Code

Wrap-up version 3.2.0#73

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Merged

fmalmeida merged 169 commits intomasterfmalmeida/MpGAP:masterfrom devfmalmeida/MpGAP:devCopy head branch name to clipboardMar 6, 2024

+1,980,252-120,348

Commits

Commits on May 10, 2023

• add illumina docker test (#44)

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• Update github actions for testing profiles (#46)

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Commits on May 18, 2023

• 30 change to unicycler v050 (#45)

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• 31 new directory called final output (#48)

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Commits on May 19, 2023

• 22 add polypolish tool (#49)

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Commits on Oct 7, 2023

• include citation information (#51)

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• Update README.md

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Commits on Oct 29, 2023

• raven does not have --weaken parameter anymore

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• allow users to change -k and -w

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• added high_quality_longreads parameter

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• add defaults for high quality reads

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• added high-quality definition for assemblers that allow it

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Commits on Oct 30, 2023

• update medaka version

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• update docker image version

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Commits on Oct 31, 2023

• update max_memory default

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Commits on Nov 4, 2023

• fixed if else statemens

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• update docker image

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• fix flye module

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Commits on Nov 10, 2023

• Add Citation

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• Add Citation

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Commits on Nov 11, 2023

• Update .readthedocs.yml

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• Update .readthedocs.yml

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• Update requirements.txt

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Commits on Nov 20, 2023

• Merge branch 'master' of https://github.com/fmalmeida/MpGAP

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• Merge branch 'master' of https://github.com/fmalmeida/MpGAP

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Commits on Dec 24, 2023

• Saving code that was wrongly merged to master instead of dev (#56)

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Commits on Dec 28, 2023

• fix input definition

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Commits on Jan 25, 2024

• update readthedocs yml

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• add mkdocs yml

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• add examples from ngs-preprocess pipeline

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• fix image link

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• updated index page

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• update colors

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• update installation page

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• update quickstart page

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• fix indentations

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• fix block indentation

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• update configs page

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• reorganize docs assets

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• start converting manual page

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• update manual page

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• increase size of table cell

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• remove unused examples.md

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• update samplesheet page

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Commits on Jan 27, 2024

• fix code block

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• update non-bacterial dataset example

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• update outputs.md page

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• trying out including example reports

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• first update on page (needs data rerun)

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• update non bacteria dataset command

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Commits on Feb 1, 2024

• fix indentation and typos

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Commits on Feb 12, 2024

• Merge branch 'dev' of https://github.com/fmalmeida/MpGAP into 58-add-example-of-non-bacterial-dataset-analysis-paper-review

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• Update changelog

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Commits on Feb 13, 2024

• update docs output overview and generated files

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• update page

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• add mention of polypolish in documentation

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• also run hybrid tests on dev PRs

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• hybid test uses pacbio

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• add missing parameter to schema

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• fix IDs of hybrid workflow

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• Merge pull request #62 from fmalmeida/58-add-example-of-non-bacterial-dataset-analysis-paper-review

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• Merge branch 'dev' of https://github.com/fmalmeida/MpGAP into 52-incomplete-pipeline-and-different-errors-when-using-nanopore-reads-files-with-different-sizes-900-mb-vs-11gb

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• fix error message

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• delete empty line

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• adjust tuple when hybrid strategy is both

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Commits on Feb 14, 2024

• skip haslr and singularity runs

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• Update test_pr_hybrid_docker.yml

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Commits on Feb 15, 2024

• add a checker to YAML samplesheet to prohibit use of corrected_longreads and high_quality_longreads at the same time for the same sample.

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• add def statements

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Commits on Feb 16, 2024

• add explanation of parameter in docs

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• Merge pull request #63 from fmalmeida/52-incomplete-pipeline-and-different-errors-when-using-nanopore-reads-files-with-different-sizes-900-mb-vs-11gb

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• change multiqc resource label

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• add new start_asm resources parameter and update defaults

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• update default resources for modules without labels, modify assembly modules to use newly added parameters and add function to parse resources for quast based on them.

