icgc-argo-workflows/sanger-wgs-variant-calling

ICGC-ARGO Sanger WGS Somatic Variant Calling Workflow

sanger-wgs-variant-calling's Issues

Update the song_score_upload and song_score_download modules to latest versions

song/score client have some fixes to address the upload/download issue:
icgc-argo/workflow-roadmap#324
icgc-argo/workflow-roadmap#333

The sanger workflow needs to update the modules to use the latest versions of song/score client.

Markduplicate issue that potentially affects CNV and SV calls

Keiran suggests to use samtools to markdup, manually perform markdup for tumour / normal pair then call sanger again to compare with original run. Affected donor DO35085, tumour aligned cram downloaded to 10.1.0.7 under /home/ubuntu/DO35085.

Manually perform new markdup then run Sanger again

Exclude gender info from QC metrics payload

related payload generation code: https://github.com/icgc-argo-workflows/sanger-wgs-variant-calling/blob/main/sanger-wgs-variant-calling/main.nf#L425

upgrade the song/score modules to 2.1.0

https://github.com/icgc-argo/dna-seq-processing-wfs/issues/49

Update workflow to use updated payload gen tool package

ticket for tool package update (new terminlogies) is here: https://github.com/icgc-argo/data-processing-utility-tools/issues/118

update payload gen variant calling package to 0.5.0

related tool pacakge update: https://github.com/icgc-argo/data-processing-utility-tools/issues/121

Options to handle incorrect contamination estimate for tumour sample in Sanger WGS workflow

I has been observed Sanger wf sometimes produce incorrect contamination estimate for tumour samples.

If there is a fix, we should be able to run it to get correct contamination estimate for tumour sample without re-running the whole Sanger WGS variant calling workflow, will then apply update to ascat_metrics SONG analysis with new result files.

If there is no fix, we should be able to remove contamination result from qc_metrics payload produced by Sanger, this change shouldn't have any impact on Sanger variant calling result at all

Error in running nextflow pipeline

Hi all,

wondering if anyone can help me with this error:

/home/ubuntu/nextflow run icgc-argo-workflows/sanger-wgs-variant-calling/sanger-wgs-variant-calling/main.nf -r sanger-wgs-variant-calling.v2.1.0-9.7.0 -params-file /home/ubuntu/variant/variant.json
N E X T F L O W ~ version 23.04.4
ERROR ~ Preview nextflow mode ('preview') is no longer supported —- use nextflow.enable.dsl=2 instead

-- Check '.nextflow.log' file for details

I've been attempting to resolve this issue for awhile now with no luck, please let me know how I can troubleshoot this.

Best,
-Ashraf