This PR, adds change for introducing new --help option for users to get the usage information for AIM next-flow pipeline.
TESTING :
In the AI_MARRVEL dir, run the command given below.
nextflow run main.nf --help
expected output :
N E X T F L O W ~ version 24.04.2
Launching `main.nf` [loquacious_bohr] DSL2 - revision: 5b9ee9fd9c
Usage:
nextflow run main.nf [All Args] [Options]
Example:
nextflow run main.nf --ref_dir path/to/aim_data_dependencies \
--input_vcf path/to/sample.vcf.gz \
--input_hpo path/to/sample/hpos.txt \
--outdir path/to/sample/Output \
--run_id [Sample ID] \
--ref_ver [hg19/hg38]
Args:
--input_vcf Path to input VCF file.
--input_hpo Path to input HPO file.
--ref_dir Path to aim pipeline dependencies directory.
--outdir Output directory.
--run_id Unique identifier for this run. (default: 1)
--ref_ver Reference genome version [hg38 or hg19] (default: hg19)
Options:
--exome_filter Enable exonic filter. Addition will filter out variants outside of exonic region (default: false)
--help Displays the usage information.
Reference Files:
--ref_loc Path to reference location file
--ref_to_sym Path to reference to symbol file
--ref_sorted_sym Path to reference sorted symbol file
--ref_exonic_filter_bed Path to exonic filter BED file
VEP Annotation:
--vep_dir_cache Path to VEP cache directory
--vep_dir_plugins Path to VEP plugins directory
--vep_custom_gnomad Path to custom gnomAD file for VEP
--vep_custom_clinvar Path to custom ClinVar file for VEP
--vep_custom_hgmd Path to custom HGMD file for VEP
For detailed information about each process,
please refer to the documentation. https://ai-marrvel.readthedocs.io/en/latest/
QA :
Happy Case: Tested cmd nextflow run main.nf --help got the expected output.
Fail Case : Tested cmd nextflow run main.nf, got error and workflow was terminated with output given below as expected.
N E X T F L O W ~ version 24.04.2
Launching `main.nf` [curious_mercator] DSL2 - revision: 5b9ee9fd9c
WARN: Access to undefined parameter `input_vcf` -- Initialise it to a default value eg. `params.input_vcf = some_value`
ERROR ~ A process input channel evaluates to null -- Invalid declaration `path vcf`
-- Check script 'main.nf' at line: 387 or see '.nextflow.log' file for more details
Changes:
--help
option for users to get the usage information for AIM next-flow pipeline.TESTING :
In the
AI_MARRVEL
dir, run the command given below.expected output :
QA :
nextflow run main.nf --help
got the expected output.nextflow run main.nf
, got error and workflow was terminated with output given below as expected.