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• fix order of inclusion

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• fix quast resources function

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• add explanation of parameter in documentation

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• add parameter in nextflow schema and update defaults

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• update changelog

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• also wrap-up 1st attempt in check_max function to avoid requesting more than what is allowed

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• update docs/assets

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• Merge pull request #64 from fmalmeida/61-add-a-simple-parameter-to-handle-starting-memory-settings

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• update docker to download latest busco datasets

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• add ignore on SAM/BAM files

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• update shasum

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Commits on Feb 17, 2024

• add busco instead of quast-busco

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• fix quast mem/cpus variable

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• update param description

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• update how busco params default is handled

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• pre-download busco db

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• update docker image

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• define automatic busco lineage control

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• add param to nextflow schema

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• add parameter in documentation

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• add BUSCO in tools listing

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• fix mqc module

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Commits on Feb 18, 2024

• add new parameter for skipping pilon or polypolish

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• add a checker to have at least one sreads polisher if running hb strategy 2

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Commits on Feb 23, 2024

• quast values are not params

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• added code to generate template samplesheet for bacannot

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• fix BUSCO samplenames

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• Update environment.yml

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• generate a versions.yml for all modules

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• fix indentation

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• include generation of versions yml

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• add lines to avoid saving versions.yml files

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• all modules use my image

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• Update test.config

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Commits on Feb 24, 2024

• fixed execution of versions file generation

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• added a proper configuration for new MultiQC

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Commits on Feb 25, 2024

• Update manual.md

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• Update nextflow.config

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• Update nextflow.config

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• Update CHANGELOG.md

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• Merge pull request #65 from fmalmeida/50-add-skip-parameter-for-sreads-polishers-and-fix-multiqc-report-names

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Commits on Feb 26, 2024

• Merge branch 'dev' of https://github.com/fmalmeida/MpGAP into 66-add-automatic-samplesheet-for-bacannot

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• re-organize configuration

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• fix container definitions

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• all use the same container

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• fix docker image

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• standardize quotation

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• update changelog

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Commits on Feb 27, 2024

• <add lines for incorporating hifiasm>

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• Merge branch 'dev' of https://github.com/fmalmeida/MpGAP into add-hifiasm-assembler

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• update docker image

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• fix module path

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• update output examples in documentation

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• add hifi testing case

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• fix container for all modules

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• skip hifiasm for non-hifi tests

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• add new testing workflow

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• min for canu

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• add def statement

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• Merge pull request #69 from fmalmeida/66-add-automatic-samplesheet-for-bacannot

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• Merge branch 'dev' of https://github.com/fmalmeida/MpGAP into add-hifiasm-assembler

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• update changelog

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• github actions cannot tun hifi (not enough mem)

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Commits on Feb 28, 2024

• add information of new tool in docs

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• Merge pull request #70 from scintilla9/add-hifiasm-assembler

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• add checker for haslr outputs

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• add checker for hifiasm outputs

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• manually build haslr

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• fix haslr installation

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Commits on Feb 29, 2024

• fixed docker image building order

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• update dockerfile and correct tool path

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• update custom error messages indentations

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• only execute hifiasm when reads are corrected or high quality

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• fix if else checker

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• fix if else

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Commits on Mar 2, 2024

• update module to have a single main script for any profile

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• update image download info

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• update changelog

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• Merge branch 'master' of https://github.com/fmalmeida/MpGAP into dev

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• fix quast resources parser

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• fix indentation

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Commits on Mar 3, 2024

• include new parameter to manage quast&busco databases

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• fix function so objects have always the correct class

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Commits on Mar 4, 2024

• add singularity runOptions to make it proper solve SIF images from docker

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Commits on Mar 5, 2024

• whitelist SINGULARITY_TMPDIR tmpdir

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• Merge branch 'dev' of https://github.com/fmalmeida/MpGAP into dev

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• add TODO

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Commits on Mar 6, 2024

• use correct image

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• fix permissions in medaka

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• use it locally to avoid problems with singularity

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• update docs assets aspergillus example results

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• update command used in example

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• is singularity git actions working?

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• update docs on singularity

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• Update CHANGELOG.md

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