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Merge branch 'develop' into BIOWDL-487

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CHANGELOG.md
+ 5
− 1
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......@@ -9,10 +9,14 @@ This document is user facing. Please word the changes in such a way
that users understand how the changes affect the new version.
-->
version 4.1.0-dev
version 5.0.0-dev
---------------------------
+ Bam2fastx: Input bam and index are now arrays.
+ Lima: Remove globs from outputs.
+ A bwa-mem2 task was created with the same interface (including usePostalt)
as the bwa mem task.
+ bwa mem and bwa kit are now one task. The usePostalt boolean can be used to
switch the postalt script on and off.
+ Added a task for GRIDSS.
+ Add wdl file for pacbio's bam2fastx tool.
......
bwa-mem2.wdl 0 → 100644
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version 1.0
# Copyright (c) 2017 Leiden University Medical Center
#
# Permission is hereby granted, free of charge, to any person obtaining a copy
# of this software and associated documentation files (the "Software"), to deal
# in the Software without restriction, including without limitation the rights
# to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
# copies of the Software, and to permit persons to whom the Software is
# furnished to do so, subject to the following conditions:
#
# The above copyright notice and this permission notice shall be included in
# all copies or substantial portions of the Software.
#
# THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
# IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
# FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
# AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
# LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
# OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
# SOFTWARE.
task Mem {
input {
File read1
File? read2
BwaIndex bwaIndex
String outputPrefix
String? readgroup
Boolean sixtyFour = false
Boolean usePostalt = false
Int threads = 4
Int? sortThreads
Int sortMemoryPerThreadGb = 2
Int compressionLevel = 1
Int? memoryGb
Int timeMinutes = 1 + ceil(size([read1, read2], "G") * 220 / threads)
# Contains bwa-mem2 2.0 bwakit 0.7.17.dev1 and samtools 1.10
String dockerImage = "quay.io/biocontainers/mulled-v2-6a15c99309c82b345497d24489bee67bbb76c2f6:1c9c3227b9bf825a8dc9726a25701aa23c0b1f12-0"
}
# Samtools sort may block the pipe while it is writing data to disk.
# This can lead to cpu underutilization.
# 1 thread if threads is 1. For 2-4 threads 2 sort threads. 3 sort threads for 5-8 threads.
Int estimatedSortThreads = if threads == 1 then 1 else 1 + ceil(threads / 4.0)
Int totalSortThreads = select_first([sortThreads, estimatedSortThreads])
# BWA-mem2's index files contain 2 BWT indexes of which only one is used. .2bit64 is used by default and
# .8bit32 is used for avx2.
# The larger one of these is the 8bit32 index. Since we do not know beforehand which one is used we need to accomodate for that.
# Using only the 8bit32 index uses 57,5% of the index files. Since bwa-mem2 uses slightly more memory than the index
# We put it at 62% as a safety factor. That means the memory usage for bwa-mem will be 53G for a human genome. Resulting in 60G total
# on 8 cores with samtools with 3 sort threads.
Int estimatedMemoryGb = 1 + ceil(size(bwaIndex.indexFiles, "G") * 0.62) + sortMemoryPerThreadGb * totalSortThreads
# The bwa postalt script is out commented as soon as usePostalt = false.
# This hack was tested with bash, dash and ash. It seems that comments in between pipes work for all of them.
command {
set -e
mkdir -p "$(dirname ~{outputPrefix})"
bwa-mem2 mem \
-t ~{threads} \
~{"-R '" + readgroup}~{true="'" false="" defined(readgroup)} \
~{bwaIndex.fastaFile} \
~{read1} \
~{read2} \
2> ~{outputPrefix}.log.bwamem | \
~{true="" false="#" usePostalt} bwa-postalt.js -p ~{outputPrefix}.hla ~{bwaIndex.fastaFile}~{true=".64.alt" false=".alt" sixtyFour} | \
samtools sort \
~{"-@ " + totalSortThreads} \
-m ~{sortMemoryPerThreadGb}G \
-l ~{compressionLevel} \
- \
-o ~{outputPrefix}.aln.bam
}
output {
File outputBam = outputPrefix + ".aln.bam"
File? outputHla = outputPrefix + ".hla"
}
runtime {
# One extra thread for bwa-postalt + samtools is not needed.
# These only use 5-10% of compute power and not always simultaneously.
cpu: threads
memory: "~{select_first([memoryGb, estimatedMemoryGb])}G"
time_minutes: timeMinutes
docker: dockerImage
}
parameter_meta {
# inputs
read1: {description: "The first-end fastq file.", category: "required"}
read2: {description: "The second-end fastq file.", category: "common"}
bwaIndex: {description: "The BWA index, including (optionally) a .alt file.", category: "required"}
usePostalt: {description: "Whether to use the postalt script from bwa kit."}
outputPrefix: {description: "The prefix of the output files, including any parent directories.", category: "required"}
readgroup: {description: "A readgroup identifier.", category: "common"}
sixtyFour: {description: "Whether or not the index uses the '.64' suffixes.", category: "common"}
threads: {description: "The number of threads to use for alignment.", category: "advanced"}
memoryGb: {description: "The amount of memory this job will use in gigabytes.", category: "advanced"}
sortThreads: {description: "The number of threads to use for sorting.", category: "advanced"}
sortMemoryPerThreadGb: {description: "The amount of memory for each sorting thread in gigabytes.", category: "advanced"}
compressionLevel: {description: "The compression level of the output BAM.", 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"}
# outputs
outputBam: "The produced BAM file."
