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| Original file line number | Diff line number | Diff line change |
|---|---|---|
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@@ -6,5 +6,4 @@ results/ | |
| testing/ | ||
| testing* | ||
| *.pyc | ||
| execution_trace* | ||
| .nf-test* | ||
| null/ | ||
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
|
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@@ -90,19 +90,23 @@ params { | |
| help = false | ||
| help_full = false | ||
| show_hidden = false | ||
| help_full = false | ||
| show_hidden = false | ||
| version = false | ||
| pipelines_testdata_base_path = 'https://raw.githubusercontent.com/nf-core/test-datasets/' | ||
| // Config options | ||
| config_profile_name = null | ||
| config_profile_description = null | ||
|
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||
|
|
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| custom_config_version = 'master' | ||
| custom_config_base = "https://raw.githubusercontent.com/nf-core/configs/${params.custom_config_version}" | ||
| config_profile_contact = null | ||
| config_profile_url = null | ||
|
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| // Schema validation default options | ||
| validate_params = true | ||
| validate_params = true | ||
| } | ||
|
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| // Load base.config by default for all pipelines | ||
|
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@@ -122,6 +126,7 @@ profiles { | |
| shifter.enabled = false | ||
| charliecloud.enabled = false | ||
| conda.channels = ['conda-forge', 'bioconda'] | ||
| conda.channels = ['conda-forge', 'bioconda'] | ||
| apptainer.enabled = false | ||
| } | ||
| mamba { | ||
|
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@@ -243,6 +248,11 @@ docker.registry = 'quay.io' | |
| podman.registry = 'quay.io' | ||
| singularity.registry = 'quay.io' | ||
| charliecloud.registry = 'quay.io' | ||
| apptainer.registry = 'quay.io' | ||
| docker.registry = 'quay.io' | ||
| podman.registry = 'quay.io' | ||
| singularity.registry = 'quay.io' | ||
| charliecloud.registry = 'quay.io' | ||
|
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| // Load igenomes.config if required | ||
| includeConfig !params.igenomes_ignore ? 'conf/igenomes.config' : 'conf/igenomes_ignored.config' | ||
|
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@@ -261,6 +271,15 @@ env { | |
| process.shell = """\ | ||
| bash | ||
| set -e # Exit if a tool returns a non-zero status/exit code | ||
| set -u # Treat unset variables and parameters as an error | ||
| set -o pipefail # Returns the status of the last command to exit with a non-zero status or zero if all successfully execute | ||
| set -C # No clobber - prevent output redirection from overwriting files. | ||
| """ | ||
| // Set bash options | ||
| process.shell = """\ | ||
| bash | ||
| set -e # Exit if a tool returns a non-zero status/exit code | ||
| set -u # Treat unset variables and parameters as an error | ||
| set -o pipefail # Returns the status of the last command to exit with a non-zero status or zero if all successfully execute | ||
|
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@@ -335,5 +354,41 @@ validation { | |
| } | ||
| } | ||
|
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| // Nextflow plugins | ||
| plugins { | ||
| id '[email protected]' // Validation of pipeline parameters and creation of an input channel from a sample sheet | ||
| } | ||
|
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| validation { | ||
| defaultIgnoreParams = ["genomes"] | ||
| help { | ||
| enabled = true | ||
| command = "nextflow run $manifest.name -profile <docker/singularity/.../institute> --input samplesheet.csv --outdir <OUTDIR>" | ||
| fullParameter = "help_full" | ||
| showHiddenParameter = "show_hidden" | ||
| beforeText = """ | ||
| -\033[2m----------------------------------------------------\033[0m- | ||
| \033[0;32m,--.\033[0;30m/\033[0;32m,-.\033[0m | ||
| \033[0;34m ___ __ __ __ ___ \033[0;32m/,-._.--~\'\033[0m | ||
| \033[0;34m |\\ | |__ __ / ` / \\ |__) |__ \033[0;33m} {\033[0m | ||
| \033[0;34m | \\| | \\__, \\__/ | \\ |___ \033[0;32m\\`-._,-`-,\033[0m | ||
| \033[0;32m`._,._,\'\033[0m | ||
| \033[0;35m ${manifest.name} ${manifest.version}\033[0m | ||
| -\033[2m----------------------------------------------------\033[0m- | ||
| """ | ||
| afterText = """${manifest.doi ? "* The pipeline\n" : ""}${manifest.doi.tokenize(",").collect { " https://doi.org/${it.trim().replace('https://doi.org/','')}"}.join("\n")}${manifest.doi ? "\n" : ""} | ||
| * The nf-core framework | ||
| https://doi.org/10.1038/s41587-020-0439-x | ||
| * Software dependencies | ||
| https://github.com/${manifest.name}/blob/master/CITATIONS.md | ||
| """ | ||
| } | ||
| summary { | ||
| beforeText = validation.help.beforeText | ||
| afterText = validation.help.afterText | ||
| } | ||
| } | ||
|
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| // Load modules.config for DSL2 module specific options | ||
| includeConfig 'conf/modules.config' | ||
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