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1.0.0 - Ratzupaltuff #135

Merged
merged 534 commits into from
Aug 1, 2023
Merged

1.0.0 - Ratzupaltuff #135

merged 534 commits into from
Aug 1, 2023
This pull request is big! We’re only showing the most recent 250 commits.

Commits on Dec 14, 2022

  1. HOLIDAYgit add subworkflows/*!

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  2. let's cheat

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  3. hmm

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  4. fix fai,gzi paths

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  5. remove unecessary .view()

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  6. fix vg_deconstruct issues

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  7. text communities and a more recent NXFv

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  8. EOL

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  9. remove dangling .view()

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  10. update test parameters for faster runtime

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  11. update test parameters for faster runtime

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Commits on Dec 15, 2022

  1. test new CI setup

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  2. maybe we can't go latest

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  3. la vie est fantastique

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  4. we want the matrix across parameters

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  5. force older Nextflow version

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  6. squeeze it!

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  7. fix --wfmash_only bug

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  8. subworkflow squeeze is ready :)

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  9. update help text and online parameter docs

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  10. Merge pull request #105 from nf-core/community 

    Community
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  11. Merge pull request #28 from nf-core/dev 

    Community update
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Commits on Dec 16, 2022

  1. we have to copy the new python files

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  2. typo [skip ci]

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  3. Merge pull request #29 from nf-core/dev 

    Update from Upstream
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  4. Update README.md

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  5. Merge pull request #30 from nf-core/dev 

    Update README.md
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Commits on Dec 19, 2022

  1. Template update for nf-core/tools version 2.7.2

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Commits on Jan 3, 2023

  1. enable trace.overwrite

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  2. update pggb docker image

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  3. Merge pull request #107 from nf-core/update_pggb 

    update pggb docker image
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  4. Merge pull request #32 from nf-core/dev 

    Update from upstream
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Commits on Jan 11, 2023

  1. the pipeline now works with all NXF versions

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  2. update README, ci

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  3. don't cheat in our tests

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  4. Merge pull request #108 from nf-core/update_pggb 

    the pipeline now works with all NXF versions
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  5. Merge pull request #33 from nf-core/dev 

    Update from upstream
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Commits on Jan 16, 2023

  1. draw 1D uncalled viz

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  2. Merge pull request #109 from nf-core/update_pggb 

    draw 1D uncalled viz
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  3. Merge pull request #35 from nf-core/dev 

    Update from upstream
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Commits on Jan 24, 2023

  1. Update README.md [no ci]

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Commits on Jan 26, 2023

  1. process odgiLayout gets publishDir option

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  2. Merge branch 'dev' of https://github.com/nf-core/pangenome into dev

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Commits on Feb 16, 2023

  1. update pggb docker

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  2. smoothxg's xpoa interface changed

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  3. Merge pull request #112 from nf-core/update_pggb 

    update pggb docker
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  4. update native_image.sh [skip ci]

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  5. Merge branch 'dev' of https://github.com/nf-core/pangenome into dev

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  6. update native_image.sh [skip ci]

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  7. Merge pull request #36 from nf-core/dev 

    update from upstream
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Commits on Feb 22, 2023

  1. update pggb

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  2. Merge pull request #113 from nf-core/update_pggb 

    update pggb
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Commits on Feb 23, 2023

  1. TEMPLATE ENGAGED!

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  2. multiqc_config.yml is ready

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  3. add intermediate test data to assets

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Commits on Feb 24, 2023

  1. remove module FASTQC

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  2. deactivate unneeded igenomes code

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  3. switch to FASTA input

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  4. grudgingly leaving in some reference genome options

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  5. removed everything igenomes related

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  6. remove unused samplesheet files and code

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  7. TABIX_BGZIP

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  8. SAMTOOLS_FAIDX

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  9. WFMASH SKELETON

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Commits on Feb 27, 2023

  1. wfmash prototype working!

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  2. update wfmash module to fix the tag issue

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Commits on Feb 28, 2023

  1. fix issue with dangling B character

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  2. Merge branch 'dev' of https://github.com/nf-core/pangenome into dev

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Commits on Mar 1, 2023

  1. adding wfmash parameters to modules.config

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  2. add wfmash parameters to schema

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Commits on Mar 2, 2023

  1. add file logic to input_check.nf

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  2. INPUT_CHECK ready!

