Merge pull request #265 from biowdl/BIOWDL-528

BIOWDL-528: Update version of tools to match new version in workflows.

Merge pull request #265 from biowdl/BIOWDL-528
d9eedf32 · Jasper · GitHub · e93b3c5e · b5558be1 · d9eedf32
Unverified Commit d9eedf32 authored 4 years ago by Jasper Committed by GitHub 4 years ago
--- a/.travis.yml
+++ b/.travis.yml
@@ -19,4 +19,5 @@ before_install:
 install:
  - conda install --file requirements-test.txt

-script: bash scripts/biowdl_lint.sh
+script:
+  - bash scripts/biowdl_lint.sh
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -10,6 +10,13 @@ that users understand how the changes affect the new version.

 version 5.0.0-dev
 ---------------------------
+ Update Lima to version 2.0.0.
+ Update IsoSeq3 to version 3.4.0.
+ Update samtools to version 1.11.
+ Update Picard to version 2.23.8.
+ Update NanoPlot to version 1.32.1.
+ Update MultiQC to version 1.9.
+ Update StringTie to version 2.1.4.
 + Complete `parameter_meta` for tasks missing the outputs.
 + DeepVariant: Add an optional input for the gvcf index.
 + Samtools: `Sort` task now has `threads` in runtime instead of `1`.

--- a/TO-DO.md
+++ b/TO-DO.md
-#TO-DO
-This file describes WDL files and tasks within those files which need
-more specific attention than just adding outputs to the parameter_meta.
-
-Some tasks have not been updated to match the new SLURM requirements and are
-missing a parameter_meta section.
-
-Some tasks are importing other WDL files.
-
-## Out of date with new cluster & parameter_meta:
-* common.wdl: `AppendToStringArray`, `CheckFileMD5`, `ConcatenateTextFiles`,
-              `Copy`, `CreateLink`, `MapMd5`, `StringArrayMd5`
-* fastqsplitter.wdl: `Fastqsplitter`
-* flash.wdl: `Flash`
-* macs2.wdl: `PeakCalling`
-* ncbi.wdl: `GenomeDownload`, `DownloadNtFasta`, `DownloadAccessionToTaxId`
-* seqtk.wdl: `Sample`
-* spades.wdl: `Spades`
-* unicycler.wdl: `Unicycler`
-* wisestork.wdl: `Count`, `GcCorrect`, `Newref`, `Zscore`
-* picard.wdl: `ScatterIntervalList`
-
-## Requires input from others:
-These tasks below are still missing descriptions `outputs` in
-the `parameter_meta`.
-* somaticseq.wdl
-* picard.wdl
--- a/VERSION
+++ b/VERSION
-4.1.0
+5.0.0
--- a/isoseq3.wdl
+++ b/isoseq3.wdl
@@ -34,7 +34,7 @@ task Refine {
        Int threads = 2
        String memory = "2G"
        Int timeMinutes = 30
-        String dockerImage = "quay.io/biocontainers/isoseq3:3.3.0--0"
+        String dockerImage = "quay.io/biocontainers/isoseq3:3.4.0--0"
    }

    command {

--- a/lima.wdl
+++ b/lima.wdl
@@ -51,7 +51,7 @@ task Lima {
        Int threads = 2
        String memory = "2G"
        Int timeMinutes = 30
-        String dockerImage = "quay.io/biocontainers/lima:1.11.0--0"
+        String dockerImage = "quay.io/biocontainers/lima:2.0.0--0"
    }

    Map[String, String] libraryDesignOptions = {"same": "--same", "different": "--different", "neighbors": "--neighbors"}

--- a/minimap2.wdl
+++ b/minimap2.wdl
@@ -33,7 +33,7 @@ task Indexing {
        Int cores = 1
        String memory = "4G"
        Int timeMinutes = 10
-        String dockerImage = "quay.io/biocontainers/minimap2:2.17--h84994c4_0"
+        String dockerImage = "quay.io/biocontainers/minimap2:2.17--hed695b0_3"
    }

    command {
@@ -100,7 +100,7 @@ task Mapping {
        Int cores = 4
        String memory = "30G"
        Int timeMinutes = 1 + ceil(size(queryFile, "G") * 200 / cores)
-        String dockerImage = "quay.io/biocontainers/minimap2:2.17--h84994c4_0"
+        String dockerImage = "quay.io/biocontainers/minimap2:2.17--hed695b0_3"
    }

    command {

--- a/multiqc.wdl
+++ b/multiqc.wdl
@@ -58,7 +58,7 @@ task MultiQC {

        String? memory
        Int timeMinutes = 2 + ceil(size(reports, "G") * 8)
-        String dockerImage = "quay.io/biocontainers/multiqc:1.7--py_1"
+        String dockerImage = "quay.io/biocontainers/multiqc:1.9--py_1"
    }

