Small variant parameters¶
Info
On the command line, prefix workflow parameters with --, e.g., --samplesheet samples.csv. Prefix Nextflow options with -, e.g., -profile hpc.
For detailed parameter documentation on the command line use --help
WORKFLOW='/gel_data_resources/workflows/rdp_small_variant/v3.1.1'
nextflow run ${WORKFLOW} -profile hpc --help
For full details of a specific parameter
Base configuration¶
| parameter | default |
|---|---|
gene_input |
${projectDir}/input/gene_list.txt |
samplesheet |
null |
outdir |
'results' |
publish_all |
false |
help |
false |
add_clinvar |
true |
use_loftee |
true |
config_profile_name |
null |
config_profile_description |
null |
config_profile_data_base |
null |
HPC-specific parameters¶
-profile hpc
| parameter | default |
|---|---|
config_profile_name |
'hpc' |
config_profile_description |
'Configuration options for GEL double helix' |
config_profile_data_base |
'/gel_data_resources,/public_data_resources' |
project_code |
'' |
cluster_options |
'-P ' |
excluded_participant_ids |
'/gel_data_resources/workflows/input_material/shared_BRS_tools/excluded_participants/excluded_participant_ids.txt' |
reference_resources.GRCh37.coord_file |
'/public_data_resources/genes_and_regions/ensembl_genes_coordinates_105_grch37.tsv' |
reference_resources.GRCh37.fasta_file |
'/public_data_resources/reference/GRCh37/Homo_sapiens.GRCh37.75.dna.primary_assembly.fa' |
reference_resources.GRCh37.vep_cache_version |
'105' |
reference_resources.GRCh37.vep_cache |
'/public_data_resources/vep_resources/VEP_105' |
reference_resources.GRCh37.vep_cache_synonyms |
'/public_data_resources/vep_resources/VEP_105/homo_sapiens/105_GRCh37/chr_synonyms.txt' |
reference_resources.GRCh37.clinvar_file |
'/public_data_resources/clinvar/20200604/clinvar/vcf_GRCh37/clinvar_20200602.vcf.gz' |
reference_resources.GRCh37.clinvar_index |
'/public_data_resources/clinvar/20200604/clinvar/vcf_GRCh37/clinvar_20200602.vcf.gz.tbi' |
reference_resources.GRCh37.loftee_human_ancestor_fa |
'/public_data_resources/vep_resources/Build-37/human_ancestor.fa.gz' |
reference_resources.GRCh37.loftee_gerp_file |
'/public_data_resources/vep_resources/Build-37/GERP_scores.final.sorted.txt.gz' |
reference_resources.GRCh37.loftee_conservation_file |
'/public_data_resources/vep_resources/Build-37/phylocsf_gerp.sql' |
reference_resources.GRCh38.coord_file |
'/public_data_resources/genes_and_regions/ensembl_genes_coordinates_105_grch38.tsv' |
reference_resources.GRCh38.fasta_file |
'/public_data_resources/reference/GRCh38/GRCh38Decoy_no_alt.fa' |
reference_resources.GRCh38.vep_cache_version |
'105' |
reference_resources.GRCh38.vep_cache |
'/public_data_resources/vep_resources/VEP_105' |
reference_resources.GRCh38.vep_cache_synonyms |
'/public_data_resources/vep_resources/VEP_105/homo_sapiens/105_GRCh38/chr_synonyms.txt' |
reference_resources.GRCh38.clinvar_file |
'/public_data_resources/clinvar/20200604/clinvar/vcf_GRCh38/clinvar_20200602.vcf.gz' |
reference_resources.GRCh38.clinvar_index |
'/public_data_resources/clinvar/20200604/clinvar/vcf_GRCh38/clinvar_20200602.vcf.gz.tbi' |
reference_resources.GRCh38.loftee_human_ancestor_fa |
'/public_data_resources/vep_resources/Build-38/human_ancestor.fa.gz' |
reference_resources.GRCh38.loftee_gerp_bigwig |
'/public_data_resources/vep_resources/Build-38/gerp_conservation_scores.homo_sapiens.GRCh38.bw' |
reference_resources.GRCh38.loftee_conservation_file |
'/public_data_resources/vep_resources/Build-38/loftee.sql' |