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  3. pggb subworkflow enganged!

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  4. make a seq wish

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Commits on Mar 3, 2023

  1. seqwish prefix

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  2. speed up communities

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  3. better channel magic for seqwish input

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  4. SMOOTHXG enganged!

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  5. SMOOTHXG schema

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Commits on Mar 6, 2023

  1. fix CI

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Commits on Mar 7, 2023

  1. update Dockerfile to match most recent pggb updates

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  2. Merge pull request #116 from nf-core/update_pggb 

    update Dockerfile to match most recent pggb updates
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  3. Merge pull request #37 from nf-core/dev 

    update from upstream
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Commits on Mar 8, 2023

  1. GFAFFIX enganged!

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  2. ODGI_BUILD engange!

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  3. ODGI_UNCHOP engange!

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  4. update modules

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Commits on Mar 21, 2023

  1. PGGB:GFAFFIX enganged!

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  2. ODIG_STATS engage!

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Commits on Mar 24, 2023

  1. update pggb docker image

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  2. Merge pull request #118 from nf-core/update_pggb 

    update pggb docker image
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Commits on Mar 27, 2023

  1. update pggb gfaffix

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  2. Merge pull request #119 from nf-core/update_pggb 

    update pggb gfaffix
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  3. ODGI_VIZ engange!

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  4. ODGI_LAYOUT ODGI_DRAW engange!

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  5. WFMASH_MAP SPLIT_APPROX_MAPPINGS_IN_CHUNKS WFMASH_ALIGN

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Commits on Mar 28, 2023

  1. update WFMASH

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  2. parallelize WFMASH across nodes: engange!

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  3. skip SMOOTHXG engange!

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  4. Update conf/modules.config 

    Co-authored-by: FriederikeHanssen <Friederike.hanssen@qbic.uni-tuebingen.de>
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  5. Update conf/modules.config 

    Co-authored-by: FriederikeHanssen <Friederike.hanssen@qbic.uni-tuebingen.de>
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  6. Update conf/modules.config 

    Co-authored-by: FriederikeHanssen <Friederike.hanssen@qbic.uni-tuebingen.de>
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  7. Update conf/modules.config 

    Co-authored-by: FriederikeHanssen <Friederike.hanssen@qbic.uni-tuebingen.de>
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  8. address review

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  9. update schema

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  10. Update conf/modules.config 

    Co-authored-by: FriederikeHanssen <Friederike.hanssen@qbic.uni-tuebingen.de>
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  11. shorten ext.args where applicable

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  12. VG_DECONSTRUCT engage!

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Commits on Mar 29, 2023

  1. enable VG_DECONSTRUCT tests

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  2. prettier

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  3. more tests

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  4. prettier

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  5. beautify modules.config

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  6. intelligible VG_DECONSTRUCT

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  7. VG_DECONSTRUCT is flexible

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  8. COMMUNITY in progress

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Commits on Mar 30, 2023

  1. fix CI

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  2. fix CI

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Commits on Apr 5, 2023

  1. NET2COMMUNITIES + EXTRACT_COMMUNITIES engange!

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  2. Update README.md

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  3. update help message to reflect mandatory argument

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  4. COMMUNITY engange!

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Commits on Apr 11, 2023

  1. moved graph quality control into its own subworkflow

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  2. fix wfmash_only

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  3. fix --wfmash_chunks --communities

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Commits on Apr 13, 2023

  1. rework ODGI_QC

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  2. fix --wfmash_only bug

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  3. MULTIQC_COMMUNITY ready

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  4. add community test

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  5. now I deserve a Radler

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  6. ODGI_VIEW --communities engage!

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  7. update odgi/squeeze

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Commits on Apr 14, 2023

  1. update CI

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  2. typo

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  3. --communities --vcf_spec engange!

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  4. update SMOOTHXG to v0.7.0

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  5. update SMOOTXG POA parameters

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  6. ignore igenomes

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Commits on Apr 17, 2023

  1. try to fix some linting issues

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  2. add some contributors

    @subwaystation
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  3. prettier!

