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Merge Haploflow into master #1015

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Merge Haploflow into master #1015

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Commits on Jul 23, 2021

  1. Use Haploflow instead of IVA

    @CBeelen
    CBeelen committed Jul 23, 2021
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Commits on Jul 30, 2021

  1. Merge branch 'master' into Haploflow to prevent splitting contigs mat… 

    …ches into pieces on the coverage map
    @CBeelen
    CBeelen committed Jul 30, 2021
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Commits on Aug 4, 2021

  1. Read in Haploflow's input arguments

    @CBeelen
    CBeelen committed Aug 4, 2021
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  2. Add debug mode to generate graphs

    @CBeelen
    CBeelen committed Aug 4, 2021
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  3. Correct default error rate

    @CBeelen
    CBeelen committed Aug 4, 2021
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Commits on Aug 9, 2021

  1. Trim and merge contigs after assembly using IVA's tools

    @CBeelen
    CBeelen committed Aug 9, 2021
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Commits on Aug 11, 2021

  1. Add optional scaffolding and patching

    @CBeelen
    CBeelen committed Aug 11, 2021
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  2. Correct contig paths

    @CBeelen
    CBeelen committed Aug 11, 2021
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  3. Handle unsuccessful scaffolding or patching

    @CBeelen
    CBeelen committed Aug 11, 2021
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  4. Better handle unsuccessful scaffolding or patching

    @CBeelen
    CBeelen committed Aug 11, 2021
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Commits on Aug 12, 2021

  1. Correct nucmer options

    @CBeelen
    CBeelen committed Aug 12, 2021
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  2. Add option for a second try at assembly with filtered reads

    @CBeelen
    CBeelen committed Aug 12, 2021
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Commits on Aug 18, 2021

  1. Merge newest changes in master, and resolve conflicts

    @CBeelen
    CBeelen committed Aug 18, 2021
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Commits on Aug 19, 2021

  1. Use information from remap.csv to separate reads

    @CBeelen
    CBeelen committed Aug 19, 2021
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  2. Correct filename

    @CBeelen
    CBeelen committed Aug 19, 2021
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Commits on Sep 1, 2021

  1. Add option for IVA assembly and modify scaffolding parameters

    @CBeelen
    CBeelen committed Sep 1, 2021
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Commits on Sep 27, 2021

  1. Merge branch 'whole-genome-consensus' into Haploflow to create whole-… 

    …genome consensus for result
    @CBeelen
    CBeelen committed Sep 27, 2021
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Commits on Sep 28, 2021

  1. Merge branch 'whole-genome-consensus' into Haploflow

    @CBeelen
    CBeelen committed Sep 28, 2021
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Commits on Sep 29, 2021

  1. Merge branch 'whole-genome-consensus' into Haploflow

    @CBeelen
    CBeelen committed Sep 29, 2021
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  2. Merge branch 'whole-genome-consensus' into Haploflow

    @CBeelen
    CBeelen committed Sep 29, 2021
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Commits on Oct 14, 2021

  1. Merge branch 'whole-genome-consensus' into Haploflow

    @CBeelen
    CBeelen committed Oct 14, 2021
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Commits on Oct 20, 2021

  1. Merge branch 'master' into Haploflow

    @CBeelen
    CBeelen committed Oct 20, 2021
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Commits on Nov 1, 2021

  1. Merge branch 'master' into Haploflow

    @CBeelen
    CBeelen committed Nov 1, 2021
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Commits on Nov 3, 2021

  1. Merge branch 'master' into Haploflow

    @CBeelen
    CBeelen committed Nov 3, 2021
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Commits on Nov 18, 2021

  1. Merge branch 'Consensus_insertions' into Haploflow

    @CBeelen
    CBeelen committed Nov 18, 2021
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Commits on Nov 19, 2021

  1. Merge branch 'Consensus_insertions' into Haploflow

    @CBeelen
    CBeelen committed Nov 19, 2021
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Commits on Nov 20, 2021

  1. Merge branch 'Consensus_insertions' into Haploflow

    @CBeelen
    CBeelen committed Nov 20, 2021
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Commits on Dec 2, 2021

  1. Merge branch 'Consensus_insertions' into Haploflow

    @CBeelen
    CBeelen committed Dec 2, 2021
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Commits on Dec 3, 2021

  1. Merge branch 'Consensus_insertions' into Haploflow

    @CBeelen
    CBeelen committed Dec 3, 2021
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Commits on Dec 9, 2021

  1. Merge branch 'Consensus_insertions' into Haploflow

    @CBeelen
    CBeelen committed Dec 9, 2021
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Commits on Dec 10, 2021

  1. Merge branch 'Consensus_insertions' into Haploflow

    @CBeelen
    CBeelen committed Dec 10, 2021
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Commits on Jan 15, 2022

  1. Merge branch 'master' into Haploflow

    @CBeelen
    CBeelen committed Jan 15, 2022
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Commits on Feb 4, 2022

  1. Merge branch 'master' into Haploflow

    @CBeelen
    CBeelen committed Feb 4, 2022
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Commits on Mar 17, 2022

  1. Merge branch 'master' into Haploflow

    @CBeelen
    CBeelen committed Mar 17, 2022
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Commits on Jun 7, 2022

  1. Merge branch 'master' into Haploflow

    @CBeelen
    CBeelen committed Jun 7, 2022
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Commits on Sep 15, 2023

  1. Merge branch 'master' into Haploflow

    @Donaim
    Donaim committed Sep 15, 2023
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Commits on Sep 19, 2023

  1. Install Haploflow during docker initialization

    @Donaim
    Donaim committed Sep 19, 2023
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  2. Install Haploflow on CI

    @Donaim
    Donaim committed Sep 19, 2023
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  3. Pin exact Haploflow version 

    Note that I am using a specific commit version for pinning.
Rationalization:

Haploflow is not developed actively, and because of that,
the last release is quite far behind master.

Thus, I think it's better to pin its version to the current master
than to the latest release tag.
    @Donaim
    Donaim committed Sep 19, 2023
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Commits on Sep 20, 2023

  1. Switch to Debian in Singularity image

    @Donaim
    Donaim committed Sep 20, 2023
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Commits on Sep 25, 2023

  1. Merge branch 'master' into Haploflow-test1

    @Donaim
    Donaim committed Sep 25, 2023
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