From 3fa0f1411831448f15e17506dfef9230b303a5f1 Mon Sep 17 00:00:00 2001
From: Redmar van den Berg <RedmarvandenBerg@lumc.nl>
Date: Thu, 15 Oct 2020 15:38:45 +0200
Subject: [PATCH] Remove most inputs
---
whatshap.wdl | 110 ++++++++-------------------------------------------
1 file changed, 16 insertions(+), 94 deletions(-)
diff --git a/whatshap.wdl b/whatshap.wdl
index 2506aa1..1334d45 100644
--- a/whatshap.wdl
+++ b/whatshap.wdl
@@ -26,33 +26,13 @@ task Phase {
String outputVCF
File? reference
File? referenceIndex
- Boolean? no_reference
String? tag
- File? output_read_list
String? algorithm
- Boolean? merge_reads
- String? internal_downsampling
- String? mapping_quality
Boolean? indels
- Boolean? ignore_read_groups
String? sample
String? chromosome
- String? error_rate
- String? maximum_error_rate
String? threshold
- String? negative_threshold
- Boolean? full_genotyping
- Boolean? distrust_genotypes
- Boolean? include_homozygous
- String? default_gq
- String? gl_regularize_r
- File? changed_genotype_list
String? ped
- File? recombination_list
- String? recomb_rate
- File? gen_map
- Boolean? no_genetic_haplo_typing
- Boolean? use_ped_samples
File vcf
File vcfIndex
File phaseInput
@@ -70,33 +50,13 @@ task Phase {
~{phaseInput} \
~{if defined(outputVCF) then ("--output " + '"' + outputVCF + '"') else ""} \
~{if defined(reference) then ("--reference " + '"' + reference + '"') else ""} \
- ~{true="--no-reference" false="" no_reference} \
~{if defined(tag) then ("--tag " + '"' + tag + '"') else ""} \
- ~{if defined(output_read_list) then ("--output-read-list " + '"' + output_read_list + '"') else ""} \
~{if defined(algorithm) then ("--algorithm " + '"' + algorithm + '"') else ""} \
- ~{true="--merge-reads" false="" merge_reads} \
- ~{if defined(internal_downsampling) then ("--internal-downsampling " + '"' + internal_downsampling + '"') else ""} \
- ~{if defined(mapping_quality) then ("--mapping-quality " + '"' + mapping_quality + '"') else ""} \
~{true="--indels" false="" indels} \
- ~{true="--ignore-read-groups" false="" ignore_read_groups} \
~{if defined(sample) then ("--sample " + '"' + sample + '"') else ""} \
~{if defined(chromosome) then ("--chromosome " + '"' + chromosome + '"') else ""} \
- ~{if defined(error_rate) then ("--error-rate " + '"' + error_rate + '"') else ""} \
- ~{if defined(maximum_error_rate) then ("--maximum-error-rate " + '"' + maximum_error_rate + '"') else ""} \
~{if defined(threshold) then ("--threshold " + '"' + threshold + '"') else ""} \
- ~{if defined(negative_threshold) then ("--negative-threshold " + '"' + negative_threshold + '"') else ""} \
- ~{true="--full-genotyping" false="" full_genotyping} \
- ~{true="--distrust-genotypes" false="" distrust_genotypes} \
- ~{true="--include-homozygous" false="" include_homozygous} \
- ~{if defined(default_gq) then ("--default-gq " + '"' + default_gq + '"') else ""} \
- ~{if defined(gl_regularize_r) then ("--gl-regularizer " + '"' + gl_regularize_r + '"') else ""} \
- ~{if defined(changed_genotype_list) then ("--changed-genotype-list " + '"' + changed_genotype_list + '"') else ""} \
~{if defined(ped) then ("--ped " + '"' + ped + '"') else ""} \
- ~{if defined(recombination_list) then ("--recombination-list " + '"' + recombination_list + '"') else ""} \
- ~{if defined(recomb_rate) then ("--recombrate " + '"' + recomb_rate + '"') else ""} \
- ~{if defined(gen_map) then ("--genmap " + '"' + gen_map + '"') else ""} \
- ~{true="--no-genetic-haplotyping" false="" no_genetic_haplo_typing} \
- ~{true="--use-ped-samples" false="" use_ped_samples} && \
tabix -p vcf ~{outputVCF}
}
@@ -114,33 +74,13 @@ task Phase {
parameter_meta {
outputVCF: {description: "Output VCF file. Add .gz to the file name to get compressed output. If omitted, use standard output.", category: "common"}
reference: {description: "Reference file. Provide this to detect alleles through re-alignment. If no index (.fai) exists, it will be created", category: "common"}
- no_reference: {description: "Detect alleles without requiring a reference, at the expense of phasing quality (in particular for long reads)", category: "common"}
tag: {description: "Store phasing information with PS tag (standardized) or HP tag (used by GATK ReadBackedPhasing) (default: {description: PS)", category: "common"}
- output_read_list: {description: "Write reads that have been used for phasing to FILE.", category: "advanced"}
algorithm: {description: "Phasing algorithm to use (default: {description: whatshap)", category: "advanced"}
- merge_reads: {description: "Merge reads which are likely to come from the same haplotype (default: {description: do not merge reads)", category: "common"}
- internal_downsampling: {description: "Coverage reduction parameter in the internal core phasing algorithm. Higher values increase runtime *exponentially* while possibly improving phasing quality marginally. Avoid using this in the normal case! (default: {description: 15)", category: "advanced"}
- mapping_quality: {description: "Minimum mapping quality (default: {description: 20)", category: "common"}