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  4. add parameter --smoothxg_poa_cpus

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  5. collect all versions of all tools

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  6. address Rike's suggestion to remove System.exit(1)

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  7. address review

    @subwaystation
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  8. fix bug2

    @subwaystation
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  9. address review

    @subwaystation
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  10. fix hardcoded pggb versions in local modules

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  11. address last review comments2

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  12. citation skeleton

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  13. prettier

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  14. update README

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Commits on Apr 19, 2023

  1. add citations for all pipeline tools

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  2. update README.md

    @subwaystation
    subwaystation committed Apr 19, 2023
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  3. minor README additions

    @subwaystation
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  4. update schema

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Commits on Apr 20, 2023

  1. update SEQWISH and WFMASH

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  2. nextflow_schema: wfmash

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  3. nextflow_schema: seqwish

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  4. nextflow_schema: smoothxg

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  5. nextflow_schema: vcf-spec, communities

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  6. nextflow_schema.json add hidden parameters

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Commits on Apr 28, 2023

  1. Template update for nf-core/tools version 2.8

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Commits on May 11, 2023

  1. update pggb Dockerfile

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  2. test merge

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Commits on May 12, 2023

  1. hopefully fixed the issues

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  2. Merge pull request #125 from nf-core/update_pggb 

    update pggb Dockerfile
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  3. fix modules

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Commits on May 15, 2023

  1. update hla.config to better match reality

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Commits on May 16, 2023

  1. fix sparse bug

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  2. update

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Commits on May 17, 2023

  1. graph and layout for odgi draw now match by meta:id

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  2. update odgi/draw

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Commits on Jun 14, 2023

  1. name clear output folders: FINAL_GFA, FINAL_ODGI

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  2. this is a risky situation

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  3. cleanup

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  4. merge dev

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  5. Merge pull request #128 from nf-core/a_brave_new_world 

    This should bring in the current status of the pipeline - A brave new world!
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Commits on Jun 15, 2023

  1. update CITATIONS.md [skip ci]

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  2. Update README.md

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  3. Update README.md [skip ci]

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  4. Update README.md [skip ci]

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  5. update usage.md [skip ci]

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  6. Merge branch 'dev' of https://github.com/nf-core/pangenome into dev

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  7. remove unused fastqc module [skip ci]

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  8. prettier usage.md

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  9. fix samtools_faidx output path2 

    2
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  10. output.md skeleton

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Commits on Jun 16, 2023

  1. add Leiden citation

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  2. step by step getting closer to you

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  3. output until wfmash

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Commits on Jun 19, 2023

  1. Update README.md [skip ci]

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  2. Update CITATIONS.md [skip ci]

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  3. gimme more

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Commits on Jun 20, 2023

  1. weiter, weiter

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  2. more dogs

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  3. prettier than barbie

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  4. playing around

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  5. Merge branch 'dev' into output.md

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  6. merge dev and be pretty

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  7. Merge pull request #129 from nf-core/output.md 

    Output Documentation
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Commits on Jun 21, 2023

  1. delete unused samplesheet files

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  2. Merge pull request #130 from nf-core/sample_sheet 

    delete unused samplesheet files
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  3. configure aws full scale test

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  4. Merge pull request #131 from nf-core/aws_large_scale_test 

    configure aws full scale test
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  5. update EXTRACT_COMMUNITIES module

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  6. remove TODOs

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  7. update README

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  8. Merge pull request #133 from nf-core/prep_1.0.0 

    remove TODOs
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  9. prepare 1.0.0 release

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  10. Merge pull request #134 from subwaystation/dev 

    prepare 1.0.0 release
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  11. Update conf/test_full.config 

    Co-authored-by: Maxime U Garcia <maxime.garcia@seqera.io>
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  12. Update modules/local/split_approx_mappings_in_chunks/main.nf 

    Co-authored-by: Maxime U Garcia <maxime.garcia@seqera.io>
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  13. Update modules/local/multiqc_community/main.nf 

    Co-authored-by: Maxime U Garcia <maxime.garcia@seqera.io>
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    subwaystation and maxulysse committed Jun 21, 2023
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  14. fix registry entries

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  15. fix text alignments

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  16. Update modules/local/net2communities/main.nf 

    Co-authored-by: Maxime U Garcia <maxime.garcia@seqera.io>
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    subwaystation and maxulysse committed Jun 21, 2023
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  17. fix module paths

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  18. remove black logo

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  19. add workflow source and update PNG

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  20. add missing logo

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  21. try Maxime's trick

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    subwaystation committed Jun 21, 2023
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  22. pangenome!

