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Add FQlint module #31

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MatthiasZepper opened this issue Oct 21, 2024 · 0 comments
Open

Add FQlint module #31

MatthiasZepper opened this issue Oct 21, 2024 · 0 comments
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@erkutilaslan
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enhancement New feature or request

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@MatthiasZepper
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Description of feature

Add the module for fq lint to the pipeline.
@MatthiasZepper MatthiasZepper added the enhancement New feature or request label Oct 21, 2024
@MatthiasZepper MatthiasZepper moved this to suggested modules to add in seqinspector project board Oct 25, 2024
@erkutilaslan erkutilaslan self-assigned this Oct 29, 2024
@erkutilaslan erkutilaslan moved this from Todo to In Progress in Hackathon October 2024 Oct 29, 2024
adamrtalbot added a commit to adamrtalbot/seqinspector that referenced this issue Nov 2, 2024
@adamrtalbot
Adds fq/lint for early validation of FASTQs
6563d8f 
Validation of FASTQS early prevents running the pipeline on invalid FASTQ files which will make the pipeline more efficient at achieving it's ultimate objective of checking FASTQ validity.

It adds 3 more parameters:
 - `--skip_linting` which enables the linting of FASTQs
 - `--fq_lint_args` which is a string of arguments to pass to the linting tool
 - `--continue_with_lint_fail` which is a boolean to determine whether to continue if the linting fails

Between these three options the user has a high degree of control over how the pipeline lints which should handle most use cases.

Closes nf-core#31
@adamrtalbot adamrtalbot mentioned this issue Nov 2, 2024
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adamrtalbot added a commit to adamrtalbot/seqinspector that referenced this issue Dec 19, 2024
@adamrtalbot
Adds fq/lint for early validation of FASTQs
7072d59 
Validation of FASTQS early prevents running the pipeline on invalid FASTQ files which will make the pipeline more efficient at achieving it's ultimate objective of checking FASTQ validity.

It adds 3 more parameters:
 - `--skip_linting` which enables the linting of FASTQs
 - `--fq_lint_args` which is a string of arguments to pass to the linting tool
 - `--continue_with_lint_fail` which is a boolean to determine whether to continue if the linting fails

Between these three options the user has a high degree of control over how the pipeline lints which should handle most use cases.

Closes nf-core#31
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@erkutilaslan erkutilaslan

Labels
enhancement New feature or request
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seqinspector project board
Status: suggested modules to add
Hackathon October 2024
Status: In Progress
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@MatthiasZepper @erkutilaslan