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Dsl2#68

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MeriamOs wants to merge 33 commits intodevnf-core/coproid:devfrom dsl2nf-core/coproid:dsl2Copy head branch name to clipboard

+16,329-11,196

Commits

Commits on Nov 4, 2022

• Merge pull request #51 from nf-core/dev

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Commits on Sep 30, 2024

• restart of a blank state

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  910675d

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• nf-core base template

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  e2da58d

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• feat: add fastp module

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Commits on Oct 5, 2024

• add modules

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Commits on Oct 24, 2024

• add modules

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Commits on Oct 28, 2024

• changes coproid.nf and added subworkflows

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Commits on Nov 4, 2024

• added genome schema and changed nf-validation to nf-schema

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Commits on Nov 7, 2024

• pipeline is running, but only fastgc, fastp and multiqc

  MeriamOs

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Commits on Nov 11, 2024

• prepare genomes working, stuck at align_index variables

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Commits on Nov 12, 2024

• pipeline running, but modified main.nf from bowtie2 and samtools sort

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  f5e1791

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• fixed fasta input for samtools, but added .sorted to output bam - otherwise they have the same name

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• fixed double kraken2

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Commits on Nov 15, 2024

• added damageprofiler and start on quarto

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Commits on Nov 19, 2024

• added pydamage and some multiQC

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• added pydamage and some multiQC

  MeriamOs

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Commits on Nov 22, 2024

• add sam2lca build db subworkflow

  maxibor

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• fixed sourcepredict module embedding, added merge sam2lca

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Commits on Nov 25, 2024

• added pydamage merge and quarto workflow

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Commits on Nov 27, 2024

• quarto is now running, but need to change qmd file to improve report

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Commits on Dec 2, 2024

• Merge pull request #66 from nf-core/sam2lca_db_build

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• tidy up and moved sourcepredict into kraken subworkflow

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Commits on Dec 3, 2024

• patched modules

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  639f43d

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• Merge branch 'dsl2' into quarto

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• Merge pull request #67 from MeriamOs/quarto

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Commits on Dec 5, 2024

• added damage profiler plots to report

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• make report prettier

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Commits on Dec 10, 2024

• changed test data, config and tidied up some code

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• added untar option for kraken database

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Commits on Dec 11, 2024

• added xz decompress for taxa_splite file, included normalisation and table in quartot report, and sorted test data

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  fc734d1

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Commits on Dec 12, 2024

• fixed sam2lca db channel, and taxa.sqlite.xz, tidying up

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Commits on Dec 17, 2024

• reporting, summary probability, fixed pydamage plot

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Commits on Jan 13, 2025

• updated samtools sort

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