcg-gd:
NGS_Automated: 4.1.0
NGS_Automated: 4.2.0
NGS_DNA: 4.2.2
ConcordanceCheck: 2.2.1
ngs-utils: 24.02.2
NGS_Demultiplexing: 2.5.4
umcg-gap:
NGS_Automated: 4.1.0
NGS_Automated: 4.2.0
GAP: 2.7.0
AGCT: 1.3.0
ngs-utils: 24.02.2
umcg-genomescan:
NGS_Automated: 4.1.0
NGS_Automated: 4.2.0
nf_ngs_dna: 1.0.0
NGS_DNA: 4.2.2
ngs-utils: 24.02.2
umcg-atd:
Expand All @@ -495,20 +505,21 @@ group_module_versions:
ngs-utils: 24.02.2
NGS_Demultiplexing: 2.5.4
umcg-gsad:
NGS_Automated: 4.1.0
NGS_Automated: 4.2.0
GAP: 2.7.0
AGCT: 1.3.0
ngs-utils: 24.02.2
umcg-gst:
NGS_Automated: 4.2.0
nf_ngs_dna: 1.0.0
NGS_DNA: 4.2.2
ngs-utils: 24.02.2
umcg-labgnkbh:
NGS_Automated: 4.1.0
NGS_Automated: 4.2.0
ngs-utils: 24.02.2
NGS_Demultiplexing: 2.5.4
umcg-patho:
NGS_Automated: 4.1.0
NGS_Automated: 4.2.0
ngs-utils: 24.02.2
# umcg-pr:
# NGS_Automated: 4.1.0
Expand Down Expand Up @@ -1109,6 +1120,13 @@ crontabs:
job: /bin/bash -c "{{ configure_env_in_cronjob }};
module load NGS_Automated/{{ group_module_versions['umcg-gst']['NGS_Automated'] }}-NGS_DNA-{{ group_module_versions['umcg-gst']['NGS_DNA'] }};
startDragenPipeline.sh -g umcg-gst"
- name: NGS_Automated_startNextflowDragenPipeline # Unique ID required to update existing cronjob: do not modify.
user: umcg-gst-ateambot
machines: "{{ groups['user_interface'] | default([]) }}"
minute: '*/10'
job: /bin/bash -c "{{ configure_env_in_cronjob }};
module load NGS_Automated/{{ group_module_versions['umcg-gst']['NGS_Automated'] }}-nf_ngs_dna-{{ group_module_versions['umcg-gst']['nf_ngs_dna'] }};
startNextflowDragenPipeline.sh -g umcg-gst"
- name: NGS_Automated_calculateProjectMd5s # Unique ID required to update existing cronjob: do not modify.
user: umcg-gst-ateambot
machines: "{{ groups['user_interface'] | default([]) }}"
Expand Down Expand Up @@ -1154,6 +1172,13 @@ crontabs:
job: /bin/bash -c "{{ configure_env_in_cronjob }};
module load NGS_Automated/{{ group_module_versions['umcg-genomescan']['NGS_Automated'] }}-NGS_DNA-{{ group_module_versions['umcg-genomescan']['NGS_DNA'] }};
startDragenPipeline.sh -g umcg-genomescan"
- name: NGS_Automated_startNextflowDragenPipeline # Unique ID required to update existing cronjob: do not modify.
user: umcg-genomescan-ateambot
machines: "{{ groups['user_interface'] | default([]) }}"
minute: '*/10'
job: /bin/bash -c "{{ configure_env_in_cronjob }};
module load NGS_Automated/{{ group_module_versions['umcg-genomescan']['NGS_Automated'] }}-nf_ngs_dna-{{ group_module_versions['umcg-genomescan']['nf_ngs_dna'] }};
startNextflowDragenPipeline.sh -g umcg-genomescan"
- name: NGS_Automated_calculateProjectMd5s # Unique ID required to update existing cronjob: do not modify.
user: umcg-genomescan-ateambot
machines: "{{ groups['user_interface'] | default([]) }}"
Expand Down Expand Up @@ -1247,6 +1272,16 @@ crontabs:
# job: /bin/bash -c "{{ configure_env_in_cronjob }};
# module load NGS_Automated/{{ group_module_versions['umcg-pr']['NGS_Automated'] }}-bare;
# copyBclDataToPrm.sh -g umcg-pr -s {{ groups['jumphost'] | first }}+{{ groups['user_interface'] | first }} -p prm56"
######################################################################################################################
# umcg-lab group
######################################################################################################################
#- name: NGS_Automated_moveSequencingData # Unique ID required to update existing cronjob: do not modify.
