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This should bring in the current status of the pipeline - A brave new world! #128

Merged
merged 123 commits into from
Jun 14, 2023
Merged

This should bring in the current status of the pipeline - A brave new world! #128

merged 123 commits into from
Jun 14, 2023

Commits on Mar 25, 2021

  1. Template update for nf-core/tools version 1.13.3

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Commits on May 11, 2021

  1. Template update for nf-core/tools version 1.14

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Commits on Jul 13, 2021

  1. Template update for nf-core/tools version 2.0

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  2. Template update for nf-core/tools version 2.0.1

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Commits on Jul 27, 2021

  1. Template update for nf-core/tools version 2.1

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Commits on Dec 14, 2021

  1. Template update for nf-core/tools version 2.2

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Commits on Mar 15, 2022

  1. Template update for nf-core/tools version 2.3

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Commits on Mar 23, 2022

  1. Template update for nf-core/tools version 2.3.1

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Commits on Mar 24, 2022

  1. Template update for nf-core/tools version 2.3.2

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Commits on May 16, 2022

  1. Template update for nf-core/tools version 2.4

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Commits on Aug 30, 2022

  1. Template update for nf-core/tools version 2.5

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Commits on Sep 1, 2022

  1. Template update for nf-core/tools version 2.5.1

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Commits on Oct 4, 2022

  1. Template update for nf-core/tools version 2.6

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Commits on Dec 8, 2022

  1. Template update for nf-core/tools version 2.7.1

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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 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 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. better channel magic for seqwish input

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  3. SMOOTHXG enganged!

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  4. SMOOTHXG schema

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Commits on Mar 6, 2023

  1. fix CI

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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 27, 2023

  1. ODGI_VIZ engange!

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  2. ODGI_LAYOUT ODGI_DRAW engange!

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  3. 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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    subwaystation and FriederikeHanssen committed Mar 28, 2023
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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. 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. add some contributors

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  2. prettier!

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  3. add parameter --smoothxg_poa_cpus

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  4. collect all versions of all tools

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

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  6. address review

    @subwaystation
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  7. fix bug2

    @subwaystation
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  8. address review

    @subwaystation
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  9. fix hardcoded pggb versions in local modules

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  10. address last review comments2

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  11. citation skeleton

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  12. prettier

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  13. 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
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  3. minor README additions

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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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    subwaystation committed Apr 20, 2023
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  4. nextflow_schema: smoothxg

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    subwaystation committed Apr 20, 2023
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  5. nextflow_schema: vcf-spec, communities

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    subwaystation committed Apr 20, 2023
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  6. nextflow_schema.json add hidden parameters

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    subwaystation committed Apr 20, 2023
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Commits on Apr 28, 2023

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

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    nf-core-bot committed Apr 28, 2023
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Commits on May 11, 2023

  1. test merge

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    subwaystation committed May 11, 2023
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Commits on May 12, 2023

  1. hopefully fixed the issues

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    subwaystation committed May 12, 2023
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  2. fix modules

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    subwaystation committed May 12, 2023
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Commits on May 15, 2023

  1. update hla.config to better match reality

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    subwaystation committed May 15, 2023
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Commits on May 16, 2023

  1. fix sparse bug

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    subwaystation committed May 16, 2023
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  2. update

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    subwaystation committed May 16, 2023
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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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    subwaystation committed May 17, 2023
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  2. update odgi/draw

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    subwaystation committed May 17, 2023
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Commits on Jun 14, 2023

  1. name clear output folders: FINAL_GFA, FINAL_ODGI

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    subwaystation committed Jun 14, 2023
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  2. merge dev

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    subwaystation committed Jun 14, 2023
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