}
}
struct BwaIndex {
File fastaFile
Array[File] indexFiles
}
bwa.wdl
+ 8
− 78
View file @ ae8ec634
......@@ -21,78 +21,6 @@ version 1.0
# SOFTWARE.
task Mem {
input {
File read1
File? read2
BwaIndex bwaIndex
String outputPath
String? readgroup
Int threads = 4
Int? sortThreads
Int sortMemoryPerThreadGb = 2
Int compressionLevel = 1
Int? memoryGb
Int timeMinutes = 1 + ceil(size([read1, read2], "G") * 200 / threads)
# This container contains: samtools (1.10), bwa (0.7.17-r1188)
String dockerImage = "quay.io/biocontainers/mulled-v2-fe8faa35dbf6dc65a0f7f5d4ea12e31a79f73e40:eabfac3657eda5818bae4090db989e3d41b01542-0"
}
# Samtools sort may block the pipe while it is writing data to disk.
# This can lead to cpu underutilization.
# 1 thread if threads is 1. For 2-4 threads 2 sort threads. 3 sort threads for 5-8 threads.
Int estimatedSortThreads = if threads == 1 then 1 else 1 + ceil(threads / 4.0)
Int totalSortThreads = select_first([sortThreads, estimatedSortThreads])
# BWA needs slightly more memory than the size of the index files (~10%). Add a margin for safety here.
Int estimatedMemoryGb = 1 + ceil(size(bwaIndex.indexFiles, "G") * 1.2) + sortMemoryPerThreadGb * totalSortThreads
command {
set -e -o pipefail
mkdir -p "$(dirname ~{outputPath})"
bwa mem \
~{"-t " + threads} \
~{"-R '" + readgroup}~{true="'" false="" defined(readgroup)} \
~{bwaIndex.fastaFile} \
~{read1} \
~{read2} \
| samtools sort \
~{"-@ " + totalSortThreads} \
-m ~{sortMemoryPerThreadGb}G \
-l ~{compressionLevel} \
- \
-o ~{outputPath}
}
output {
File outputBam = outputPath
}
runtime {
cpu: threads
memory: "~{select_first([memoryGb, estimatedMemoryGb])}G"
time_minutes: timeMinutes
docker: dockerImage
}
parameter_meta {
read1: {description: "The first or single end fastq file.", category: "required"}
read2: {description: "The second end fastq file.", category: "common"}
bwaIndex: {description: "The BWA index files.", category: "required"}
outputPath: {description: "The location the output BAM file should be written to.", category: "required"}
readgroup: {description: "The readgroup to be assigned to the reads. See BWA mem's `-R` option.", category: "common"}
threads: {description: "The number of threads to use.", category: "advanced"}
memoryGb: {description: "The amount of memory this job will use in gigabytes.", category: "advanced"}
sortThreads: {description: "The number of threads to use for sorting.", category: "advanced"}
sortMemoryPerThreadGb: {description: "The amount of memory for each sorting thread in gigabytes.", category: "advanced"}
compressionLevel: {description: "The compression level of the output BAM.", 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"}
}
}
task Kit {
input {
File read1
File? read2
......@@ -100,7 +28,7 @@ task Kit {
String outputPrefix
String? readgroup
Boolean sixtyFour = false
Boolean usePostalt = false
Int threads = 4
Int? sortThreads
Int sortMemoryPerThreadGb = 2
......@@ -119,6 +47,8 @@ task Kit {
# BWA needs slightly more memory than the size of the index files (~10%). Add a margin for safety here.
Int estimatedMemoryGb = 1 + ceil(size(bwaIndex.indexFiles, "G") * 1.2) + sortMemoryPerThreadGb * totalSortThreads
# The bwa postalt script is out commented as soon as usePostalt = false.
# This hack was tested with bash, dash and ash. It seems that comments in between pipes work for all of them.
command {
set -e
mkdir -p "$(dirname ~{outputPrefix})"
......@@ -129,10 +59,8 @@ task Kit {
~{read1} \
~{read2} \
2> ~{outputPrefix}.log.bwamem | \
bwa-postalt.js \
-p ~{outputPrefix}.hla \
~{bwaIndex.fastaFile}~{true=".64.alt" false=".alt" sixtyFour} | \
samtools sort \
~{true="" false="#" usePostalt} bwa-postalt.js -p ~{outputPrefix}.hla ~{bwaIndex.fastaFile}~{true=".64.alt" false=".alt" sixtyFour} | \
samtools sort \
~{"-@ " + totalSortThreads} \
-m ~{sortMemoryPerThreadGb}G \
-l ~{compressionLevel} \
......@@ -142,6 +70,7 @@ task Kit {
output {
File outputBam = outputPrefix + ".aln.bam"
File? outputHla = outputPrefix + ".hla"
}
runtime {
......@@ -157,7 +86,8 @@ task Kit {
# inputs
read1: {description: "The first-end fastq file.", category: "required"}
read2: {description: "The second-end fastq file.", category: "common"}
bwaIndex: {description: "The BWA index, including a .alt file.", category: "required"}
bwaIndex: {description: "The BWA index, including (optionally) a .alt file.", category: "required"}
usePostalt: {description: "Whether to use the postalt script from bwa kit."}
outputPrefix: {description: "The prefix of the output files, including any parent directories.", category: "required"}
readgroup: {description: "A readgroup identifier.", category: "common"}
sixtyFour: {description: "Whether or not the index uses the '.64' suffixes.", category: "common"}
......
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