diff --git a/roles/archive-upload-ws/defaults/main.yml b/roles/archive-upload-ws/defaults/main.yml index 781f9b47..3eeba71e 100644 --- a/roles/archive-upload-ws/defaults/main.yml +++ b/roles/archive-upload-ws/defaults/main.yml @@ -1,14 +1,14 @@ --- -# If deploying to staging one should call with +# If deploying to staging one should call with # -e deployment_environment=staging -# One can also override the default installed version -# by overriding the archive_upload_version on the command line. +# One can also override the default installed version +# by overriding the archive_upload_version on the command line. # -# This will set corresponding paths and use the appropriate port. +# This will set corresponding paths and use the appropriate port. archive_upload_repo: https://github.com/Molmed/snpseq-archive-upload.git -archive_upload_version: v1.0.2 +archive_upload_version: v1.0.3 # in production this should be /proj/ngi2016001/nobackup/NGI/ANALYSIS/ archive_upload_monitored_path_prod: "/proj/{{ ngi_pipeline_upps_delivery }}/nobackup/NGI/ANALYSIS/" @@ -27,11 +27,11 @@ archive_upload_logger_config: "{{ archive_upload_config_root }}/logger.config" archive_upload_log_dir: "/proj/{{ ngi_pipeline_upps_delivery }}/private/log/arteria/archive-upload-ws" archive_upload_port_prod: 10480 -archive_upload_port_stage: 10481 +archive_upload_port_stage: 10481 archive_upload_cores_to_use: 2 # We want to fake a successful return code for the dsmc subprocess for some certain warnings. -# Otherwise the Arteria workflow in Stackstorm would be marked as failed when it actually suceeded. +# Otherwise the Arteria workflow in Stackstorm would be marked as failed when it actually suceeded. # # ANS1809W = a session with the TSM server has been disconnected: will retry again # ANS2042W = a symblic link to a file on other fs has been uploaded: acls/extended attributes might not be backed up diff --git a/roles/multiqc/defaults/main.yml b/roles/multiqc/defaults/main.yml index 21b656a7..49e53a26 100644 --- a/roles/multiqc/defaults/main.yml +++ b/roles/multiqc/defaults/main.yml @@ -1,6 +1,6 @@ multiqc_repo: https://github.com/ewels/MultiQC.git multiqc_dest: "{{ sw_path }}/multiqc" -multiqc_version: "v1.10" +multiqc_version: "v1.10.1" multiqc_ngi_repo: https://github.com/NationalGenomicsInfrastructure/MultiQC_NGI.git multiqc_ngi_dest: "{{ sw_path }}/multiqc_ngi" diff --git a/roles/nf-core/defaults/main.yml b/roles/nf-core/defaults/main.yml index 6f1d120a..76593def 100644 --- a/roles/nf-core/defaults/main.yml +++ b/roles/nf-core/defaults/main.yml @@ -4,11 +4,11 @@ nextflow_download_url: "https://github.com/nextflow-io/nextflow/releases/downloa nf_core_env: "/lupus/ngi/irma3/nf-core-env" pipelines: - name: methylseq - release: 1.6 + release: 1.6.1 - name: ampliseq - release: 1.1.2 + release: 1.2.0 - name: atacseq - release: 1.1.0 + release: 1.2.1 - name: viralrecon release: 1.1.0 - name: rnafusion diff --git a/roles/ngi_pipeline/templates/create_ngi_pipeline_dirs.sh.j2 b/roles/ngi_pipeline/templates/create_ngi_pipeline_dirs.sh.j2 index a6bc94c8..d04f28cb 100755 --- a/roles/ngi_pipeline/templates/create_ngi_pipeline_dirs.sh.j2 +++ b/roles/ngi_pipeline/templates/create_ngi_pipeline_dirs.sh.j2 @@ -39,5 +39,5 @@ ln -s /lupus/ngi/{{ deployment_environment }}/latest/sw/ngi_pipeline/$ACKNOWLEDG #if sthlm, source delivery readme script if [ $1 == "ngi2016003" ]; then -. create_delivery_readme_softlinks.sh +. {{ ngi_resources }}/create_delivery_readme_softlinks.sh fi diff --git a/roles/taca/defaults/main.yml b/roles/taca/defaults/main.yml index 1f29c6eb..30fca6d3 100644 --- a/roles/taca/defaults/main.yml +++ b/roles/taca/defaults/main.yml @@ -1,7 +1,7 @@ --- taca_ngi_repo: https://github.com/SciLifeLab/taca-ngi-pipeline.git taca_ngi_dest: "{{ sw_path }}/taca-ngi-pipeline" -taca_ngi_version: 1d7ca548099ed3b08dd33fff59f6b8652b323707 +taca_ngi_version: 79d6f1b38dd5808b0ab4a3e7a732c989e5cc7ec1 statusdb_repo: "https://github.com/SciLifeLab/statusdb.git" statusdb_dest: "{{ sw_path }}/statusdb" diff --git a/roles/taca/templates/create_delivery_readme_softlinks.sh.j2 b/roles/taca/templates/create_delivery_readme_softlinks.sh.j2 index 67fce716..b5d46a3b 100755 --- a/roles/taca/templates/create_delivery_readme_softlinks.sh.j2 +++ b/roles/taca/templates/create_delivery_readme_softlinks.sh.j2 @@ -16,4 +16,4 @@ fi ln -s /lupus/ngi/{{ deployment_environment }}/latest/sw/taca-ngi-pipeline/delivery_readmes/DELIVERY.README.RAW_DATA.txt {{ proj_root }}/$1/nobackup/NGI/softlinks/DELIVERY.README.RAW_DATA.txt ln -s /lupus/ngi/{{ deployment_environment }}/latest/sw/taca-ngi-pipeline/delivery_readmes/DELIVERY.README.MethylSeq.txt {{ proj_root }}/$1/nobackup/NGI/softlinks/DELIVERY.README.MethylSeq.txt ln -s /lupus/ngi/{{ deployment_environment }}/latest/sw/taca-ngi-pipeline/delivery_readmes/DELIVERY.README.RNASeq.txt {{ proj_root }}/$1/nobackup/NGI/softlinks/DELIVERY.README.RNASeq.txt -ln -s /lupus/ngi/{{ deployment_environment }}/latest/sw/taca-ngi-pipeline/delivery_readmes/DELIVERY.README.Sarek.txt {{ ngi_resources }}/TACA/sthlm/DELIVERY.README.SAREK.txt +ln -s /lupus/ngi/{{ deployment_environment }}/latest/sw/taca-ngi-pipeline/delivery_readmes/DELIVERY.README.Sarek.txt {{ proj_root }}/$1/nobackup/NGI/softlinks/DELIVERY.README.SAREK.txt diff --git a/roles/taca/templates/site_taca_sarek_delivery.yml.j2 b/roles/taca/templates/site_taca_sarek_delivery.yml.j2 index 2258e1ec..2b6fb054 100644 --- a/roles/taca/templates/site_taca_sarek_delivery.yml.j2 +++ b/roles/taca/templates/site_taca_sarek_delivery.yml.j2 @@ -7,8 +7,8 @@ deliver: stagingpath: /DELIVERY/ operator: "{{ recipient_mail }}" hash_algorithm: md5 - files_to_deliver: {% if "upps" == site %} + files_to_deliver: - - /seqreports/* - /00-Reports/SequenceQC/ @@ -21,17 +21,6 @@ deliver: - /multiqc_ngi/*multiqc_report_data.zip - /00-Reports/ - required: True -{% endif %} -{% if "sthlm" == site %} - - - - /sarek_ngi/*multiqc_report.html - - /00-Reports/ - - required: True - - - - /reports/* - - /00-Reports/ - - required: True -{% endif %} - - //SarekGermlineAnalysis/results/Annotation/* - //results/Annotation/ @@ -68,3 +57,59 @@ deliver: - {{ ngi_resources }}/TACA/apply_recalibration.sh - /01-Resources/ - required: True +{% endif %} +{% if "sthlm" == site %} + datapath: /DATA/ + stagingpathhard: /DELIVERY_HARD/ + files_to_deliver: + - + - //*/* + - //02-FASTQ + - required: True + - + - //SarekGermlineAnalysis/results/Annotation/* + - //01-SarekGermline-Results/Annotation/ + - required: True + - + - //SarekGermlineAnalysis/results/pipeline_info/results_description.html + - //01-SarekGermline-Results/pipeline_info + - required: True + - + - //SarekGermlineAnalysis/results/pipeline_info/software_versions.csv + - //01-SarekGermline-Results/pipeline_info + - required: True + - + - //SarekGermlineAnalysis/results/Preprocessing/TSV/duplicates_marked*.tsv* + - //01-SarekGermline-Results/Preprocessing/TSV + - required: True + - + - //SarekGermlineAnalysis/results/Preprocessing//DuplicatesMarked/* + - //01-SarekGermline-Results/Preprocessing/DuplicatesMarked + - required: True + - + - //SarekGermlineAnalysis/results/Preprocessing//Recalibrated/* + - //01-SarekGermline-Results/Preprocessing/Recalibrated + - required: True + - + - //SarekGermlineAnalysis/results/Reports/* + - //01-SarekGermline-Results/Reports + - required: True + - + - //SarekGermlineAnalysis/results/VariantCalling//* + - //01-SarekGermline-Results/VariantCalling/ + - required: True + misc_files_to_deliver: + - + - {{ ngi_site_softlinks }}/ACKNOWLEDGEMENTS.txt + - + - + - {{ ngi_site_softlinks }}/DELIVERY.README.SAREK.txt + - + - + - /reports/* + - /00-Reports + - + - /*multiqc_report.html + - /00-Reports + save_meta_info: True +{% endif %}