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Update from grunwaldlab fork #88

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Update from grunwaldlab fork #88

wants to merge 609 commits into from
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Commits on Mar 6, 2024

  1. fix bug that ignored groups using only refseq for references

    @zachary-foster
    zachary-foster committed Mar 6, 2024
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  2. fix bug

    @zachary-foster
    zachary-foster committed Mar 6, 2024
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  3. update docker file for main report

    @zachary-foster
    zachary-foster committed Mar 6, 2024
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  4. Adds more detail to the status table.

    @cahuparo
    cahuparo committed Mar 6, 2024
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  5. add missing dependency for adgenet in report docker container

    @zachary-foster
    zachary-foster committed Mar 6, 2024
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  6. Merge branch 'master' of github.com:grunwaldlab/pathogensurveillance

    @zachary-foster
    zachary-foster committed Mar 6, 2024
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Commits on Mar 10, 2024

  1. Fix color-by typo in sample data sheet

    Martha Sudermann committed Mar 10, 2024
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  2. Update report with MSN function

    Martha Sudermann committed Mar 10, 2024
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Commits on Mar 13, 2024

  1. Update MSN function so it is more generalizable

    Martha Sudermann authored and Martha Sudermann committed Mar 13, 2024
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  2. Update MSN

    Martha Sudermann authored and Martha Sudermann committed Mar 13, 2024
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Commits on Mar 14, 2024

  1. add abstract

    @zachary-foster
    zachary-foster committed Mar 14, 2024
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  2. fix fake warning

    @zachary-foster
    zachary-foster committed Mar 14, 2024
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  3. update report dockerfile

    @zachary-foster
    zachary-foster committed Mar 14, 2024
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  4. add test dataset

    @zachary-foster
    zachary-foster committed Mar 14, 2024
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  5. specify resources for some processes

    @zachary-foster
    zachary-foster committed Mar 14, 2024
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  6. Merge branch 'master' of github.com:grunwaldlab/pathogensurveillance

    @zachary-foster
    zachary-foster committed Mar 14, 2024
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  7. add bakta --skip-crispr

    @zachary-foster
    zachary-foster committed Mar 14, 2024
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Commits on Mar 15, 2024

  1. Update main report doc

    Martha Sudermann authored and Martha Sudermann committed Mar 15, 2024
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  2. Merge branch 'master' of github.com:grunwaldlab/pathogensurveillance

    Martha Sudermann authored and Martha Sudermann committed Mar 15, 2024
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  3. update report

    Martha Sudermann authored and Martha Sudermann committed Mar 15, 2024
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  4. read2tree formater step 1

    @ricardoi
    ricardoi committed Mar 15, 2024
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  5. faa and fna format

    @ricardoi
    ricardoi committed Mar 15, 2024
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  6. fix OOM error for vcf_concatenate:

    @masudermann
    masudermann committed Mar 15, 2024
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Commits on Mar 18, 2024

  1. Merge branch 'master' of github.com:grunwaldlab/pathogensurveillance

    @masudermann
    masudermann committed Mar 18, 2024
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  2. Update Kpneum test database-remove two bad samples

    @masudermann
    masudermann committed Mar 18, 2024
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Commits on Mar 20, 2024

  1. update test datasets

    @zachary-foster
    zachary-foster committed Mar 20, 2024
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  2. Merge branch 'master' of github.com:grunwaldlab/pathogensurveillance

    @zachary-foster
    zachary-foster committed Mar 20, 2024
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Commits on Mar 25, 2024

  1. remove debug print statements

    @zachary-foster
    zachary-foster committed Mar 25, 2024
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  2. remove whitespace around report group ids

    @zachary-foster
    zachary-foster committed Mar 25, 2024
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Commits on Mar 26, 2024

  1. fix bug with drop=FALSE

    @cahuparo
    cahuparo authored Mar 26, 2024
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Commits on Mar 29, 2024

