Lighter #6626
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Lighter #6626
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nvnieuwk
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Sep 23, 2024
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| val genome_size //Estimated or user specified genome size | ||
| val kmer_size //K_mer size | ||
| val alpha // define alpha is optional, because "When using "-K" instead of "-k", Lighter will go through the reads an extra pass to decide C. " | ||
| val output_dir |
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Are these required values for the module to run?
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| tuple val(meta), path("*.fq.gz"), emit: outfastq | ||
| path "versions.yml" , emit: versions |
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| tuple val(meta), path("*.fq.gz"), emit: outfastq | |
| path "versions.yml" , emit: versions | |
| tuple val(meta), path("*.fq.gz"), emit: outfastq | |
| path "versions.yml" , emit: versions |
| -r ${readList.join(' -r ')} \\ | ||
| $k_par \\ | ||
| -t $task.cpus \\ | ||
| -od ${output_dir} \\ |
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| -od ${output_dir} \\ | |
| -od ${prefix} \\ |
I think it makes more sense to use the prefix here
| --- | ||
| # yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/meta-schema.json | ||
| name: "lighter" | ||
| ## TODO nf-core: Add a description of the module and list keywords |
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| ## TODO nf-core: Add a description of the module and list keywords |
| doi: "10.1186/s13059-014-0509-9" | ||
| licence: ["MIT"] | ||
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| ## TODO nf-core: Add a description of all of the variables used as input |
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| ## TODO nf-core: Add a description of all of the variables used as input |
| when { | ||
| process { | ||
| """ | ||
| // TODO nf-core: define inputs of the process here. Example: |
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| // TODO nf-core: define inputs of the process here. Example: |
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| //TODO nf-core: Add all required assertions to verify the test output. | ||
| // See https://nf-co.re/docs/contributing/tutorials/nf-test_assertions for more information and examples. |
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| //TODO nf-core: Add all required assertions to verify the test output. | |
| // See https://nf-co.re/docs/contributing/tutorials/nf-test_assertions for more information and examples. |
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| } | ||
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| // TODO nf-core: Change the test name preferably indicating the test-data and file-format used but keep the " - stub" suffix. |
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| // TODO nf-core: Change the test name preferably indicating the test-data and file-format used but keep the " - stub" suffix. |
| when { | ||
| process { | ||
| """ | ||
| // TODO nf-core: define inputs of the process here. Example: |
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| // TODO nf-core: define inputs of the process here. Example: |
| assertAll( | ||
| { assert process.success }, | ||
| { assert snapshot(process.out).match() } | ||
| //TODO nf-core: Add all required assertions to verify the test output. |
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| //TODO nf-core: Add all required assertions to verify the test output. |
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PR checklist
Closes #XXX
versions.ymlfile.labelnf-core modules test <MODULE> --profile dockernf-core modules test <MODULE> --profile singularitynf-core modules test <MODULE> --profile condanf-core subworkflows test <SUBWORKFLOW> --profile dockernf-core subworkflows test <SUBWORKFLOW> --profile singularitynf-core subworkflows test <SUBWORKFLOW> --profile conda