diff --git a/samtools.wdl b/samtools.wdl
index e123e6356e99df28a9e7311204230572be89c482..5648eb1cf403fbe3c877fe72f3cae066514d7026 100644
--- a/samtools.wdl
+++ b/samtools.wdl
@@ -98,297 +98,301 @@ task Faidx {
}
}
-task Index {
+task Fastq {
input {
- File bamFile
- String? outputBamPath
- String memory = "2G"
- Int timeMinutes = 1 + ceil(size(bamFile, "G") * 4)
+ File inputBam
+ String outputRead1
+ String? outputRead2
+ String? outputRead0
+ Int? includeFilter
+ Int? excludeFilter
+ Int? excludeSpecificFilter
+ Boolean appendReadNumber = false
+ Boolean outputQuality = false
+ Int? compressionLevel
+
+ Int threads = 1
+ String memory = "1G"
+ Int timeMinutes = 1 + ceil(size(inputBam) * 2)
String dockerImage = "quay.io/biocontainers/samtools:1.8--h46bd0b3_5"
}
- # Select_first is needed, otherwise womtool validate fails.
- String outputPath = select_first([outputBamPath, basename(bamFile)])
- String bamIndexPath = sub(outputPath, "\.bam$", ".bai")
-
command {
- bash -c '
- set -e
- # Make sure outputBamPath does not exist.
- if [ ! -f ~{outputPath} ]
- then
- mkdir -p "$(dirname ~{outputPath})"
- ln ~{bamFile} ~{outputPath}
- fi
- samtools index ~{outputPath} ~{bamIndexPath}
- '
+ samtools fastq \
+ ~{true="-1" false="-s" defined(outputRead2)} ~{outputRead1} \
+ ~{"-2 " + outputRead2} \
+ ~{"-0 " + outputRead0} \
+ ~{"-f " + includeFilter} \
+ ~{"-F " + excludeFilter} \
+ ~{"-G " + excludeSpecificFilter} \
+ ~{true="-N" false="-n" appendReadNumber} \
+ ~{true="-O" false="" outputQuality} \
+ ~{"-c " + compressionLevel} \
+ ~{"--threads " + threads} \
+ ~{inputBam}
}
output {
- File indexedBam = outputPath
- File index = bamIndexPath
+ File read1 = outputRead1
+ File? read2 = outputRead2
+ File? read0 = outputRead0
}
runtime {
+ cpu: threads
memory: memory
- time_minutes: timeMinutes
docker: dockerImage
+ time_minutes: timeMinutes
}
parameter_meta {
# inputs
- bamFile: {description: "The BAM file for which an index should be made.", category: "required"}
- outputBamPath: {description: "The location where the BAM file should be written to. The index will appear alongside this link to the BAM file.",
- category: "common"}
- memory: {description: "The amount of memory needed for the job.", category: "advanced"}
+ inputBam: {description: "The bam file to process.", category: "required"}
+ outputRead1: {description: "The location the reads (first reads for pairs, in case of paired-end sequencing) should be written to.", category: "required"}
+ outputRead2: {description: "The location the second reads from pairs should be written to.", category: "common"}
+ outputRead0: {description: "The location the unpaired reads should be written to (in case of paired-end sequenicng).", category: "advanced"}
+ includeFilter: {description: "Include reads with ALL of these flags. Corresponds to `-f`", category: "advanced"}
+ excludeFilter: {description: "Exclude reads with ONE OR MORE of these flags. Corresponds to `-F`", category: "advanced"}
+ excludeSpecificFilter: {description: "Exclude reads with ALL of these flags. Corresponds to `-G`", category: "advanced"}
+ appendReadNumber: {description: "Append /1 and /2 to the read name, or don't. Corresponds to `-n/N`", category: "advanced"}
+ outputQuality: {description: "Equivalent to samtools fastq's `-O` flag.", category: "advanced"}
+ threads: {description: "The number of threads to use.", category: "advanced"}
+ 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"}
}
}
-task Merge {
+task FilterShortReadsBam {
input {
- Array[File]+ bamFiles
- String outputBamPath = "merged.bam"
- Boolean force = true
-
- Int timeMinutes = 1 + ceil(size(bamFiles, "G") * 2)
+ File bamFile
+ String outputPathBam
+ String memory = "1G"
+ Int timeMinutes = 1 + ceil(size(bamFile, "G") * 8)
String dockerImage = "quay.io/biocontainers/samtools:1.8--h46bd0b3_5"
}
- String indexPath = sub(outputBamPath, "\.bam$",".bai")
+
+ String outputPathBamIndex = sub(outputPathBam, "\.bam$", ".bai")
command {
set -e
- mkdir -p "$(dirname ~{outputBamPath})"
- samtools merge ~{true="-f" false="" force} ~{outputBamPath} ~{sep=' ' bamFiles}
- samtools index ~{outputBamPath} ~{indexPath}
+ mkdir -p "$(dirname ~{outputPathBam})"
