Merge pull request #295 from NationalGenomicsInfrastructure/monthly

Monthly Merge Dec 24

Author: slohse

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

roles/arteria-sequencing-report-ws/templates/nextflow_configs/demultiplex.config.j2

@@ -50,8 +50,4 @@ process {
         ]
     }
 
-    withName: MD5SUM {
-        publishDir = []
-    }
 }
-

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}

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

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"

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"