  1. Fix typo in metadata-nursery not nusery, otherwise we get error in MSN

    Martha Sudermann committed Mar 29, 2024
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  2. Fix typos in metadata

    Martha Sudermann committed Mar 29, 2024
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  3. Update MSN portion of report to handle different scenarios, like not … 

    …enough samples in alignment file
    Martha Sudermann committed Mar 29, 2024
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  4. Fix tabs-MSN outputs

    Martha Sudermann committed Mar 29, 2024
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  5. Update main report

    Martha Sudermann committed Mar 29, 2024
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Commits on Mar 30, 2024

  1. debug outputs for msn fxn

    Martha Sudermann committed Mar 30, 2024
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Commits on Apr 1, 2024

  1. Revise MSN code so network headers and tabs render properly

    Martha Sudermann committed Apr 1, 2024
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  2. trying to fix report not being run if there are no status messages

    @zachary-foster
    zachary-foster committed Apr 1, 2024
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  3. added new presenation

    @zachary-foster
    zachary-foster committed Apr 1, 2024
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  4. Merge branch 'master' of github.com:grunwaldlab/pathogensurveillance

    @zachary-foster
    zachary-foster committed Apr 1, 2024
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  5. fix typo in test metadata

    @zachary-foster
    zachary-foster committed Apr 1, 2024
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  6. add temp_dir option to specify location of temporary files for PICARD… 

    …_SORTSAM; relates to nf-core#48
    @zachary-foster
    zachary-foster committed Apr 1, 2024
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Commits on Apr 2, 2024

  1. Upate MSN code chunk-still bizarre formatting concerns

    Martha Sudermann committed Apr 2, 2024
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  2. Add header message back to MSN plots

    Martha Sudermann committed Apr 2, 2024
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  3. beginning r2tdir

    @ricardoi
    ricardoi committed Apr 2, 2024
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  4. ammended r2tdir

    @ricardoi
    ricardoi committed Apr 2, 2024
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Commits on Apr 3, 2024

  1. add warnings when samples are removed from the core gene phylogeny

    @zachary-foster
    zachary-foster committed Apr 3, 2024
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  2. removed install code for psminer from report

    @zachary-foster
    zachary-foster committed Apr 3, 2024
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  3. add a way to specify the temporary directory for some processes

    @zachary-foster
    zachary-foster committed Apr 3, 2024
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  4. merge

    @zachary-foster
    zachary-foster committed Apr 3, 2024
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Commits on Apr 4, 2024

  1. update test datasets

    @zachary-foster
    zachary-foster committed Apr 4, 2024
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  2. update citation

    @zachary-foster
    zachary-foster committed Apr 4, 2024
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Commits on Apr 9, 2024

  1. Add new mixed bacterial test dataset

    Martha Sudermann committed Apr 9, 2024
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  2. updated report to add dropdown menu to select MSN

    @zachary-foster
    zachary-foster committed Apr 9, 2024
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  3. Merge branch 'master' of github.com:grunwaldlab/pathogensurveillance

    @zachary-foster
    zachary-foster committed Apr 9, 2024
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  4. fixed bug when running single sample

    @zachary-foster
    zachary-foster committed Apr 9, 2024
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Commits on Apr 10, 2024

  1. Revised mixed dataset

    Martha Sudermann committed Apr 10, 2024
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  2. revised mixed dataset

    Martha Sudermann committed Apr 10, 2024
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  3. inital support of long reads by cutting into 150mers

    @zachary-foster
    zachary-foster committed Apr 10, 2024
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  4. Merge branch 'master' of github.com:grunwaldlab/pathogensurveillance

    @zachary-foster
    zachary-foster committed Apr 10, 2024
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  5. fixed bug

    @zachary-foster
    zachary-foster committed Apr 10, 2024
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  6. Revise mixed dataset again

    Martha Sudermann committed Apr 10, 2024
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  7. minor

    @zachary-foster
    zachary-foster committed Apr 10, 2024
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  8. Merge branch 'master' of github.com:grunwaldlab/pathogensurveillance

