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Commits on Apr 7, 2025

• new version of centrifuge

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Commits on Mar 28, 2025

• scripts/Makefile: modify *_dbest targets to change json with jq

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• add gff file for NC_000962.3

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• Merge branch 'master' of https://github.com/ranlib/varpipe4

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• add .vscode to .gitignore

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• update multiqc docker image

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• task_multiqc.wdl: update multiqc version

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• scripts/Makefile: add new target run_tb_profiler_dbest

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• update gatk and multiqc docker images

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Commits on Mar 18, 2025

• scripts/Makefile: use cromwell script to manage cromwell versions better

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• staphb/minimap2:2.25 ==> staphb/minimap2:2.28

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• dbest/snpeff:v5.2a ==> dbest/snpeff:v5.2f; multiqc/multiqc:v1.21 ==> dbest/snpeff:v5.2f; broadinstitute/gatk:4.5.0.0 ==> broadinstitute/gatk:4.6.1.0

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• multiqc: multiqc/multiqc:v1.21 ==> multiqc/multiqc:v1.27.1

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• snpEff: dbest/snpeff:v5.2a ==> dbest/snpeff:v5.2f

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• Makefile: switch to womtool script, better management of womtool version

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Commits on Feb 5, 2025

• wf_ngs_pipeline.json: update version of gatk, snpeff, multiqc

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Commits on Mar 1, 2024

• wf_tbprofiler.wdl: add fastq_screen output to multiqc and workflow output section

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Commits on Feb 29, 2024

• task_freebayes: update documentation

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• update wf_varpipe_tasks.md

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• update wf_varpipe_tasks.md

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• add more md files with documentation of workflows

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• update and add more documentation to wdl workflows

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Commits on Feb 28, 2024

• add directory wdldocs

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• wf_delly.wdl: update documentation

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• wf_delly: change output array from Array[File] to Array[File?]

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• update to use docker image multiqc/multiqc:v1.21

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• add wf_varpipe.wdlviz.pdf: varpipe flowchart generated by wdlviz

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Commits on Feb 20, 2024

• wf_varpipe.wdl: add more parameter documentation

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Commits on Feb 15, 2024

• wf_varpipe.wdl: add centrifuge kraken style output to multiQC

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Commits on Feb 13, 2024

• wf_varpipe.json: switch to newer version for multiqc: v1.20

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Commits on Feb 12, 2024

• wf_varpipe_terra_configuration_2.json: switch to using cdc_v2 clockwork decontamination database

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• task_kraken2.wdl: switch from input index files to input gzipped tar file for kraken database

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• task_bracken.wdl/wf_kraken2.wdl: switch from input index files to input gzipped tar file for kraken database

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• Makefile: add kraken_large and centrifuge_dbest, use cdc_v2 clockwork decontamination database in varpipe_dbest.json

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• make_clockwork_contamination_cdc_v2.sh: make sure reference not included twice

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