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modify argument formatting, container setup
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@emmarousseau
emmarousseau committed Oct 5, 2024
1 parent c623706 commit 1ed80fb
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155 changes: 76 additions & 79 deletions src/snpeff/config.vsh.yaml
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Expand Up @@ -14,269 +14,267 @@ license: MIT
argument_groups:
- name: Inputs
arguments:
- name: -input
- name: --input
type: file
description: Input variants file.
example: test.vcf
direction: input
required: true
- name: -genome_version
- name: --genome_version
type: string
description: Reference genome version.
example: GRCh37.75
direction: input
required: true
- name: Outputs
arguments:
- name: -output
- name: --output
type: file
description: The output file.
example: out.vcf
direction: output
required: true
- name: -summary
- name: --summary
type: file
description: Summary file directory.
example: summary_dir
direction: output
required: false
- name: -genes
- name: --genes
type: file
description: Txt file directory.
example: genes_dir
direction: output
required: false
- name: Options
arguments:
- name: -chr
- name: --chr
type: string
description: |
Prepend 'string' to chromosome name (e.g. 'chr1' instead of '1'). Only on TXT output.
- name: -classic
- name: --classic
type: boolean_true
description: Use old style annotations instead of Sequence Ontology and Hgvs.
- name: -csv_stats
- name: --csv_stats
type: file
description: Create CSV summary file.
- name: -download
- name: --download
type: boolean_true
description: Download reference genome if not available.
- name: -input_format
- name: --input_format
alternatives: [-i]
type: string
description: |
Input format [ vcf, bed ]. Default: VCF.
- name: -file_list
example: "VCF"
- name: --file_list
type: boolean_true
description: Input actually contains a list of files to process.
- name: -output_format
- name: --output_format
alternatives: [-o]
type: string
description: |
Output format [ vcf, gatk, bed, bedAnn ]. Default: VCF.
- name: -stats
alternatives: [-s, -htmlStats]
example: "VCF"
- name: --stats
alternatives: [-s, --htmlStats]
type: boolean_true
description: Create HTML summary file.
- name: -no_stats
- name: --no_stats
type: boolean_false
description: Do not create stats (summary) file.
- name: Results filter options
arguments:
- name: -fi
alternatives: [-filterInterval]
- name: --fi
alternatives: [--filterInterval]
type: file
description: |
Only analyze changes that intersect with the intervals
specified in this file. This option can be used several times.
- name: -no_downstream
- name: --no_downstream
type: boolean_false
description: Do not show DOWNSTREAM changes
- name: -no_intergenic
- name: --no_intergenic
type: boolean_false
description: Do not show INTERGENIC changes.
- name: -no_intron
- name: --no_intron
type: boolean_false
description: Do not show INTRON changes.
- name: -no_upstream
- name: --no_upstream
type: boolean_false
description: Do not show UPSTREAM changes.
- name: -no_utr
- name: --no_utr
type: boolean_false
description: Do not show 5_PRIME_UTR or 3_PRIME_UTR changes.
- name: -no
- name: --no
type: string
description: |
Do not show 'EffectType'. This option can be used several times.
- name: Annotations options
arguments:
- name: -cancer
- name: --cancer
type: boolean_true
description: Perform 'cancer' comparisons (Somatic vs Germline).
- name: -cancer_samples
- name: --cancer_samples
type: file
description: Two column TXT file defining 'original \t derived' samples.
- name: -fastaprot
- name: --fastaprot
type: file
description: |
Create an output file containing the resulting protein sequences.
- name: -format_eff
- name: --format_eff
type: boolean_true
description: |
Use 'EFF' field compatible with older versions (instead of 'ANN').
- name: -gene_id
- name: --gene_id
type: boolean_true
description: Use gene ID instead of gene name (VCF output).
- name: -hgvs
- name: --hgvs
type: boolean_true
description: Use HGVS annotations for amino acid sub-field.
- name: -hgvs_old
- name: --hgvs_old
type: boolean_true
description: Use old HGVS notation.
- name: -hgvs1_letter_aa
- name: --hgvs1_letter_aa
type: boolean_true
description: Use one letter Amino acid codes in HGVS notation.
- name: -hgvs_tr_id
- name: --hgvs_tr_id
type: boolean_true
description: Use transcript ID in HGVS notation.
- name: -lof
- name: --lof
type: boolean_true
description: |
Add loss of function (LOF) and Nonsense mediated decay (NMD) tags.
- name: -no_hgvs
type: boolean_false
description: Do not add HGVS annotations.
- name: -no_lof
- name: --no_lof
type: boolean_false
description: Do not add LOF and NMD annotations.
- name: -no_shift_hgvs
- name: --no_shift_hgvs
type: boolean_false
description: |
Do not shift variants according to HGVS notation (most 3prime end).
- name: -oicr
- name: --oicr
type: boolean_true
description: Add OICR tag in VCF file.
- name: -sequence_ontology
- name: --sequence_ontology
type: boolean_true
description: Use Sequence Ontology terms.
