A pipeline to pre-process raw NGS data for downstream reuse across various pipelines
Define where the pipeline should find input data and save output data.
| Parameter | Description | Type | Default | Required | Hidden |
|---|---|---|---|---|---|
input |
Path to comma-separated file containing information about the samples in the experiment. | string |
True | ||
cat_by_group |
Concatenate samples by group and save group-level FastQ files | boolean |
True | ||
save_group_fasta |
Save group level Fasta files in addition to FastQ files | boolean |
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outdir |
The output directory where the results will be saved. You have to use absolute paths to storage on Cloud infrastructure. | string |
True | ||
email |
Email address for completion summary. | string |
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multiqc_title |
MultiQC report title. Printed as page header, used for filename if not otherwise specified. | string |
| Parameter | Description | Type | Default | Required | Hidden |
|---|---|---|---|---|---|
skip_trimming |
Skip adapter trimming step | boolean |
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save_trimmed_fail |
Save the trimmed FastQ files in the results directory | boolean |
True | ||
min_trimmed_reads |
Minimum number of trimmed reads below which samples are removed from further processing | integer |
10000 | ||
additional_adapters |
Fasta file containing additional adapter for trimming | string |
${projectDir}/assets/adapters.fasta | ||
extra_fastp_args |
Extra arguments to pass to fastp command in addition to defaults defined by the pipeline | string |
Parameters used to describe centralised config profiles. These should not be edited.
| Parameter | Description | Type | Default | Required | Hidden |
|---|---|---|---|---|---|
custom_config_version |
Git commit id for Institutional configs. | string |
master | True | |
custom_config_base |
Base directory for Institutional configs. | string |
https://raw.githubusercontent.com/nf-core/configs/master | True | |
config_profile_name |
Institutional config name. | string |
True | ||
config_profile_description |
Institutional config description. | string |
True | ||
config_profile_contact |
Institutional config contact information. | string |
True | ||
config_profile_url |
Institutional config URL link. | string |
True |
Set the top limit for requested resources for any single job.
| Parameter | Description | Type | Default | Required | Hidden |
|---|---|---|---|---|---|
max_cpus |
Maximum number of CPUs that can be requested for any single job. | integer |
12 | True | |
max_memory |
Maximum amount of memory that can be requested for any single job. | string |
72.GB | True | |
max_time |
Maximum amount of time that can be requested for any single job. | string |
12.h | True |
Less common options for the pipeline, typically set in a config file.
| Parameter | Description | Type | Default | Required | Hidden |
|---|---|---|---|---|---|
help |
Display help text. | boolean |
True | ||
version |
Display version and exit. | boolean |
True | ||
publish_dir_mode |
Method used to save pipeline results to output directory. | string |
copy | True | |
email_on_fail |
Email address for completion summary, only when pipeline fails. | string |
True | ||
plaintext_email |
Send plain-text email instead of HTML. | boolean |
True | ||
max_multiqc_email_size |
File size limit when attaching MultiQC reports to summary emails. | string |
25.MB | True | |
monochrome_logs |
Do not use coloured log outputs. | boolean |
True | ||
monochromeLogs |
Do not use coloured log outputs. | boolean |
True | ||
hook_url |
Incoming hook URL for messaging service | string |
True | ||
multiqc_config |
Custom config file to supply to MultiQC. | string |
True | ||
multiqc_logo |
Custom logo file to supply to MultiQC. File name must also be set in the MultiQC config file | string |
True | ||
multiqc_methods_description |
Custom MultiQC yaml file containing HTML including a methods description. | string |
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validate_params |
Boolean whether to validate parameters against the schema at runtime | boolean |
True | True | |
validationShowHiddenParams |
Show all params when using --help |
boolean |
True | ||
validationFailUnrecognisedParams |
Validation of parameters fails when an unrecognised parameter is found. | boolean |
True | ||
validationLenientMode |
Validation of parameters in lenient more. | boolean |
True | ||
pipelines_testdata_base_path |
Base URL or local path to location of pipeline test dataset files | string |
https://raw.githubusercontent.com/nf-core/test-datasets/ | True |