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theiagen / public_health_viral_genomics

Bioinformatics workflows for genomic characterization, submission preparation, and genomic epidemiology of viral pathogens of concern, especially SARS-CoV-2
https://public-health-viral-genomics-theiagen.readthedocs.io/
GNU Affero General Public License v3.0
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Task and workflow review to ensure best practices are being applied #5

Closed kevinlibuit closed 3 years ago

kevinlibuit commented 3 years ago

Need for manual review of workflows and tasks to ensure consistent and best-practice coding practices are being applied throughout repo

kevinlibuit commented 3 years ago

Need to harmonize use of ivar container to 1.3.1_Titan

rpetit3 commented 3 years ago

Unique list of containers used: https://github.com/rpetit3/public_health_viral_genomics/blob/rp3-titan-cli/conf/containers.txt

rpetit3 commented 3 years ago 
find ~/repos/public_health_viral_genomics/ -name "*.wdl" | xargs -I {} grep -H docker {} | awk '{split($
0, b, ".wdl:"); print b[2]}' | grep "/" | sed 's/"/\t/g' | cut -f 2  | sort | uniq -c
      1 genomicpariscentre/guppy
      2 ncbi/sra-human-scrubber:1.0.2021-05-05
      1 neherlab/nextclade:0.14.4
     15 nextstrain/base:build-20210218T081251Z
      1 quay.io/biocontainers/multiqc:1.8--py_2
      1 quay.io/biocontainers/snp-sites:2.5.1--hed695b0_0
      1 quay.io/broadinstitute/viral-assemble:2.1.16.1
      1 quay.io/broadinstitute/viral-baseimage:0.1.20
      1 quay.io/broadinstitute/viral-classify:2.1.16.0
     11 quay.io/broadinstitute/viral-core:2.1.19
     10 quay.io/broadinstitute/viral-phylo:2.1.19.1
      1 staphb/artic-ncov2019:1.3.0
      2 staphb/bbtools:38.76
      2 staphb/fastqc:0.11.8
      1 staphb/iqtree:1.6.7
      6 staphb/ivar:1.2.2_artic20200528
      1 staphb/ivar:1.3.1
      1 staphb/kraken2:2.0.8-beta_hv
      1 staphb/mafft:7.450
      4 staphb/multiqc:1.7
      1 staphb/pangolin:1.1.14
      5 staphb/pangolin:3.1.3-pangolearn-2021-06-15
      1 staphb/samtools:1.10
     11 staphb/seqyclean:1.10.09
      1 staphb/snp-dists:0.6.2
      2 staphb/trimmomatic:0.39
      1 staphb/vadr:1.1.2
      1 staphb/vadr:1.2.1
      1 theiagen/artic-ncov2019:1.1.3
      1 theiagen/cluster-report-env:1.2
      3 theiagen/utility:1.0
      1 theiagen/utility:1.1
rpetit3 commented 3 years ago

List of different versions of same program used

ivar_variant_version    iVar version 1.2.2
ivar_version_consensus  iVar version 1.2.2
ivar_version_primtrim   iVar version 1.3.1
samtools_version    samtools 1.9
samtools_version_consensus  samtools 1.9
samtools_version_primtrim   samtools 1.12
samtools_version_stats  samtools 1.10
kevinlibuit commented 3 years ago

Fixed in [recent PR merge](Remove unused files and harmonize docker images per software)