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    subwaystation committed Jun 21, 2023
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  23. WRONG BRANCH

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    subwaystation committed Jun 21, 2023
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  24. try Maxime's trick

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    subwaystation committed Jun 21, 2023
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Commits on Jun 23, 2023

  1. update vg_deconstruct container

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    subwaystation committed Jun 23, 2023
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Commits on Jun 26, 2023

  1. update local modules to pggb:0.5.4

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    subwaystation committed Jun 26, 2023
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  2. Update modules/local/net2communities/main.nf 

    Co-authored-by: Maxime U Garcia <maxime.garcia@seqera.io>
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    subwaystation and maxulysse committed Jun 26, 2023
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  3. Update modules/local/split_approx_mappings_in_chunks/main.nf 

    Co-authored-by: Maxime U Garcia <maxime.garcia@seqera.io>
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    subwaystation and maxulysse committed Jun 26, 2023
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  4. remove quay.io from modules

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    subwaystation committed Jun 26, 2023
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  5. Update nextflow_schema.json 

    Co-authored-by: Maxime U Garcia <maxime.garcia@seqera.io>
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    subwaystation and maxulysse committed Jun 26, 2023
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  6. Update nextflow_schema.json 

    Co-authored-by: Maxime U Garcia <maxime.garcia@seqera.io>
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    subwaystation and maxulysse committed Jun 26, 2023
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  7. Update nextflow_schema.json 

    Co-authored-by: Maxime U Garcia <maxime.garcia@seqera.io>
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    subwaystation and maxulysse committed Jun 26, 2023
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  8. Update nextflow_schema.json 

    Co-authored-by: Maxime U Garcia <maxime.garcia@seqera.io>
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    subwaystation and maxulysse committed Jun 26, 2023
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  9. Update nextflow_schema.json 

    Co-authored-by: Maxime U Garcia <maxime.garcia@seqera.io>
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    subwaystation and maxulysse committed Jun 26, 2023
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  10. Update nextflow_schema.json 

    Co-authored-by: Maxime U Garcia <maxime.garcia@seqera.io>
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    subwaystation and maxulysse committed Jun 26, 2023
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  11. Update nextflow_schema.json 

    Co-authored-by: Maxime U Garcia <maxime.garcia@seqera.io>
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    subwaystation and maxulysse committed Jun 26, 2023
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Commits on Jun 27, 2023

  1. update wfmash v0.10.4

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    subwaystation committed Jun 27, 2023
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Commits on Jun 28, 2023

  1. fix ODGI_QC reporting issue in non-community-mode

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    subwaystation committed Jun 28, 2023
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  2. remove .view()

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    subwaystation committed Jun 28, 2023
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Commits on Jun 30, 2023

  1. Template update for nf-core/tools version 2.9

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    nf-core-bot committed Jun 30, 2023
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Commits on Jul 3, 2023

  1. merge template v2.9.0

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    subwaystation committed Jul 3, 2023
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  2. correct for TEMPLATE issues

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    subwaystation committed Jul 3, 2023
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  3. please be fixed2

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    subwaystation committed Jul 3, 2023
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  4. fix mandatory NXF version

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    subwaystation committed Jul 3, 2023
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  5. Merge pull request #136 from nf-core/nf-core-template-merge-2.9 

    Important! Template update for nf-core/tools v2.9
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    subwaystation committed Jul 3, 2023
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Commits on Jul 17, 2023

  1. address review by @heuermh

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    subwaystation committed Jul 17, 2023
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Commits on Jul 18, 2023

  1. address missing docs for MultiQC output

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    subwaystation committed Jul 18, 2023
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Commits on Jul 19, 2023

  1. Update README.md 

    Co-authored-by: Michael L Heuer <heuermh@acm.org>
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    subwaystation and heuermh committed Jul 19, 2023
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  2. update affiliations

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    subwaystation committed Jul 19, 2023
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