    @zachary-foster
    zachary-foster committed Apr 10, 2024
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  9. starting to add long read support

    @zachary-foster
    zachary-foster committed Apr 10, 2024
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  10. updated main report docker image

    @zachary-foster
    zachary-foster committed Apr 10, 2024
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  11. update main report docker images

    @zachary-foster
    zachary-foster committed Apr 10, 2024
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Commits on Apr 12, 2024

  1. add header to MSN plots

    @zachary-foster
    zachary-foster committed Apr 12, 2024
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  2. change id to fasta

    @ricardoi
    ricardoi committed Apr 12, 2024
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  3. change fasta to buscoid

    @ricardoi
    ricardoi committed Apr 12, 2024
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  4. rtbinder.py to bin

    @ricardoi
    ricardoi committed Apr 12, 2024
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  5. busco binder module

    @ricardoi
    ricardoi committed Apr 12, 2024
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  6. Create boxwood.csv 

    new test dataset 81 fungal isolates
    @cahuparo
    cahuparo authored Apr 12, 2024
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  7. Create fungi_n81.config

    @cahuparo
    cahuparo authored Apr 12, 2024
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  8. Update fungi_n81.config

    @cahuparo
    cahuparo authored Apr 12, 2024
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  9. r2tbinder update $markers

    @ricardoi
    ricardoi committed Apr 12, 2024
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  10. Quick fix to MSN headers. Should be number of samples in snp alignmen… 

    …ts minus 1, to exclude REF in count.
    Martha Sudermann committed Apr 12, 2024
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  11. Remove loading psminer package from local directory

    Martha Sudermann committed Apr 12, 2024
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  12. added flye for genome assembly of long reads

    @zachary-foster
    zachary-foster committed Apr 12, 2024
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  13. added option to change minimum ANI between samples and selected refer… 

    …ences for variant calling
    @zachary-foster
    zachary-foster committed Apr 12, 2024
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  14. Merge branch 'master' of github.com:grunwaldlab/pathogensurveillance

    @zachary-foster
    zachary-foster committed Apr 12, 2024
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Commits on Apr 15, 2024

  1. rt2bin working

    @ricardoi
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Commits on Apr 16, 2024

  1. make temp_dir option apply to SRATOOLS_FASTERQDUMP

    @zachary-foster
    zachary-foster committed Apr 16, 2024
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Commits on Apr 19, 2024

  1. Allows more flexibility in column names from user input data

    Logan Blair committed Apr 19, 2024
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Commits on Apr 20, 2024

  1. change input format for reads; add required reads_type column

    @zachary-foster
    zachary-foster committed Apr 20, 2024
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Commits on Apr 22, 2024

  1. add test dataset for nanopore

    @zachary-foster
    zachary-foster committed Apr 22, 2024
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Commits on Apr 24, 2024

  1. Update mixed_bacteria.config 

    Quick revision to mixed_bacteria config file
    @masudermann
    masudermann authored Apr 24, 2024
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Commits on Apr 25, 2024

  1. add channels to run read2tree

    @zachary-foster
    zachary-foster committed Apr 25, 2024
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Commits on Apr 26, 2024

  1. fix no messages causing report not to render

    @zachary-foster
    zachary-foster committed Apr 26, 2024
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  2. Merge branch 'master' of github.com:grunwaldlab/pathogensurveillance

    @zachary-foster
    zachary-foster committed Apr 26, 2024
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Commits on Apr 30, 2024

  1. Update pathogensurveillance.nf 

    typo: passigned_refs > assigned_refs
    @logankblair
    logankblair authored Apr 30, 2024
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  2. Update assign_group_reference.R 

    fixed error when sample names are all integers
    @logankblair
    logankblair authored Apr 30, 2024
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  3. Update subset_core_gene.R 

    Changed how fractional values were read away from as.integer to as.numeric
    @logankblair
    logankblair authored Apr 30, 2024
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Commits on May 1, 2024

