Releases: moka-guys/automate_demultiplex
Fix to ensure full runfolder uploaded to DNANexus
Fix an error where the full runfolder was not uploaded because the location of the samplesheets folder had been changed from samplesheets to samplesheets_dir. upload_and_setoff_workflows.py updated.
Support MokaCAN
Add support for MokaCAN v1.0
Update MokaAMP to v1.7 ( varscan variant callers to v1.3.2) which allows for samplename to be specified. This aids ainterpretation of multiple VCfs in one QCI analysis.
NA12878 samples are excluded form the congenica upload command
The demultiplex script has been changed to improve the logic around missing samplesheets.
The logic which counts the number of samples in the samplesheet (used to update smartsheet) has also been updated.
Update description of Pan4314 to R229 from R266 inn config
Update config.testing statement to allow for all testing variables to be easily replaced - this removes the now obsolete debug flag.
Update VCP3 bed file to add support for SNORD118
Create fastqc/multiqc report for OnePGT samples
Upgrade to upload_multiqc_v1.4.0
This release upgrades to the DNA NExus app upload_multiqc_v1.4.0
correct missing comma in vcp3 panel list in config
Merge pull request #335 from moka-guys/v39.1 V39.1
V39
Add support for archerdx runs. These are uploaded to DNANexus, fastqc run per sample and multiqc report generated. OPMS queries also sent
To ensure bcl2fastq stats are present for multiqc, this stats file is uploaded seperately to the rest of the runfolder backup.
Some extra pan numbers have been added
BED files for VCP1 and 3 have been changed (including STG samples) to reflect LAMA2 mapping issues
v38.0.0
Automated SNP Genotyping pipeline
Added new VCP panels
Updated BED files for VCP panels
Updated MokaOnc and MokaAMP pipeline versions (adds the genome build to the VCF header)
v37
move to congenica pan numbers
Merge pull request #306 from moka-guys/automate_trios new congenica pan numbers