CloudOS-specific parameters¶
-profile cloudos
| parameter | default |
|---|---|
config_profile_name |
'cloudos' |
config_profile_description |
'Configuration options for LifeBit CloudOS' |
config_profile_data_base |
's3://512426816668-gel-data-resources,s3://512426816668-public-data-resources,s3://512426816668-genomes,s3://gel-lifebit-featured-datasets' |
reference_resources.GRCh37.coord_file |
's3://512426816668-public-data-resources/genes_and_regions/ensembl_genes_coordinates_105_grch37.tsv' |
reference_resources.GRCh37.fasta_file |
's3://512426816668-genomes/reference/illumina_nsv2/Homo_sapiens.GRCh37.75.dna.primary_assembly.fa' |
reference_resources.GRCh37.vep_cache_version |
'105' |
reference_resources.GRCh37.vep_cache |
's3://gel-lifebit-featured-datasets/containers/vep/vep_cache_GRCh37_v105' |
reference_resources.GRCh37.vep_cache_synonyms |
's3://gel-lifebit-featured-datasets/containers/vep/vep_cache_GRCh37_v105/homo_sapiens/105_GRCh37/chr_synonyms.txt' |
reference_resources.GRCh37.clinvar_file |
's3://512426816668-public-data-resources/clinvar/20200604/clinvar/vcf_GRCh37/clinvar_20200602.vcf.gz' |
reference_resources.GRCh37.clinvar_index |
's3://512426816668-public-data-resources/clinvar/20200604/clinvar/vcf_GRCh37/clinvar_20200602.vcf.gz.tbi' |
reference_resources.GRCh37.loftee_human_ancestor_fa |
's3://512426816668-public-data-resources/vep_resources/LOFTEE/Build-37/human_ancestor.fa.gz' |
reference_resources.GRCh37.loftee_gerp_file |
's3://512426816668-public-data-resources/vep_resources/LOFTEE/Build-37/GERP_scores.final.sorted.txt.gz' |
reference_resources.GRCh37.loftee_conservation_file |
's3://512426816668-public-data-resources/vep_resources/LOFTEE/Build-37/phylocsf_gerp.sql' |
reference_resources.GRCh38.coord_file |
's3://512426816668-public-data-resources/genes_and_regions/ensembl_genes_coordinates_105_grch38.tsv' |
reference_resources.GRCh38.fasta_file |
's3://512426816668-genomes/reference/illumina_nsv4/GRCh38Decoy_no_alt.fa' |
reference_resources.GRCh38.vep_cache_version |
'105' |
reference_resources.GRCh38.vep_cache |
's3://gel-lifebit-featured-datasets/containers/vep/vep_cache_GRCh38_v105' |
reference_resources.GRCh38.vep_cache_synonyms |
's3://gel-lifebit-featured-datasets/containers/vep/vep_cache_GRCh38_v105/homo_sapiens/105_GRCh38/chr_synonyms.txt' |
reference_resources.GRCh38.clinvar_file |
's3://512426816668-public-data-resources/clinvar/20200604/clinvar/vcf_GRCh38/clinvar_20200602.vcf.gz' |
reference_resources.GRCh38.clinvar_index |
's3://512426816668-public-data-resources/clinvar/20200604/clinvar/vcf_GRCh38/clinvar_20200602.vcf.gz.tbi' |
reference_resources.GRCh38.loftee_human_ancestor_fa |
's3://512426816668-public-data-resources/vep_resources/LOFTEE/Build-38/human_ancestor.fa.gz' |
reference_resources.GRCh38.loftee_gerp_bigwig |
's3://512426816668-public-data-resources/vep_resources/LOFTEE/Build-38/gerp_conservation_scores.homo_sapiens.GRCh38.bw' |
reference_resources.GRCh38.loftee_conservation_file |
's3://512426816668-public-data-resources/vep_resources/LOFTEE/Build-38/loftee.sql' |
lb_bcftools_container |
'docker-quay-io.artifactory.aws.gel.ac/kenhanscombe/bcftools:1.17' |
lb_vep_container |
'docker-quay-io.artifactory.aws.gel.ac/lifebitai/brs_tools_genevariantworkflow-vep:105.2' |
excluded_participant_ids |
's3://512426816668-gel-data-resources/brs-workflows/input_material/shared_BRS_tools/excluded_participants/excluded_participant_ids.txt' |