# user: umcg-lab-ateambot
# machines: "{{ groups['user_interface'] | default([]) }}"
# minute: '*/10'
# job: /bin/bash -c "{{ configure_env_in_cronjob }};
# module load NGS_Automated/{{ group_module_versions['umcg-lab']['NGS_Automated'] }}-bare;
# moveSequencingData.sh -t tmp06"

#
# Sources, software and reference data to install/fetch.
Expand Down
80 changes: 58 additions & 22 deletions group_vars/wingedhelix_cluster/vars.yml
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -242,6 +242,16 @@ group_subfolder_structure:
# owner: umcg-pr-dm
# subfolders: "{{ analysis_folders['BclDataToPrm']['prm'] }}"
# machines: "{{ groups['chaperone'] }}"
######################################################################################################################
# umcg-lab group
######################################################################################################################
- group: umcg-lab
lfs: tmp06
user: umcg-lab-ateambot
type: notification_webhooks
analysis_phases: [moveSequencingData]
notification_target: hpc-helpdesk
machines: "{{ groups['user_interface'] }}"
#
# Symlinks to enable sending notifications to certain target when notification are enabled for an anlysis phase in NGS_Automated.
#
Expand Down Expand Up @@ -475,18 +485,19 @@ group_notification_targets:
#
group_module_versions:
umcg-gd:
NGS_Automated: 4.1.0
NGS_Automated: 4.2.0
NGS_DNA: 4.2.2
ConcordanceCheck: 2.2.1
ngs-utils: 24.02.2
NGS_Demultiplexing: 2.5.4
umcg-gap:
NGS_Automated: 4.1.0
NGS_Automated: 4.2.0
GAP: 2.7.0
AGCT: 1.3.0
ngs-utils: 24.02.2
umcg-genomescan:
NGS_Automated: 4.1.0
NGS_Automated: 4.2.0
nf_ngs_dna: 1.0.0
NGS_DNA: 4.2.2
ngs-utils: 24.02.2
umcg-atd:
Expand All @@ -496,20 +507,21 @@ group_module_versions:
ngs-utils: 24.02.2
NGS_Demultiplexing: 2.5.4
umcg-gsad:
NGS_Automated: 4.1.0
NGS_Automated: 4.2.0
GAP: 2.7.0
AGCT: 1.3.0
ngs-utils: 24.02.2
umcg-gst:
NGS_Automated: 4.2.0
nf_ngs_dna: 1.0.0
NGS_DNA: 4.2.2
ngs-utils: 24.02.2
umcg-labgnkbh:
NGS_Automated: 4.1.0
NGS_Automated: 4.2.0
ngs-utils: 24.02.2
NGS_Demultiplexing: 2.5.4
umcg-patho:
NGS_Automated: 4.1.0
NGS_Automated: 4.2.0
ngs-utils: 24.02.2
# umcg-pr:
# NGS_Automated: 4.1.0
Expand Down Expand Up @@ -1110,6 +1122,13 @@ crontabs:
job: /bin/bash -c "{{ configure_env_in_cronjob }};
module load NGS_Automated/{{ group_module_versions['umcg-gst']['NGS_Automated'] }}-NGS_DNA-{{ group_module_versions['umcg-gst']['NGS_DNA'] }};
startDragenPipeline.sh -g umcg-gst"
- name: NGS_Automated_startNextflowDragenPipeline # Unique ID required to update existing cronjob: do not modify.
