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Refactor POC#188

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adamrtalbot merged 220 commits intodevnf-core/fetchngs:devfrom refactornf-core/fetchngs:refactorCopy head branch name to clipboardOct 18, 2023

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Commits on Aug 23, 2023

• remove public aws ecr profile

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• split up config files to be more modular

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• Merge pull request #185 from maxulysse/remove_public_aws_ecr

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• no cascade inclusion of config files

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• use schema_ignore_params to remove warnings

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• fix lint

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Commits on Aug 24, 2023

• Adds emit statement for FASTQs and metadata to SRA workflow

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• Update nextflow.config

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• remove if statement

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• Merge pull request #187 from maxulysse/fix_tests

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• Add emit statement to synpase workflow

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• Update CHANGELOG.md

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• Merge pull request #184 from adamrtalbot/emit_statement_to_SRA_workflow

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• Merge pull request #186 from maxulysse/split_configs

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• move out multiqc and versions

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• enable tests in refactor

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• Apply suggestions from code review

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• Apply suggestions from code review

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• fix syntax

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• Merge pull request #189 from maxulysse/move_things

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Commits on Aug 25, 2023

• small refactor

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• staging

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• validate input in main.nf

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• use error

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• Merge pull request #190 from maxulysse/better_syntax

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• Merge branch 'refactor' into better_tests

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• use workflow testing

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• update snapshot

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• restore versions

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• update workflow

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• update snapshot

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• just one id to test

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• one emit statement at a time

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• polish

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• update snapshot

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• disable autosort channel

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• update snapshot

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Commits on Aug 28, 2023

• order

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• update test and snapshots

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• update test

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• update tests and snapshot

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• update snapshot

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• update test

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• need to update snapshot

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• add nextflow.log to test output when failures

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• add nextflow.log to test output when failures

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Commits on Aug 29, 2023

• Merge pull request #191 from maxulysse/better_tests

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Commits on Sep 11, 2023

• test rc

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• re-able autoSort

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• add .nf-test.log to gitignore

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• simplify tests

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• update snapshot

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• update snapshot

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• relative path

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• update tests and snapshot

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Commits on Sep 12, 2023

• Merge pull request #192 from maxulysse/fix_test

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• implement changes in GHA CI

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• add tags

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• fix path to tags

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• rename files

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• add tests to tags

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• alphabetical order

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• add modules to changes

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• Merge pull request #193 from maxulysse/check_changes

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Commits on Sep 18, 2023

• Remove public_aws_ecr profile

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• Replace large config file with individual configs per module

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• Inherit Synapse related configuration via separate files

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• Revert switch for inheritance of correct config

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• Handle custom/dumpsoftwareversions via config

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• Update multiqc to v1.15

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• Use switch statement to avoid nested if-else

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• Moved workflows configuration to workflows/nextflow.config

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• Addition of subworkflow specific configuration file

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• Add empty config for sratoolsncbisettings to make it consistent

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• CHANGELOG

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• Update change tags

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Commits on Sep 20, 2023

• Merge pull request #195 from adamrtalbot/inherit_configs_recursively

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Commits on Sep 21, 2023

• Merge branch 'dev' into refactor

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• Merge pull request #198 from maxulysse/only_refactor

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• restore nf-test tests for sra workflow

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• restore module tests

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• restore CI

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• forgot some files

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Commits on Sep 22, 2023

• fix NXF_VER

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• Delete .github/tags.yml

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• fix linting

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• Delete conf/modules/base.config

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• Apply suggestions from code review

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• Merge branch 'refactor' into nf-test

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• restore file

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• do some tests

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• 2 *

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• Merge pull request #200 from maxulysse/nf-test

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• forgot this file

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• Merge pull request #202 from maxulysse/test_data

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• fix path to file to include and update snapshots

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• Merge pull request #203 from maxulysse/nf-test

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• use initialise subworkflows

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• Merge branch 'dev' into refactor

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Commits on Sep 25, 2023

• Merge branch 'nf-core:refactor' into refactor

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• Merge branch 'dev' into refactor

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• code polish

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• more code polish

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• params

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• more code polish

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• typo

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• Apply suggestions from code review

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• use initialise subworkflows

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• move scripts

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• no need to test on push on dev, pr are enough

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• more code polish

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• code polish

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• more code polish

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• params

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• more code polish

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• typo

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• use rc2

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• regenerate tests and snapshots