indels: {description: "Also phase indels (default: {description: do not phase indels)", category: "common"}
- ignore_read_groups: {description: "Ignore read groups in BAM/CRAM header and assume all reads come from the same sample.", category: "advanced"}
sample: {description: "Name of a sample to phase. If not given, all samples in the input VCF are phased. Can be used multiple times.", category: "common"}
chromosome: {description: "Name of chromosome to phase. If not given, all chromosomes in the input VCF are phased. Can be used multiple times.", category: "common"}
- error_rate: {description: "The probability that a nucleotide is wrong in read merging model (default: {description: 0.15).", category: "advanced"}
- maximum_error_rate: {description: "The maximum error rate of any edge of the read merging graph before discarding it (default: {description: 0.25).", category: "advanced"}
threshold: {description: "The threshold of the ratio between the probabilities that a pair of reads come from the same haplotype and different haplotypes in the read merging model (default: {description: 1000000).", category: "advanced"}
- negative_threshold: {description: "The threshold of the ratio between the probabilities that a pair of reads come from different haplotypes and the same haplotype in the read merging model (default: {description: 1000).", category: "advanced"}
- full_genotyping: {description: "Completely re-genotype all variants based on read data, ignores all genotype data that might be present in the VCF (EXPERIMENTAL FEATURE).", category: "experimental"}
- distrust_genotypes: {description: "Allow switching variants from hetero- to homozygous in an optimal solution (see documentation).", category: "advanced"}
- include_homozygous: {description: "Also work on homozygous variants, which might be turned to heterozygous", category: "advanced"}
- default_gq: {description: "Default genotype quality used as cost of changing a genotype when no genotype likelihoods are available (default 30)", category: "advanced"}
- gl_regularize_r: {description: "Constant (float) to be used to regularize genotype likelihoods read from input VCF (default None).", category: "advanced"}
- changed_genotype_list: {description: "Write list of changed genotypes to FILE.", category: "advanced"}
ped: {description: "Use pedigree information in PED file to improve phasing (switches to PedMEC algorithm). Columns 2, 3, 4 must refer to child, mother, and father sample names as used in the VCF and BAM/CRAM. Other columns are ignored.", category: "advanced"}
- recombination_list: {description: "Write putative recombination events to FILE.", category: "advanced"}
- recomb_rate: {description: "Recombination rate in cM/Mb (used with --ped). If given, a constant recombination rate is assumed (default: {description: 1.26cM/Mb).", category: "advanced"}
- gen_map: {description: "File with genetic map (used with --ped) to be used instead of constant recombination rate, i.e. overrides option --recombrate.", category: "advanced"}
- no_genetic_haplo_typing: {description: "Do not merge blocks that are not connected by reads (i.e. solely based on genotype status). Default: {description: when in --ped mode, merge all blocks that contain at least one homozygous genotype in at least one individual into one block.", category: "advanced"}
- use_ped_samples: {description: "Only work on samples mentioned in the provided PED file.", category: "advanced"}
vcf: {description: "VCF or BCF file with variants to be phased (can be gzip-compressed)", category: "required"}
vcfIndex: {description: "Index for the VCF or BCF file with variants to be phased", category: "required"}
phaseInput: {description: "BAM, CRAM, VCF or BCF file(s) with phase information, either through sequencing reads (BAM, CRAM) or through phased blocks (VCF, BCF)", category: "required"}
@@ -154,10 +94,8 @@ task Stats {
input {
String? gtf
String? sample
- String? chr_lengths
String? tsv
- Boolean? only_sn_vs
- String? block_list
+ String? blockList
String? chromosome
File vcf
@@ -168,21 +106,19 @@ task Stats {
}
command {
- whatshap stats \
+ whatshap stats \
~{vcf} \
~{if defined(gtf) then ("--gtf " + '"' + gtf + '"') else ""} \
~{if defined(sample) then ("--sample " + '"' + sample + '"') else ""} \
- ~{if defined(chr_lengths) then ("--chr-lengths " + '"' + chr_lengths + '"') else ""} \
~{if defined(tsv) then ("--tsv " + '"' + tsv + '"') else ""} \
- ~{true="--only-snvs" false="" only_sn_vs} \
- ~{if defined(block_list) then ("--block-list " + '"' + block_list + '"') else ""} \
+ ~{if defined(blockList) then ("--block-list " + '"' + blockList + '"') else ""} \
~{if defined(chromosome) then ("--chromosome " + '"' + chromosome + '"') else ""}
}
output {
- File? phasedGTF = gtf
- File? phasedTSV = tsv
- File? phasedBlockList = block_list
+ File? phasedGTF = gtf
+ File? phasedTSV = tsv
+ File? phasedBlockList = blockList
}
runtime {
@@ -194,10 +130,8 @@ task Stats {
parameter_meta {
gtf: "Write phased blocks to GTF file."
sample: "Name of the sample to process. If not given, use first sample found in VCF."