+ samtools view -h ~{bamFile} | \
+ awk 'length($10) > 30 || $1 ~/^@/' | \
+ samtools view -bS -> ~{outputPathBam}
+ samtools index ~{outputPathBam} ~{outputPathBamIndex}
}
output {
- File outputBam = outputBamPath
- File outputBamIndex = indexPath
+ File filteredBam = outputPathBam
+ File filteredBamIndex = outputPathBamIndex
}
runtime {
- docker: dockerImage
+ memory: memory
time_minutes: timeMinutes
+ docker: dockerImage
}
parameter_meta {
- # inputs
- bamFiles: {description: "The BAM files to merge.", category: "required"}
- outputBamPath: {description: "The location the merged BAM file should be written to.", category: "common"}
- force: {description: "Equivalent to samtools merge's `-f` flag.", category: "advanced"}
+ bamFile: {description: "The bam file to process.", category: "required"}
+ outputPathBam: {description: "The filtered bam file.", category: "common"}
+ memory: {description: "The amount of memory this job will use.", category: "advanced"}
timeMinutes: {description: "The maximum amount of time the job will run in minutes.", category: "advanced"}
- dockerImage: {description: "The docker image used for this task. Changing this may result in errors which the developers may choose not to address.",
- category: "advanced"}
+ dockerImage: {description: "The docker image used for this task. Changing this may result in errors which the developers may choose not to address.", category: "advanced"}
}
}
-task Sort {
+task Flagstat {
input {
File inputBam
String outputPath
- Boolean sortByName = false
- Int compressionLevel = 1
- String memory = "2G"
- String dockerImage = "quay.io/biocontainers/samtools:1.10--h9402c20_2"
- Int timeMinutes = 1 + ceil(size(inputBam, "G") * 2)
- Int? threads
+ String memory = "1G"
+ Int timeMinutes = 1 + ceil(size(inputBam, "G"))
+ String dockerImage = "quay.io/biocontainers/samtools:1.8--h46bd0b3_5"
}
command {
set -e
mkdir -p "$(dirname ~{outputPath})"
- samtools sort \
- -l ~{compressionLevel} \
- ~{true="-n" false="" sortByName} \
- ~{"--threads " + threads} \
- -o ~{outputPath} \
- ~{inputBam}
+ samtools flagstat ~{inputBam} > ~{outputPath}
}
output {
- File outputSortedBam = outputPath
+ File flagstat = outputPath
}
runtime {
- cpu: 1 + select_first([threads, 0])
memory: memory
- docker: dockerImage
time_minutes: timeMinutes
+ docker: dockerImage
}
parameter_meta {
# inputs
- inputBam: {description: "The input SAM file.", category: "required"}
- outputPath: {description: "Output directory path + output file.", category: "required"}
- sortByName: {description: "Sort the inputBam by read name instead of position.", category: "advanced"}
- compressionLevel: {description: "Compression level from 0 (uncompressed) to 9 (best).", category: "advanced"}
- memory: {description: "The amount of memory available to the job.", 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"}
- threads: {description: "The number of additional threads that will be used for this task.", category: "advanced"}
+ inputBam: {description: "The BAM file for which statistics should be retrieved.", category: "required"}
+ outputPath: {description: "The location the ouput should be written to.", category: "required"}
+ memory: {description: "The amount of memory needed for the job.", category: "advanced"}
timeMinutes: {description: "The maximum amount of time the job will run in minutes.", category: "advanced"}
- # outputs
- outputSortedBam: {description: "Sorted BAM file."}
+ 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 Markdup {
+task Index {
input {
- File inputBam
- String outputBamPath
-
- Int timeMinutes = 1 + ceil(size(inputBam, "G") * 2)
+ File bamFile
+ String? outputBamPath
+ String memory = "2G"
+ Int timeMinutes = 1 + ceil(size(bamFile, "G") * 4)
String dockerImage = "quay.io/biocontainers/samtools:1.8--h46bd0b3_5"
}
+ # Select_first is needed, otherwise womtool validate fails.
+ String outputPath = select_first([outputBamPath, basename(bamFile)])
+ String bamIndexPath = sub(outputPath, "\.bam$", ".bai")
+
command {
+ bash -c '
set -e
- mkdir -p "$(dirname ~{outputBamPath})"
- samtools markdup ~{inputBam} ~{outputBamPath}
+ # Make sure outputBamPath does not exist.
