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biowdl
tasks
Commits
67116dfe
Commit
67116dfe
authored
4 years ago
by
JasperBoom
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Update version of tools.
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e93b3c5e
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CHANGELOG.md
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CHANGELOG.md
TO-DO.md
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TO-DO.md
cutadapt.wdl
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cutadapt.wdl
stringtie.wdl
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stringtie.wdl
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30 deletions
CHANGELOG.md
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View file @
67116dfe
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@@ -10,6 +10,8 @@ that users understand how the changes affect the new version.
version 5.0.0-dev
---------------------------
+
Update CutAdapt to version 3.0.0.
+
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`
.
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TO-DO.md
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#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## Out of date with new cluster & parameter_meta: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
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cutadapt.wdl
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@@ -85,7 +85,7 @@ task Cutadapt {
Int cores = 4
String memory = "~{300 + 100 * cores}M"
Int timeMinutes = 1 + ceil(size([read1, read2], "G") * 12.0 / cores)
String dockerImage = "quay.io/biocontainers/cutadapt:
2.1
0--py37hf01694f_
1
"
String dockerImage = "quay.io/biocontainers/cutadapt:
3.
0--py37hf01694f_
0
"
}
String realRead2output = select_first([read2output, "cut_r2.fq.gz"])
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stringtie.wdl
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@@ -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 {
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@@ -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 {
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