user: umcg-gst-ateambot
machines: "{{ groups['user_interface'] | default([]) }}"
minute: '*/10'
job: /bin/bash -c "{{ configure_env_in_cronjob }};
module load NGS_Automated/{{ group_module_versions['umcg-gst']['NGS_Automated'] }}-nf_ngs_dna-{{ group_module_versions['umcg-gst']['nf_ngs_dna'] }};
startNextflowDragenPipeline.sh -g umcg-gst"
- name: NGS_Automated_calculateProjectMd5s # Unique ID required to update existing cronjob: do not modify.
user: umcg-gst-ateambot
machines: "{{ groups['user_interface'] | default([]) }}"
Expand Down Expand Up @@ -1155,6 +1174,13 @@ crontabs:
job: /bin/bash -c "{{ configure_env_in_cronjob }};
module load NGS_Automated/{{ group_module_versions['umcg-genomescan']['NGS_Automated'] }}-NGS_DNA-{{ group_module_versions['umcg-genomescan']['NGS_DNA'] }};
startDragenPipeline.sh -g umcg-genomescan"
- name: NGS_Automated_startNextflowDragenPipeline # Unique ID required to update existing cronjob: do not modify.
user: umcg-genomescan-ateambot
machines: "{{ groups['user_interface'] | default([]) }}"
minute: '*/10'
job: /bin/bash -c "{{ configure_env_in_cronjob }};
module load NGS_Automated/{{ group_module_versions['umcg-genomescan']['NGS_Automated'] }}-nf_ngs_dna-{{ group_module_versions['umcg-genomescan']['nf_ngs_dna'] }};
startNextflowDragenPipeline.sh -g umcg-genomescan"
- name: NGS_Automated_calculateProjectMd5s # Unique ID required to update existing cronjob: do not modify.
user: umcg-genomescan-ateambot
machines: "{{ groups['user_interface'] | default([]) }}"
Expand Down Expand Up @@ -1248,6 +1274,16 @@ crontabs:
# job: /bin/bash -c "{{ configure_env_in_cronjob }};
# module load NGS_Automated/{{ group_module_versions['umcg-pr']['NGS_Automated'] }}-bare;
# copyBclDataToPrm.sh -g umcg-pr -s {{ groups['jumphost'] | first }}+{{ groups['user_interface'] | first }} -p prm57"
######################################################################################################################
# umcg-lab group
######################################################################################################################
#- name: NGS_Automated_moveSequencingData # Unique ID required to update existing cronjob: do not modify.
# user: umcg-lab-ateambot
# machines: "{{ groups['user_interface'] | default([]) }}"
# minute: '*/10'
# job: /bin/bash -c "{{ configure_env_in_cronjob }};
# module load NGS_Automated/{{ group_module_versions['umcg-lab']['NGS_Automated'] }}-bare;
# moveSequencingData.sh -t tmp07"

#
# Sources, software and reference data to install/fetch.
Expand All @@ -1256,24 +1292,24 @@ public_sources: [
]
private_sources: []
refdata: [
# 'GRC/Hg19toHumanG1kV37.chain',
# 'dbSNP',
'GRC/Hg19toHumanG1kV37.chain',
'dbSNP',
'1000G',
'Agilent',
# 'CGD',
# 'ClinVar',
# 'Controls_Convading_XHMM',
# 'GSAarray',
# 'Ensembl',
# 'Prepkits',
# 'ExAC',
# 'ManVarList',
# 'gnomAD/release-170228',
# 'GAVIN',
# 'UMCG',
# 'gonl',
# 'inSilico',
# 'snpEff-4.3',
'CGD',
'ClinVar',
'Controls_Convading_XHMM',
'GSAarray',
'Ensembl',
'Prepkits',
'ExAC',
'ManVarList',
'gnomAD/release-170228',
'GAVIN',
'UMCG',
'gonl',
'inSilico',
'snpEff-4.3',
]
static_easyconfigs:
- 'c/cluster-utils/cluster-utils-v24.01.1-GCCcore-11.3.0.eb'
Expand Down