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Update sequencing report service #230

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merged 10 commits into from
Apr 23, 2024
+147 −32
Merged

Update sequencing report service #230

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78d9a22
Update arteria_sequencing_report_service
Aratz Mar 5, 2024
082f555
Set seqreport_service_version to v1.5.0-rc2
Aratz Mar 14, 2024
6dd6405
Put the singularity containers in `biocontainers`
Aratz Apr 3, 2024
2dc5e7b
Fix demultiplex workflow path
Aratz Apr 3, 2024
cb68ae2
Include schema in deployment
Aratz Apr 3, 2024
0ac7f61
Fix pipeline config files
Aratz Apr 3, 2024
d312066
Update sequencing-report-service to v1.5.0-rc3
Aratz Apr 3, 2024
b94606b
Fix pipeline config path
Aratz Apr 3, 2024
9537b34
Update arteria sequencing-report-service to v1.5.0-rc4
Aratz Apr 5, 2024
4f2d976
Remove left-over comment
Aratz Apr 10, 2024
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Put the singularity containers in biocontainers 
instead of having separate folders for each pipeline
@Aratz
Aratz committed Apr 22, 2024
commit 6dd640507d6cbbd8223eab71343119c94c7eef54
2 changes: 1 addition & 1 deletion roles/arteria-sequencing-report-ws/tasks/install.yml
View file
Original file line number Diff line number Diff line change
@@ -39,7 +39,7 @@
args:
chdir: "{{ tempfolder.path }}"
environment:
NXF_SINGULARITY_CACHEDIR: "{{ ngi_containers }}/seqreports"
NXF_SINGULARITY_CACHEDIR: "{{ ngi_containers }}/biocontainers"
NXF_HOME: "{{ nextflow_dest }}/workfiles"
NXF_JAVA_HOME: "{{ nextflow_env.NXF_JAVA_HOME }}"
NXF_TEMP: "{{ tempfolder.path }}"
2 changes: 1 addition & 1 deletion roles/arteria-sequencing-report-ws/templates/pipeline_configs/demultiplex.yml.j2
View file
Original file line number Diff line number Diff line change
@@ -13,7 +13,7 @@ nextflow_parameters:
environment:
NXF_TEMP: {{nextflow_env.NXF_TEMP}}
NXF_WORK: "{runfolder_path}/.nextflow"
NXF_SINGULARITY_CACHEDIR: {{ ngi_containers }}/demultiplex
NXF_SINGULARITY_CACHEDIR: {{ ngi_containers }}/biocontainers
NXF_ANSI_LOG: false
parameters:
input: "{input_samplesheet}"
2 changes: 1 addition & 1 deletion roles/arteria-sequencing-report-ws/templates/pipeline_configs/seqreports.yml.j2
View file
Original file line number Diff line number Diff line change
@@ -14,7 +14,7 @@ nextflow_parameters:
environment:
NXF_TEMP: {{nextflow_env.NXF_TEMP}}
NXF_WORK: "{runfolder_path}/.nextflow"
NXF_SINGULARITY_CACHEDIR: "{{ ngi_containers }}/seqreports"
NXF_SINGULARITY_CACHEDIR: "{{ ngi_containers }}/biocontainers"
NXF_ANSI_LOG: false
parameters:
run_folder: "{runfolder_path}"