+ if [ ! -f ~{outputPath} ]
+ then
+ mkdir -p "$(dirname ~{outputPath})"
+ ln ~{bamFile} ~{outputPath}
+ fi
+ samtools index ~{outputPath} ~{bamIndexPath}
+ '
}
output {
- File outputBam = outputBamPath
+ File indexedBam = outputPath
+ File index = bamIndexPath
}
runtime {
- docker: dockerImage
+ memory: memory
time_minutes: timeMinutes
+ docker: dockerImage
}
parameter_meta {
# inputs
- inputBam: {description: "The BAM file to be processed.", category: "required"}
- outputBamPath: {description: "The location of the output BAM file.", category: "required"}
+ bamFile: {description: "The BAM file for which an index should be made.", category: "required"}
+ outputBamPath: {description: "The location where the BAM file should be written to. The index will appear alongside this link to the BAM file.",
+ category: "common"}
+ memory: {description: "The amount of memory needed for the job.", category: "advanced"}
timeMinutes: {description: "The maximum amount of time the job will run in minutes.", category: "advanced"}
dockerImage: {description: "The docker image used for this task. Changing this may result in errors which the developers may choose not to address.",
category: "advanced"}
}
}
-task FilterShortReadsBam {
+task Markdup {
input {
- File bamFile
- String outputPathBam
- String memory = "1G"
- Int timeMinutes = 1 + ceil(size(bamFile, "G") * 8)
+ File inputBam
+ String outputBamPath
+
+ Int timeMinutes = 1 + ceil(size(inputBam, "G") * 2)
String dockerImage = "quay.io/biocontainers/samtools:1.8--h46bd0b3_5"
}
- String outputPathBamIndex = sub(outputPathBam, "\.bam$", ".bai")
-
command {
set -e
- mkdir -p "$(dirname ~{outputPathBam})"
- samtools view -h ~{bamFile} | \
- awk 'length($10) > 30 || $1 ~/^@/' | \
- samtools view -bS -> ~{outputPathBam}
- samtools index ~{outputPathBam} ~{outputPathBamIndex}
+ mkdir -p "$(dirname ~{outputBamPath})"
+ samtools markdup ~{inputBam} ~{outputBamPath}
}
output {
- File filteredBam = outputPathBam
- File filteredBamIndex = outputPathBamIndex
+ File outputBam = outputBamPath
}
runtime {
- memory: memory
- time_minutes: timeMinutes
docker: dockerImage
+ time_minutes: timeMinutes
}
parameter_meta {
- bamFile: {description: "The bam file to process.", category: "required"}
- outputPathBam: {description: "The filtered bam file.", category: "common"}
- memory: {description: "The amount of memory this job will use.", category: "advanced"}
+ # inputs
+ inputBam: {description: "The BAM file to be processed.", category: "required"}
+ outputBamPath: {description: "The location of the output BAM file.", category: "required"}
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"}
+ 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 Flagstat {
+task Merge {
input {
- File inputBam
- String outputPath
+ Array[File]+ bamFiles
+ String outputBamPath = "merged.bam"
+ Boolean force = true
- String memory = "1G"
- Int timeMinutes = 1 + ceil(size(inputBam, "G"))
+ Int timeMinutes = 1 + ceil(size(bamFiles, "G") * 2)
String dockerImage = "quay.io/biocontainers/samtools:1.8--h46bd0b3_5"
}
+ String indexPath = sub(outputBamPath, "\.bam$",".bai")
command {
set -e
- mkdir -p "$(dirname ~{outputPath})"
- samtools flagstat ~{inputBam} > ~{outputPath}
+ mkdir -p "$(dirname ~{outputBamPath})"
+ samtools merge ~{true="-f" false="" force} ~{outputBamPath} ~{sep=' ' bamFiles}
+ samtools index ~{outputBamPath} ~{indexPath}
}
output {
- File flagstat = outputPath
+ File outputBam = outputBamPath
+ File outputBamIndex = indexPath
}
runtime {
- memory: memory
- time_minutes: timeMinutes
docker: dockerImage
+ time_minutes: timeMinutes
}
parameter_meta {
# inputs
- inputBam: {description: "The BAM file for which statistics should be retrieved.", category: "required"}
- outputPath: {description: "The location the ouput should be written to.", category: "required"}
- memory: {description: "The amount of memory needed for the job.", category: "advanced"}
+ bamFiles: {description: "The BAM files to merge.", category: "required"}
+ outputBamPath: {description: "The location the merged BAM file should be written to.", category: "common"}
+ force: {description: "Equivalent to samtools merge's `-f` flag.", 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 Fastq {
+task Sort {
input {
File inputBam
- String outputRead1
- String? outputRead2
- String? outputRead0
