diff --git a/CHANGELOG.md b/CHANGELOG.md
index 67ea94a03e31ffcbc7ee591ecb4bbf52bea1cec4..a0964883666a89e028314eaa5973cdc95d90abbe 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -9,7 +9,11 @@ This document is user facing. Please word the changes in such a way
that users understand how the changes affect the new version.
-->
-version 4.0.0-develop
+version 5.0.0-dev
+---------------------------
++ Add wdl file for pacbio's bam2fastx tool.
+
+version 4.0.0
---------------------------
+ Added a task for GRIDSS.
+ Picard MergeVcf now uses compression level 1 by default.
diff --git a/VERSION b/VERSION
index 944880fa15e85084780c290b929924d3f8b6085f..ee74734aa2258df77aa09402d55798a1e2e55212 100644
--- a/VERSION
+++ b/VERSION
@@ -1 +1 @@
-3.2.0
+4.1.0
diff --git a/bam2fastx.wdl b/bam2fastx.wdl
new file mode 100644
index 0000000000000000000000000000000000000000..5e5fb50afe854af5ea404f977f835da00f4e1c1f
--- /dev/null
+++ b/bam2fastx.wdl
@@ -0,0 +1,127 @@
+version 1.0
+
+# Copyright (c) 2020 Sequencing Analysis Support Core - 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 Bam2Fasta {
+ input {
+ File inputFile
+ File bamIndex
+ String outputPrefix
+ Int compressionLevel = 1
+ Boolean splitByBarcode = false
+
+ String? seqIdPrefix
+
+ String memory = "2G"
+ Int timeMinutes = 15
+ String dockerImage = "quay.io/biocontainers/bam2fastx:1.3.0--he1c1bb9_8"
+ }
+
+ command {
+ set -e
+ mkdir -p "$(dirname ~{outputPrefix})"
+ bam2fasta \
+ --output ~{outputPrefix} \
+ -c ~{compressionLevel} \
+ ~{true="--split-barcodes" false="" splitByBarcode} \
+ ~{"--seqid-prefix " + seqIdPrefix} \
+ ~{inputFile}
+ }
+
+ output {
+ File fastaFile = outputPrefix + ".fasta.gz"
+ }
+
+ runtime {
+ memory: memory
+ time_minutes: timeMinutes
+ docker: dockerImage
+ }
+
+ parameter_meta {
+ # inputs
+ inputFile: {description: "The input pacbio bam file.", category: "required"}
+ bamIndex: {description: "The .pbi index for the input file.", category: "required"}
+ outputPrefix: {description: "Output directory path + output file prefix.", category: "required"}
+ compressionLevel: {description: "Gzip compression level [1-9]", category: "advanced"}
+ splitByBarcode: {description: "Split output into multiple fasta files, by barcode pairs.", category: "advanced"}
+ seqIdPrefix: {description: "Prefix for sequence IDs in headers.", category: "advanced"}
+ memory: {description: "The amount of memory available to the job.", category: "advanced"}
+ timeMinutes: {description: "The maximum amount of time the job will run in minutes.", category: "advanced"}
+ dockerImage: {description: "The docker image used for this task. Changing this may result in errors which the developers may choose not to address.", category: "advanced"}
+
+ # outputs
+ fastaFile: {description: "The fasta output file."}
+ }
+}
+
+task Bam2Fastq {
+ input {
+ File inputFile
+ File bamIndex
+ String outputPrefix
+ Int compressionLevel = 1
+ Boolean splitByBarcode = false
+
+ String? seqIdPrefix
+
+ String memory = "2G"
+ Int timeMinutes = 15
+ String dockerImage = "quay.io/biocontainers/bam2fastx:1.3.0--he1c1bb9_8"
+ }
+
+ command {
+ set -e
+ mkdir -p "$(dirname ~{outputPrefix})"
+ bam2fastq \
+ --output ~{outputPrefix} \
+ -c ~{compressionLevel} \
+ ~{true="--split-barcodes" false="" splitByBarcode} \
+ ~{"--seqid-prefix " + seqIdPrefix} \
+ ~{inputFile}
+ }
+
+ output {
+ File fastqFile = outputPrefix + ".fastq.gz"
+ }
+
+ runtime {
+ memory: memory
+ time_minutes: timeMinutes
+ docker: dockerImage
+ }
+
+ parameter_meta {
+ # inputs
+ inputFile: {description: "The input pacbio bam file.", category: "required"}
+ bamIndex: {description: "The .pbi index for the input file.", category: "required"}
+ outputPrefix: {description: "Output directory path + output file prefix.", category: "required"}
+ compressionLevel: {description: "Gzip compression level [1-9]", category: "advanced"}
+ splitByBarcode: {description: "Split output into multiple fastq files, by barcode pairs.", category: "advanced"}
+ seqIdPrefix: {description: "Prefix for sequence IDs in headers.", category: "advanced"}
+ memory: {description: "The amount of memory available to 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"}
+
+ # outputs
+ fastqFile: {description: "The fastq output file."}
+ }
+}
diff --git a/bcftools.wdl b/bcftools.wdl
index 2677899be23d70b102a357a9ff9b593c2fbb2832..8875903b2a6ac9126a794b891cc72df10c5dacef 100644
--- a/bcftools.wdl
+++ b/bcftools.wdl
@@ -58,7 +58,7 @@ task View {
parameter_meta {
inputFile: {description: "A vcf or bcf file.", category: "required"}
outputPath: {description: "The location the output VCF file should be written.", category: "common"}
- outputType: {description: "Output type: v=vcf, z=vcf.gz, b=bcf, u=uncompressed bcf"}
+ outputType: {description: "Output type: v=vcf, z=vcf.gz, b=bcf, u=uncompressed bcf", category: "advanced"}
memory: {description: "The amount of memory this job will use.", category: "advanced"}
compressionLevel: {description: "Compression level from 0 (uncompressed) to 9 (best).", category: "advanced"}
timeMinutes: {description: "The maximum amount of time the job will run in minutes.", category: "advanced"}
diff --git a/scripts b/scripts
index 325a129c14de56b2055ee0e9e0da7dc74df5fec4..c0b48b0a916913d1e6751d7744d1cec37559a81f 160000
--- a/scripts
+++ b/scripts
@@ -1 +1 @@
-Subproject commit 325a129c14de56b2055ee0e9e0da7dc74df5fec4
+Subproject commit c0b48b0a916913d1e6751d7744d1cec37559a81f