diff --git a/roles/arteria-sequencing-report-ws/files/hiseq.rsync b/roles/arteria-sequencing-report-ws/files/hiseq.rsync index 6de43274..502e3e45 100644 --- a/roles/arteria-sequencing-report-ws/files/hiseq.rsync +++ b/roles/arteria-sequencing-report-ws/files/hiseq.rsync @@ -5,6 +5,13 @@ # rsync -av --prune-empty-dirs --include-from hiseq.rsync $PWD/ biologin:~/incoming/runfolders/$runfolder > $PWD/rsync.log # +# Exclude all .nextflow directory +# This works if rsync is called with src dest +- /*/.nextflow/*** + +# This works if rsync is called with src/ dest +- .nextflow + + */ # Include some files regardless of location in tree diff --git a/roles/arteria-sequencing-report-ws/templates/nextflow_configs/demultiplex.config.j2 b/roles/arteria-sequencing-report-ws/templates/nextflow_configs/demultiplex.config.j2 index 4209150e..13391552 100644 --- a/roles/arteria-sequencing-report-ws/templates/nextflow_configs/demultiplex.config.j2 +++ b/roles/arteria-sequencing-report-ws/templates/nextflow_configs/demultiplex.config.j2 @@ -50,8 +50,4 @@ process { ] } - withName: MD5SUM { - publishDir = [] - } } - diff --git a/roles/arteria-sequencing-report-ws/templates/pipeline_configs/demultiplex.yml.j2 b/roles/arteria-sequencing-report-ws/templates/pipeline_configs/demultiplex.yml.j2 index 886ef574..39d9fa0f 100644 --- a/roles/arteria-sequencing-report-ws/templates/pipeline_configs/demultiplex.yml.j2 +++ b/roles/arteria-sequencing-report-ws/templates/pipeline_configs/demultiplex.yml.j2 @@ -20,7 +20,7 @@ pipeline_parameters: outdir: "{runfolder_path}" project: {{uppmax_project}} demultiplexer: "bcl2fastq" - skip_tools: "fastp,falco,multiqc" + skip_tools: "fastp,falco,multiqc,md5sum" input_samplesheet_content: | id,samplesheet,lane,flowcell {runfolder_name},{runfolder_path}/SampleSheet.csv,,{runfolder_path} diff --git a/roles/func_accounts/templates/crontab.j2 b/roles/func_accounts/templates/crontab.j2 index 956661c2..1e0eb298 100644 --- a/roles/func_accounts/templates/crontab.j2 +++ b/roles/func_accounts/templates/crontab.j2 @@ -6,6 +6,9 @@ SHELL=/bin/bash # restart supervisord if it has died for some reason 11 * * * * bash {{ ngi_resources }}/start_supervisord_{{ site }}.sh &> /dev/null +# Check disk usage every Monday +0 7 * * 1 echo "Disk usage Miarka:" && /vulpes/ngi/production/latest/sw/standalone_scripts/du_miarka.py /proj/ngi2016001 + {% endif %} # updates charon with locally stored run info for sarek diff --git a/roles/multiqc/defaults/main.yml b/roles/multiqc/defaults/main.yml index c0c6a735..16f9f900 100644 --- a/roles/multiqc/defaults/main.yml +++ b/roles/multiqc/defaults/main.yml @@ -1,7 +1,7 @@ -multiqc_repo: https://github.com/ewels/MultiQC.git +multiqc_repo: https://github.com/MultiQC/MultiQC.git multiqc_dest: "{{ sw_path }}/multiqc" -multiqc_version: "v1.25.1" +multiqc_version: "v1.25.2" multiqc_ngi_repo: https://github.com/NationalGenomicsInfrastructure/MultiQC_NGI.git multiqc_ngi_dest: "{{ sw_path }}/multiqc_ngi" -multiqc_ngi_version: "0.8.2" +multiqc_ngi_version: "0.9.2" diff --git a/roles/taca/defaults/main.yml b/roles/taca/defaults/main.yml index 0a135f3f..7380f1e0 100644 --- a/roles/taca/defaults/main.yml +++ b/roles/taca/defaults/main.yml @@ -7,9 +7,9 @@ flowcell_parser_repo: https://github.com/NationalGenomicsInfrastructure/flowcell flowcell_parser_dest: "{{ sw_path }}/flowcell_parser" flowcell_parser_version: cfe18abb6b758a6389a9d6aa75f1866d517dc36e -taca_repo: https://github.com/SciLifeLab/TACA.git +taca_repo: https://github.com/NationalGenomicsInfrastructure/TACA.git taca_dest: "{{ sw_path }}/TACA" -taca_version: c08d3f3ca4ed2f0f8ef7e669b6d7313b746e33f0 +taca_version: 43b763b44be324c9d8ef6841d9c56e2a85cd2d62 ngi_pipeline_analysisdir: "{{ ngi_pipeline_workdir }}/ANALYSIS" ngi_pipeline_datadir: "{{ ngi_pipeline_workdir }}/DATA"