- name: Generic options
arguments:
- name: -config
- name: --config
alternatives: [-c]
type: file
description: Specify config file
- name: -config_option
- name: --config_option
type: string
description: Override a config file option (name=value).
- name: -debug
- name: --debug
alternatives: [-d]
type: boolean_true
description: Debug mode (very verbose).
- name: -data_dir
- name: --data_dir
type: file
description: Override data_dir parameter from config file.
# - name: -download
# type: boolean_true
# description: Download a SnpEff database, if not available locally.
- name: -no_download
- name: --no_download
type: boolean_false
description: Do not download a SnpEff database, if not available locally.
- name: -no_log
- name: --no_log
type: boolean_false
description: Do not report usage statistics to server.
- name: -quiet
- name: --quiet
alternatives: [-q]
type: boolean_true
description: Quiet mode (do not show any messages or errors)
- name: -verbose
- name: --verbose
alternatives: [-v]
type: boolean_true
description: Verbose mode.
- name: Database options
arguments:
- name: -canon
- name: --canon
type: boolean_true
description: Only use canonical transcripts.
- name: -canon_list
- name: --canon_list
type: file
description: |
Only use canonical transcripts, replace some transcripts using the 'gene_id
transcript_id' entries in <file>.
- name: -tag
- name: --tag
type: string
description: |
Only use transcript having a tag 'tagName'. This option can be used multiple times.
- name: -no_tag
- name: --no_tag
type: boolean_false
description: |
Filter out transcript having a tag 'tagName'. This option can be used multiple times.
- name: -interaction
- name: --interaction
type: boolean_true
description: Annotate using interactions (requires interaction database).
- name: -interval
- name: --interval
type: file
description: |
Use a custom intervals in TXT/BED/BigBed/VCF/GFF file (you may use this option many times).
- name: -max_tsl
- name: --max_tsl
type: integer
description: Only use transcripts having Transcript Support Level lower than <TSL_number>.
- name: -motif
- name: --motif
type: boolean_true
description: Annotate using motifs (requires Motif database).
- name: -nextprot
- name: --nextprot
type: boolean_true
description: Annotate using NextProt (requires NextProt database).
- name: -no_genome
- name: --no_genome
type: boolean_false
description: Do not load any genomic database (e.g. annotate using custom files).
- name: -no_expand_iub
- name: --no_expand_iub
type: boolean_false
description: Disable IUB code expansion in input variants.
- name: -no_interaction
- name: --no_interaction
type: boolean_false
description: Disable inteaction annotations.
- name: -no_motif
- name: --no_motif
type: boolean_false
description: Disable motif annotations.
- name: -no_nextprot
- name: --no_nextprot
type: boolean_false
description: Disable NextProt annotations.
- name: -only_reg
- name: --only_reg
type: boolean_true
description: Only use regulation tracks.
- name: -only_protein
- name: --only_protein
type: boolean_true
description: Only use protein coding transcripts.
- name: -only_tr
- name: --only_tr
type: file
description: |
Only use the transcripts in this file. Format: One transcript ID per line.
example: file.txt
- name: -reg
- name: --reg
type: string
description: Regulation track to use (this option can be used add several times).
- name: -ss
alternatives: [-spliceSiteSize]
- name: --ss
alternatives: [--spliceSiteSize]
type: integer
description: |
Set size for splice sites (donor and acceptor) in bases. Default: 2.
- name: -splice_region_exon_size
- name: --splice_region_exon_size
type: integer
description: |
Set size for splice site region within exons. Default: 3 bases.
- name: -splice_region_intron_min
- name: --splice_region_intron_min
type: integer
description: |
Set minimum number of bases for splice site region within intron. Default: 3 bases.
- name: -splice_region_intron_max
- name: --splice_region_intron_max
type: integer
description: |
Set maximum number of bases for splice site region within intron. Default: 8 bases.
- name: -strict
- name: --strict
type: boolean_true
description: Only use 'validated' transcripts (i.e. sequence has been checked).
- name: -ud
alternatives: [-upDownStreamLen]
- name: --ud
alternatives: [--upDownStreamLen]
type: integer
description: Set upstream downstream interval length (in bases).
resources:
Expand All @@ -293,10 +291,9 @@ engines:
setup:
- type: docker
run: |
# touch ./var/software_versions.txt && \
# version=$(snpEff -version) && \
# version_trimmed=$(echo "$version" | awk '{print $1, $2}') && \
# echo "$version_trimmed" > ./var/software_versions.txt
version=$(snpEff -version) && \
version_trimmed=$(echo "$version" | awk '{print $1, $2}') && \
echo "$version_trimmed" > /var/software_versions.txt
runners:
- type: executable
- type: nextflow
4 changes: 3 additions & 1 deletion src/snpeff/script.sh
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Original file line number Diff line number Diff line change
Expand Up @@ -150,4 +150,6 @@ if [ -z "$par_no_stats" ]; then
else
mv -f snpEff_genes.txt "$directory_path"
fi
fi
fi

exit 0
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