  1. added number of variants used in SNP alignments to report output

    @zachary-foster
    zachary-foster committed May 1, 2024
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Commits on May 2, 2024

  1. split cluster work in progress

    Logan Blair committed May 2, 2024
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  2. test

    Logan Blair committed May 2, 2024
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  3. working on integrating core gene clustering into the rest of the pipl… 

    …eine
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Commits on May 6, 2024

  1. downgraded bakta version to make it work on nanopore data

    @zachary-foster
    zachary-foster committed May 6, 2024
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  2. ignore lab meeting presentations

    @zachary-foster
    zachary-foster committed May 6, 2024
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Commits on May 8, 2024

  1. new clustering method to select core genes

    @zachary-foster
    zachary-foster committed May 8, 2024
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  2. working on integrating clustering of core genes into the rest of the … 

    …pipeline
    @zachary-foster
    zachary-foster committed May 8, 2024
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  3. subsetting of core gene phylgoeny seems to be working

    @zachary-foster
    zachary-foster committed May 8, 2024
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  4. Merge branch 'master' of github.com:grunwaldlab/pathogensurveillance

    @zachary-foster
    zachary-foster committed May 8, 2024
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  5. merge 

    Merge branch 'cluster_core_gene_samples'

# Conflicts:
#	assets/main_report/index.qmd
    @zachary-foster
    zachary-foster committed May 8, 2024
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  6. Update modules.config to include improved PIRATE args

    @cahuparo
    cahuparo authored May 8, 2024
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  7. Update modules.config

    @cahuparo
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Commits on May 9, 2024

  1. added draft code for selecting a representative subset of downloaded … 

    …references
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  2. Merge branch 'master' of github.com:grunwaldlab/pathogensurveillance

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  3. }

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Commits on May 10, 2024

  1. fixes to selecting genera for each family

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  2. read2tree seems to be working

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Commits on May 14, 2024

  1. Update references.bib 

    Updated reference list
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  2. Update references.bib

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  3. Update references.bib

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  1. ?

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  2. merge

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  3. Main report citations

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  1. New citation instructions in readme

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  2. Changed MAFFT conda channel to conda-forge and version to 7.526

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  1. added subsetting for contextual references

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Commits on May 21, 2024

  1. Update mixed.csv 

    Clean up mixed dataset, replace contaminated or non-DNA samples.
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  2. fixed bwa mem failing when there are more than 2 read files for SRA d… 

    …ownloads
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  1. working on making subset references be used instead of all references

    @zachary-foster
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  2. added journal

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  1. Storage improvements

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  1. journal update

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  2. merge

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  1. working on new metadata format

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  1. working on adding reference metadata validation

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  2. Merge branch 'master' of github.com:grunwaldlab/pathogensurveillance

    @zachary-foster
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  3. integrating NCBI queries into the input CSV processing

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  4. updated main report docker container

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  5. midwork

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  6. add unzip to download_assemblies.nf conda environment

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  1. add journal

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  2. add proof of concept docker file for aps workshop

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  3. Merge branch 'master' of github.com:grunwaldlab/pathogensurveillance

    @zachary-foster
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  4. allow reference data to be specified in the sample data CSV

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  5. added code to look up sequence type for accessions with one defined

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  6. added code to validate reference usage columns

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  7. add code to validate the ploidy column

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  1. add defaults for some columns and validate color_by column

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  2. added limits to ncbi_query columns

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  1. added description of new columns to the README

    @zachary-foster
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  2. changed modules.config to publish PREPARE_REPORT_INPUT

    @logankblair
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  3. Create aps.config

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  4. starting to apply changes to input format to workflows

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  1. Update nextflow.config

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  2. working on apply input format changes

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  3. Fix conf file

    @masudermann
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  4. midwork

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  5. trying to get gitpod working

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  6. fix bug from location of check_prior on new nextflow version