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• Apply suggestions from code review

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• Merge branch 'refactor' into nf-test

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• final code polish

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• Merge branch 'refactor' into nf-test

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• Apply suggestions from code review

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• update snapshots

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• Update main.nf

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• Merge branch 'dev' into refactor

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• Merge branch 'dev' into refactor

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Commits on Oct 6, 2023

• Merge branch 'dev' into refactor

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• Update main.nf

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• Merge branch 'refactor' into nf-test

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• update snapshots

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Commits on Oct 8, 2023

• Merge pull request #201 from nf-core/nf-test

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Commits on Oct 9, 2023

• Merge branch 'dev' into refactor

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• fix conflicts + update initialise + code polish

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• fix linting

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• prettier

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• use /tmp for nf-test tests

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• update snapshots

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Commits on Oct 10, 2023

• Remove nf-test files from .gitattributes

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• Remove unused multiqc_config.yml

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• Update main.nf

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• Apply suggestions from code review

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• Apply suggestions from code review

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• Per module/subworkflow tags.yml file

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• Escape single quotes

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• Trying to use cat

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• fixup

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• Merge pull request #212 from nf-core/separate_tags_into_individual_files

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Commits on Oct 11, 2023

• Remove all files in lib directory

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• Remove nf-core/initialise subworkflow

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• Update workflow main scripts

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• Add subworkflows to replace files in lib directory

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• Merge branch 'refactor' into nf-test-review

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• Invoke imNotification in completion subworkflow

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• Merge pull request #213 from drpatelh/nf-test-review

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• EC lint

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• update nf-core modules

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• update nf-test version

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Commits on Oct 12, 2023

• Merge pull request #214 from maxulysse/refactor

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• Use relative paths for main script location for nf-test

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• Remove nf-test branch from ci.yml

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• Update CHANGELOG and author contributions

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• Add nf-test citation

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• update custom/dumpsoftwareversions

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• Remove workflows/nextflow.config

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• same install

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• fix env

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• Merge pull request #215 from maxulysse/refactor

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• Add nf-test authors to credits for release

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Commits on Oct 13, 2023

• Re-order tags in workflow nf-test files

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• add pipeline level tests

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• add tags

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• update tags

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• use proper tag

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• extends files to trigger test

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• Update conf/test.config

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• Merge pull request #216 from maxulysse/pipeline_test

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• use same IDs as profile test

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• Merge pull request #217 from drpatelh/nf-test-review

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• update snap

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• add file for sratools/prefetch

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• update modules

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• use nextflowpipelineutils from nf-core/modules

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• tags

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Commits on Oct 16, 2023

• Merge pull request #218 from maxulysse/update_workflows_tests

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• Merge pull request #219 from maxulysse/ncbi_user_settings

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• Use nf-core nfvalidation subworkflow

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• fix

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• Use nf-core subworkflow: NFCORE_PIPELINE_UTILS

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• Update nextflowpipelineutils

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• path fix

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• Update subworkflows/local/nf_core_fetchngs_utils/main.nf

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• Merge pull request #222 from nf-core/use-nfcore-validation-subworkflow

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• Merge pull request #224 from nf-core/update-nextflow-pipeline-utils

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• Merge branch 'refactor' into use-nfcore-pipeline-utils-subworkflow

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• Merge pull request #223 from nf-core/use-nfcore-pipeline-utils-subworkflow

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Commits on Oct 17, 2023

• update modules

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• patch custom-dumpsoftwareversions snap

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• update snaps

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• Replace CUSTOM_DUMPSOFTWAREVERSIONS with collectFile operator

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• fixup

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• gitignore

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• Use software versions file that matches MultiQC input

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• tidy

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• Merge pull request #225 from maxulysse/fix_all

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• forgot patch

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• add data

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• Merge pull request #227 from maxulysse/fix_all_again

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• Merge branch 'refactor' of github.com:nf-core/fetchngs into collect-software-versions-via-collectfile and remove CUSTOM_DUMPSOFTWAREVERSIONS

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Commits on Oct 18, 2023

• Merge pull request #226 from nf-core/collect-software-versions-via-collectfile

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• tinier tests + patch fasterdump

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• diff file

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• one last test

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• Merge pull request #228 from maxulysse/refactor

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• Update CHANGELOG.md

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• qwqUpdate snaps

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• Merge remote-tracking branch 'origin/dev' into refactor

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• Update .github/workflows/ci.yml

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