- chr_lengths: "File with chromosome lengths (one line per chromosome, tab separated '<chr> <length>') needed to compute N50 values."
tsv: "Filename to write statistics to (tab-separated)."
- only_sn_vs: "Only process SNVs and ignore all other variants."
- block_list: "Filename to write list of all blocks to (one block per line)."
+ blockList: "Filename to write list of all blocks to (one block per line)."
chromosome: "Name of chromosome to process. If not given, all chromosomes in the input VCF are considered."
vcf: "Phased VCF file"
memory: {description: "The amount of memory this job will use.", category: "advanced"}
@@ -212,12 +146,7 @@ task Haplotag {
File? reference
File? referenceFastaIndex
String? regions
- Boolean? ignore_linked_read
- String? linked_read_distance_cut_off
- Boolean? ignore_read_groups
String? sample
- String? output_haplo_tag_list
- Boolean? tag_supplementary
File vcf
File vcfIndex
File alignments
@@ -230,24 +159,19 @@ task Haplotag {
}
command {
- whatshap haplotag \
+ whatshap haplotag \
~{vcf} \
~{alignments} \
~{if defined(outputFile) then ("--output " + '"' + outputFile+ '"') else ""} \
~{if defined(reference) then ("--reference " + '"' + reference + '"') else ""} \
~{if defined(regions) then ("--regions " + '"' + regions + '"') else ""} \
- ~{true="--ignore-linked-read" false="" ignore_linked_read} \
- ~{if defined(linked_read_distance_cut_off) then ("--linked-read-distance-cutoff " + '"' + linked_read_distance_cut_off + '"') else ""} \
- ~{true="--ignore-read-groups" false="" ignore_read_groups} \
~{if defined(sample) then ("--sample " + '"' + sample + '"') else ""} \
- ~{if defined(output_haplo_tag_list) then ("--output-haplotag-list " + '"' + output_haplo_tag_list + '"') else ""} \
- ~{true="--tag-supplementary" false="" tag_supplementary} && \
python3 -c "import pysam; pysam.index('~{outputFile}')"
}
output {
- File bam = outputFile
- File bamIndex = outputFile + ".bai"
+ File bam = outputFile
+ File bamIndex = outputFile + ".bai"
}
runtime {
@@ -258,16 +182,14 @@ task Haplotag {
parameter_meta {
outputFile: "Output file. If omitted, use standard output."
- reference: "Reference file. Provide this to detect alleles through re-alignment. If no index (.fai) exists, it will be created"
+ reference: "Reference file. Provide this to detect alleles through re-alignment. If no index (.fai) exists, it will be created."
+ referenceIndex: "Index for the reference file."
regions: "Specify region(s) of interest to limit the tagging to reads/variants overlapping those regions. You can specify a space-separated list of regions in the form of chrom:start-end, chrom (consider entire chromosome), or chrom:start (consider region from this start to end of chromosome)."
- ignore_linked_read: "Ignore linkage information stored in BX tags of the reads."
- linked_read_distance_cut_off: "Assume reads with identical BX tags belong to different read clouds if their distance is larger than LINKEDREADDISTANCE (default: 50000)."
- ignore_read_groups: "Ignore read groups in BAM/CRAM header and assume all reads come from the same sample."
sample: "Name of a sample to phase. If not given, all samples in the input VCF are phased. Can be used multiple times."
- output_haplo_tag_list: "Write assignments of read names to haplotypes (tab separated) to given output file. If filename ends in .gz, then output is gzipped."
- tag_supplementary: "Also tag supplementary alignments. Supplementary alignments are assigned to the same haplotype the primary alignment has been assigned to (default: only tag primary alignments)."
- vcf: "VCF file with phased variants (must be gzip-compressed and indexed)"
- alignments: "File (BAM/CRAM) with read alignments to be tagged by haplotype"
+ vcf: "VCF file with phased variants (must be gzip-compressed and indexed)."
+ vcfIndex: "Index for the VCF or BCF file with variants to be phased."
+ alignments: "File (BAM/CRAM) with read alignments to be tagged by haplotype."
+ alignmentsIndex: "Index for the alignment file."
memory: {description: "The amount of memory this job will use.", category: "advanced"}
timeMinutes: {description: "The maximum amount of time the job will run in minutes.", category: "advanced"}
dockerImage: {description: "The docker image used for this task. Changing this may result in errors which the developers may choose not to address.", category: "advanced"}
--
GitLab