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  1. midwork

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  1. midwork

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  2. draft docker container to combine trim-low-abund and sourmash compare

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  1. midwork

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  1. added nanoplot

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Commits on Jun 14, 2024

  1. got assign_mapping_referenece working

    @zachary-foster
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  1. midowrk

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Commits on Jun 20, 2024

  1. make fasterqdump work with storeDir directive

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  1. Change defualt baktadb to light

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  2. add command line option for which baktadb to use

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  1. variant analysis updated

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Commits on Jun 24, 2024

  1. midwork:

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  2. use nf-core/gitpod for workshop

    @zachary-foster
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  1. replace depreciated docker option

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  2. core gene phylogeny subworkflow updated

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  3. working on updating busco analysis

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  4. busco analysis updated

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  5. midwork

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  6. midwork

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  7. add quast back in

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Commits on Jun 26, 2024

  1. preparing inputs for the main report

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  1. midwork

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  2. report input preparation working

    @zachary-foster
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  3. make multiqc output named by report group

    @zachary-foster
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  1. midwork

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  1. fix kingdom parsing and cache bug

    @zachary-foster
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  2. merge

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  3. update out_dir name

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  1. updated all test datasets to new input format

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  1. add xan small outputs to _test_data dir

    @masudermann
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  2. add ramorum output dirs to _test_data

    @masudermann
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  3. updated report outputs

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Commits on Jul 4, 2024

  1. fix metadata file path in config file

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  1. fix error when essages are empty

    @masudermann
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  2. add mycobacteroides test datase to _test_data

    @masudermann
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  3. add xan dataset to _test_data dir

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  4. fix busco r2tf bug

    @zachary-foster
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  5. Merge branch 'dev' of github.com:grunwaldlab/pathogensurveillance int… 

    …o dev
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Commits on Jul 6, 2024

  1. add another test dataset output

    @masudermann
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  2. fix mixed.csv file so basil powdery mildew is genomic dna

    @masudermann
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  3. revise metadata sheet

    @masudermann
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  4. revise mixed bacteria conf file

    @masudermann
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  5. incorporate mixed bacteria dataset

    @masudermann
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Commits on Jul 8, 2024

  1. add mixed_bacteria outputs to _test_data

    @masudermann
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  2. minimal update of report code

    @zachary-foster
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  3. merge

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  4. make report ignore messages when there are none

    @zachary-foster
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  5. Update main_report.nf 

    Add available conda packages
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  6. Update main_report.nf 

    add conda packages line
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  7. minor

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  8. Merge branch 'master' of github.com:grunwaldlab/pathogensurveillance

    @zachary-foster
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Commits on Jul 9, 2024

  1. Update main_report.nf 

    Add ggtree
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  2. Update main_report.nf

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  3. Update index.qmd to include installation of packages not in conda. 

    The module for the main report should have the r packages that are available in conda and anything else included here.
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Commits on Jul 11, 2024

  1. Update busco_download.nf

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Commits on Jul 12, 2024

  1. making changes to track changes in psminer

    @zachary-foster
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  2. making changes to track changes in psminer

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  3. finshed replacing path handling code with psminer functions

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Commits on Jul 15, 2024

  1. update metadata sheets

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  2. add new dir to _test_data

    @masudermann
    masudermann committed Jul 15, 2024
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Commits on Jul 16, 2024

  1. added cache_type option

    @zachary-foster
    zachary-foster committed Jul 16, 2024
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  2. Merge branch 'master' of github.com:grunwaldlab/pathogensurveillance

    @zachary-foster
    zachary-foster committed Jul 16, 2024
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  3. fix error when looking up sequence type 

    issue nf-core#83
    @zachary-foster
    zachary-foster committed Jul 16, 2024
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Commits on Jul 17, 2024

  1. increase SRA download limt

    @zachary-foster
    zachary-foster committed Jul 17, 2024
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  2. Remove limit on number of genomes/reads downloaded 

    resolves nf-core#84
    @zachary-foster
    zachary-foster committed Jul 17, 2024
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  3. dont download SRA reads with very low coverage

