Closed kevinlibuit closed 3 years ago
Need to harmonize use of ivar container to 1.3.1_Titan
Unique list of containers used: https://github.com/rpetit3/public_health_viral_genomics/blob/rp3-titan-cli/conf/containers.txt
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
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
Fixed in [recent PR merge](Remove unused files and harmonize docker images per software)
Need for manual review of workflows and tasks to ensure consistent and best-practice coding practices are being applied throughout repo