- Int? includeFilter
- Int? excludeFilter
- Int? excludeSpecificFilter
- Boolean appendReadNumber = false
- Boolean outputQuality = false
- Int? compressionLevel
+ String outputPath
+ Boolean sortByName = false
+ Int compressionLevel = 1
- Int threads = 1
- String memory = "1G"
- Int timeMinutes = 1 + ceil(size(inputBam) * 2)
- String dockerImage = "quay.io/biocontainers/samtools:1.8--h46bd0b3_5"
+ String memory = "2G"
+ String dockerImage = "quay.io/biocontainers/samtools:1.10--h9402c20_2"
+ Int timeMinutes = 1 + ceil(size(inputBam, "G") * 2)
+ Int? threads
}
command {
- samtools fastq \
- ~{true="-1" false="-s" defined(outputRead2)} ~{outputRead1} \
- ~{"-2 " + outputRead2} \
- ~{"-0 " + outputRead0} \
- ~{"-f " + includeFilter} \
- ~{"-F " + excludeFilter} \
- ~{"-G " + excludeSpecificFilter} \
- ~{true="-N" false="-n" appendReadNumber} \
- ~{true="-O" false="" outputQuality} \
- ~{"-c " + compressionLevel} \
+ set -e
+ mkdir -p "$(dirname ~{outputPath})"
+ samtools sort \
+ -l ~{compressionLevel} \
+ ~{true="-n" false="" sortByName} \
~{"--threads " + threads} \
+ -o ~{outputPath} \
~{inputBam}
}
output {
- File read1 = outputRead1
- File? read2 = outputRead2
- File? read0 = outputRead0
+ File outputSortedBam = outputPath
}
runtime {
- cpu: threads
+ cpu: 1 + select_first([threads, 0])
memory: memory
docker: dockerImage
time_minutes: timeMinutes
@@ -396,20 +400,16 @@ task Fastq {
parameter_meta {
# inputs
- inputBam: {description: "The bam file to process.", category: "required"}
- outputRead1: {description: "The location the reads (first reads for pairs, in case of paired-end sequencing) should be written to.", category: "required"}
- outputRead2: {description: "The location the second reads from pairs should be written to.", category: "common"}
- outputRead0: {description: "The location the unpaired reads should be written to (in case of paired-end sequenicng).", category: "advanced"}
- includeFilter: {description: "Include reads with ALL of these flags. Corresponds to `-f`", category: "advanced"}
- excludeFilter: {description: "Exclude reads with ONE OR MORE of these flags. Corresponds to `-F`", category: "advanced"}
- excludeSpecificFilter: {description: "Exclude reads with ALL of these flags. Corresponds to `-G`", category: "advanced"}
- appendReadNumber: {description: "Append /1 and /2 to the read name, or don't. Corresponds to `-n/N`", category: "advanced"}
- outputQuality: {description: "Equivalent to samtools fastq's `-O` flag.", category: "advanced"}
- threads: {description: "The number of threads to use.", category: "advanced"}
- memory: {description: "The amount of memory this job will use.", category: "advanced"}
+ inputBam: {description: "The input SAM file.", category: "required"}
+ outputPath: {description: "Output directory path + output file.", category: "required"}
+ sortByName: {description: "Sort the inputBam by read name instead of position.", category: "advanced"}
+ compressionLevel: {description: "Compression level from 0 (uncompressed) to 9 (best).", category: "advanced"}
+ memory: {description: "The amount of memory available to the job.", 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"}
+ threads: {description: "The number of additional threads that will be used for this task.", 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
+ outputSortedBam: {description: "Sorted BAM file."}
}
}
@@ -518,38 +518,4 @@ task View {
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 FilterShortReadsBam {
- input {
- File bamFile
- String outputPathBam
- String dockerImage = "quay.io/biocontainers/samtools:1.8--h46bd0b3_5"
- }
-
- String outputPathBamIndex = sub(outputPathBam, "\.bam$", ".bai")
-
- command {
- set -e
- mkdir -p "$(dirname ~{outputPathBam})"
- samtools view -h ~{bamFile} | \
- awk 'length($10) > 30 || $1 ~/^@/' | \
- samtools view -bS -> ~{outputPathBam}
- samtools index ~{outputPathBam} ~{outputPathBamIndex}
- }
-
- output {
- File filteredBam = outputPathBam
- File filteredBamIndex = outputPathBamIndex
- }
-
- runtime {
- docker: dockerImage
- }
-
- parameter_meta {
- bamFile: {description: "The bam file to process.", category: "required"}
- outputPathBam: {description: "The filtered bam file.", category: "common"}
- 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"}
- }
-}
+}
\ No newline at end of file