    Int memoryGb = 2 + ceil(size(reports, "G"))

--- a/nanopack.wdl
+++ b/nanopack.wdl
@@ -42,7 +42,7 @@ task NanoPlot {
        Int threads = 2
        String memory = "2G"
        Int timeMinutes = 15
-        String dockerImage = "quay.io/biocontainers/nanoplot:1.32.0--py_0"
+        String dockerImage = "quay.io/biocontainers/nanoplot:1.32.1--py_0"
    }

    Map[String, String] fileTypeOptions = {"fastq": "--fastq ", "fasta": "--fasta ", "fastq_rich": "--fastq_rich ", "fastq_minimal": "--fastq_minimal ", "summary": "--summary ", "bam": "--bam ", "ubam": "--ubam ", "cram": "--cram ", "pickle": "--pickle ", "feather": "--feather "}

--- a/picard.wdl
+++ b/picard.wdl
@@ -29,7 +29,7 @@ task BedToIntervalList {
        String javaXmx = "3G"
        String memory = "4G"
        Int timeMinutes = 5
-        String dockerImage = "quay.io/biocontainers/picard:2.20.5--0"
+        String dockerImage = "quay.io/biocontainers/picard:2.23.8--0"
    }

    command {
@@ -89,7 +89,7 @@ task CollectHsMetrics {
        # Additional * 2 because picard multiple metrics reads the
        # reference fasta twice.
        Int timeMinutes = 1 + ceil(size(referenceFasta, "G") * 3 * 2) + ceil(size(inputBam, "G") * 6)
-        String dockerImage = "quay.io/biocontainers/picard:2.23.2--0"
+        String dockerImage = "quay.io/biocontainers/picard:2.23.8--0"
    }

    command {
@@ -158,7 +158,7 @@ task CollectMultipleMetrics {
        Int memoryMb = javaXmxMb + 512
        # Additional * 2 because picard multiple metrics reads the reference fasta twice.
        Int timeMinutes = 1 + ceil(size(referenceFasta, "G") * 3 * 2) + ceil(size(inputBam, "G") * 6)
-        String dockerImage = "quay.io/biocontainers/picard:2.23.2--0"
+        String dockerImage = "quay.io/biocontainers/picard:2.23.8--0"
    }

    command {
@@ -284,7 +284,7 @@ task CollectRnaSeqMetrics {
        String memory = "9G"
        # With 6 minutes per G there were several timeouts.
        Int timeMinutes = 1 + ceil(size(inputBam, "G") * 12)
-        String dockerImage = "quay.io/biocontainers/picard:2.23.2--0"
+        String dockerImage = "quay.io/biocontainers/picard:2.23.8--0"
    }

    command {
@@ -342,7 +342,7 @@ task CollectTargetedPcrMetrics {
        String javaXmx = "3G"
        String memory = "4G"
        Int timeMinutes = 1 + ceil(size(inputBam, "G") * 6)
-        String dockerImage = "quay.io/biocontainers/picard:2.23.2--0"
+        String dockerImage = "quay.io/biocontainers/picard:2.23.8--0"
    }

    command {
@@ -404,7 +404,7 @@ task CollectVariantCallingMetrics {
        String javaXmx =  "8G"
        String memory = "9G"
        Int timeMinutes = 1440
-        String dockerImage = "quay.io/biocontainers/picard:2.23.2--0"
+        String dockerImage = "quay.io/biocontainers/picard:2.23.8--0"
    }

    command {
@@ -453,7 +453,7 @@ task CreateSequenceDictionary {

        String javaXmx = "2G"
        String memory = "3G"
-        String dockerImage = "quay.io/biocontainers/picard:2.23.2--0"
+        String dockerImage = "quay.io/biocontainers/picard:2.23.8--0"
    }