    @zachary-foster
    zachary-foster committed Jul 17, 2024
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Commits on Jul 18, 2024

  1. fix NCBI query error caused by 1 vs 0 based indexing

    @zachary-foster
    zachary-foster committed Jul 18, 2024
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  2. Fix bug when ncbi_accession is the only column in input.csv

    @logankblair
    logankblair committed Jul 18, 2024
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Commits on Jul 19, 2024

  1. updates for new psminer plotting

    @zachary-foster
    zachary-foster committed Jul 19, 2024
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  2. Merge branch 'master' of github.com:grunwaldlab/pathogensurveillance

    @zachary-foster
    zachary-foster committed Jul 19, 2024
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  3. add aps nanopore data

    @zachary-foster
    zachary-foster committed Jul 19, 2024
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  4. add aps nanopore data

    @zachary-foster
    zachary-foster committed Jul 19, 2024
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  5. fix aps profile

    @zachary-foster
    zachary-foster committed Jul 19, 2024
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  6. updated SNP tree plotting

    @zachary-foster
    zachary-foster committed Jul 19, 2024
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Commits on Jul 22, 2024

  1. MSN code more updated and mostly working

    @zachary-foster
    zachary-foster committed Jul 22, 2024
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  2. updates

    @zachary-foster
    zachary-foster committed Jul 22, 2024
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  3. improve scaling of zooming plots

    @zachary-foster
    zachary-foster committed Jul 22, 2024
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Commits on Jul 23, 2024

  1. updated status messsage printing

    @zachary-foster
    zachary-foster committed Jul 23, 2024
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  2. Merge branch 'master' of github.com:grunwaldlab/pathogensurveillance

    @zachary-foster
    zachary-foster committed Jul 23, 2024
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  3. ignore rdata

    @zachary-foster
    zachary-foster committed Jul 23, 2024
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  4. ignore rdata

    @zachary-foster
    zachary-foster committed Jul 23, 2024
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  5. Merge branch 'master' of github.com:grunwaldlab/pathogensurveillance

    @zachary-foster
    zachary-foster committed Jul 23, 2024
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  6. remove fungal sample

    @zachary-foster
    zachary-foster committed Jul 23, 2024
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  7. allow bgiseq input

    @zachary-foster
    zachary-foster committed Jul 23, 2024
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Commits on Jul 24, 2024

  1. comment out test paths

    @zachary-foster
    zachary-foster committed Jul 24, 2024
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  2. adding data to workshop docker image

    @zachary-foster
    zachary-foster committed Jul 24, 2024
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  3. update multiqc docker container

    @zachary-foster
    zachary-foster committed Jul 24, 2024
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  4. disable quarto cacheing to avoid permissions error on gitpod

    @zachary-foster
    zachary-foster committed Jul 24, 2024
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  5. trying to fix gitpod error

    @zachary-foster
    zachary-foster committed Jul 24, 2024
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  6. fixing conda erros on gitpod

    @zachary-foster
    zachary-foster committed Jul 24, 2024
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  7. fix mafft conda error on gitpod

    @zachary-foster
    zachary-foster committed Jul 24, 2024
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  8. update conda dependencies for main report

    @zachary-foster
    zachary-foster committed Jul 24, 2024
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Commits on Jul 25, 2024

  1. workshop release

    @zachary-foster
    zachary-foster committed Jul 25, 2024
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  2. add nextflow to gc env

    @zachary-foster
    zachary-foster committed Jul 25, 2024
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  3. typo fix

    @zachary-foster
    zachary-foster committed Jul 25, 2024
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Commits on Jul 27, 2024

  1. reduced dataset size

    @zachary-foster
    zachary-foster committed Jul 27, 2024
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  2. Merge branch 'master' of github.com:grunwaldlab/pathogensurveillance

    @zachary-foster
    zachary-foster committed Jul 27, 2024
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