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czbiohub-sf / sc2-illumina-pipeline

Bioinformatics pipeline for SARS-CoV-2 sequencing at CZ Biohub
GNU Affero General Public License v3.0
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coverage plot per pool #86

Open aspitaleri opened 3 years ago

aspitaleri commented 3 years ago

Hi I was trying to use this approach: https://github.com/Psy-Fer/CoVarPlot to plot the coverage as function of the pool in the artic V3 (see the example at the bottom of the page). The only bam present in the outdir is the align_reads/file.primertrimmed.bam If I do: artic_make_depth_mask --store-rg-depths /softw/artic-ncov2019/primer_schemes/nCoV-2019/V3/nCoV-2019.reference.fasta file.primertrimmed.bam file.cov_mask

I only get: file.cov_mask.txt and file.cov_mask.txt.nCoV-2019.depths instead that file.cov_mask.txt.nCoV-2019_1.depths and file.cov_mask.txt.nCoV-2019_2.depths

probably due to the different align_trim step (there is two align_stemp to generate the bam)

Is there anyway to generate a bam to run the covarplot.py? Actually I can follow the instructions there but I am wondering if there is already in the workdir temporary bam to be used for this.

my command is: nextflow run czbiohub/sc2-illumina-pipeline -profile artic --reads '/Covid19/DIR/FILES/_R{1,2}.fastq.gz' --outdir '/Covid19/DIR/FILES/outdir' --kraken2_db '/Covid19/DIR/kraken_coronavirus_db_only'

Thanks!