    command {
@@ -503,7 +503,7 @@ task GatherBamFiles {
        Int memoryMb = javaXmxMb + 512
        # One minute per input gigabyte.
        Int timeMinutes = 1 + ceil(size(inputBams, "G") * 1)
-        String dockerImage = "quay.io/biocontainers/picard:2.23.2--0"
+        String dockerImage = "quay.io/biocontainers/picard:2.23.8--0"
    }

    command {
@@ -558,7 +558,7 @@ task GatherVcfs {
        String javaXmx = "4G"
        String memory = "5G"
        Int timeMinutes = 1 + ceil(size(inputVcfs, "G") * 2)
-        String dockerImage = "quay.io/biocontainers/picard:2.23.2--0"
+        String dockerImage = "quay.io/biocontainers/picard:2.23.8--0"
    }

    command {
@@ -622,7 +622,7 @@ task MarkDuplicates {
        String memoryMb = javaXmxMb + 512

        Int timeMinutes = 1 + ceil(size(inputBams, "G") * 8)
-        String dockerImage = "quay.io/biocontainers/picard:2.23.2--0"
+        String dockerImage = "quay.io/biocontainers/picard:2.23.8--0"
    }

    # Task is assuming query-sorted input so that the Secondary and Supplementary reads get
@@ -701,7 +701,7 @@ task MergeVCFs {
        String javaXmx = "4G"
        String memory = "5G"
        Int timeMinutes = 1 + ceil(size(inputVCFs, "G")) * 2
-        String dockerImage = "quay.io/biocontainers/picard:2.23.2--0"
+        String dockerImage = "quay.io/biocontainers/picard:2.23.8--0"
    }

    # Using MergeVcfs instead of GatherVcfs so we can create indices.
@@ -757,7 +757,7 @@ task SamToFastq {
        String javaXmx = "16G" # High memory default to avoid crashes.
        String memory = "17G"
        Int timeMinutes = 30
-        String dockerImage = "quay.io/biocontainers/picard:2.23.2--0"
+        String dockerImage = "quay.io/biocontainers/picard:2.23.8--0"

        File? noneFile
    }
@@ -818,7 +818,7 @@ task ScatterIntervalList {

        String javaXmx = "3G"
        String memory = "4G"
-        String dockerImage = "quay.io/biocontainers/picard:2.23.2--0"
+        String dockerImage = "quay.io/biocontainers/picard:2.23.8--0"
    }

    command {
@@ -859,7 +859,7 @@ task SortSam {
        # GATK Best practices uses 75000 here: https://github.com/gatk-workflows/broad-prod-wgs-germline-snps-indels/blob/d2934ed656ade44801f9cfe1c0e78d4f80684b7b/PairedEndSingleSampleWf-fc-hg38.wdl#L778
        Int XmxGb = ceil(maxRecordsInRam / 125001.0)
        Int timeMinutes = 1 + ceil(size(inputBam, "G") * 3)
-        String dockerImage = "quay.io/biocontainers/picard:2.23.2--0"
+        String dockerImage = "quay.io/biocontainers/picard:2.23.8--0"
    }

    command {
@@ -917,7 +917,7 @@ task SortVcf {
        String javaXmx = "8G"
        String memory = "9G"
        Int timeMinutes = 1 + ceil(size(vcfFiles, "G") * 5)
-        String dockerImage = "quay.io/biocontainers/picard:2.20.5--0"
+        String dockerImage = "quay.io/biocontainers/picard:2.23.8--0"
    }


@@ -967,7 +967,7 @@ task RenameSample {
        String javaXmx = "8G"
        String memory = "9G"
        Int timeMinutes = 1 + ceil(size(inputVcf, "G") * 2)
-        String dockerImage = "quay.io/biocontainers/picard:2.19.0--0"
+        String dockerImage = "quay.io/biocontainers/picard:2.23.8--0"
    }

    command {

--- a/samtools.wdl
+++ b/samtools.wdl
@@ -69,7 +69,7 @@ task Faidx {
        String outputDir

        String memory = "2G"
-        String dockerImage = "quay.io/biocontainers/samtools:1.10--h9402c20_2"
+        String dockerImage = "quay.io/biocontainers/samtools:1.11--h6270b1f_0"
    }

    command {
@@ -118,7 +118,7 @@ task Fastq {
        Int threads = 1
        String memory = "1G"
        Int timeMinutes = 1 + ceil(size(inputBam) * 2)
-        String dockerImage = "quay.io/biocontainers/samtools:1.10--h9402c20_2"
+        String dockerImage = "quay.io/biocontainers/samtools:1.11--h6270b1f_0"
    }

    command {
@@ -180,7 +180,7 @@ task FilterShortReadsBam {

        String memory = "1G"
        Int timeMinutes = 1 + ceil(size(bamFile, "G") * 8)
-        String dockerImage = "quay.io/biocontainers/samtools:1.10--h9402c20_2"
+        String dockerImage = "quay.io/biocontainers/samtools:1.11--h6270b1f_0"
    }

    String outputPathBamIndex = sub(outputPathBam, "\.bam$", ".bai")
@@ -226,7 +226,7 @@ task Flagstat {

        String memory = "256M"  # Only 40.5 MiB used for 150G bam file.
        Int timeMinutes = 1 + ceil(size(inputBam, "G"))
-        String dockerImage = "quay.io/biocontainers/samtools:1.10--h9402c20_2"
+        String dockerImage = "quay.io/biocontainers/samtools:1.11--h6270b1f_0"
    }

    command {
@@ -266,7 +266,7 @@ task Index {

        String memory = "2G"
        Int timeMinutes = 1 + ceil(size(bamFile, "G") * 4)
-        String dockerImage = "quay.io/biocontainers/samtools:1.10--h9402c20_2"
+        String dockerImage = "quay.io/biocontainers/samtools:1.11--h6270b1f_0"
    }

    # Select_first is needed, otherwise womtool validate fails.
@@ -317,7 +317,7 @@ task Markdup {
        String outputBamPath

        Int timeMinutes = 1 + ceil(size(inputBam, "G") * 2)
-        String dockerImage = "quay.io/biocontainers/samtools:1.10--h9402c20_2"
+        String dockerImage = "quay.io/biocontainers/samtools:1.11--h6270b1f_0"
    }

    command {
@@ -356,7 +356,7 @@ task Merge {
        Int threads = 1
        String memory = "4G"
        Int timeMinutes = 1 + ceil(size(bamFiles, "G") * 2)
-        String dockerImage = "quay.io/biocontainers/samtools:1.10--h9402c20_2"
+        String dockerImage = "quay.io/biocontainers/samtools:1.11--h6270b1f_0"
    }

    String indexPath = sub(outputBamPath, "\.bam$",".bai")
@@ -411,7 +411,7 @@ task Sort {
        Int threads = 1
        Int memoryGb = 1 + threads * memoryPerThreadGb
        Int timeMinutes = 1 + ceil(size(inputBam, "G") * 3)
-        String dockerImage = "quay.io/biocontainers/samtools:1.10--h9402c20_2"
+        String dockerImage = "quay.io/biocontainers/samtools:1.11--h6270b1f_0"
    }

    # Select first needed as outputPath is optional input (bug in cromwell).
@@ -523,7 +523,7 @@ task View {
        Int threads = 1
        String memory = "1G"
        Int timeMinutes = 1 + ceil(size(inFile, "G") * 5)
-        String dockerImage = "quay.io/biocontainers/samtools:1.10--h9402c20_2"
+        String dockerImage = "quay.io/biocontainers/samtools:1.11--h6270b1f_0"
    }

    String outputIndexPath = basename(outputFileName) + ".bai"

--- a/scripts @ 85e2ec54
+++ b/scripts @ 85e2ec54
-Subproject commit 0cca0f40a8e9121e8dcc9e76838f85835a0d8e94
+Subproject commit 85e2ec542b65be5f2a25c22db05c28700fbe6db5
--- a/stringtie.wdl
+++ b/stringtie.wdl
@@ -35,7 +35,7 @@ task Stringtie {
        Int threads = 1
        String memory = "2G"
        Int timeMinutes = 1 + ceil(size(bam, "G") * 60 / threads)
-        String dockerImage = "quay.io/biocontainers/stringtie:1.3.4--py35_0"
+        String dockerImage = "quay.io/biocontainers/stringtie:2.1.4--h7e0af3c_0"
    }

    command {
@@ -101,7 +101,7 @@ task Merge {

        String memory = "10G"
        Int timeMinutes = 1 + ceil(size(gtfFiles, "G") * 20)
-        String dockerImage = "quay.io/biocontainers/stringtie:1.3.4--py35_0"
+        String dockerImage = "quay.io/biocontainers/stringtie:2.1.4--h7e0af3c_0"
    }

    command {