Unverified Commit f438bf4d authored by Cedrick Agaser's avatar Cedrick Agaser Committed by GitHub
Browse files

Merge pull request #273 from biowdl/addNewMultiPackageContainerWithUmiAndSamtools

Add new multi package container with umi and samtools
parents 2d04addf c791c96a
......@@ -10,7 +10,9 @@ that users understand how the changes affect the new version.
version 5.0.0-dev
---------------------------
+ UMI-tools (dedup): Add tempdir
+ UMI-tools: re-introduce samtools indexing
+ UMI-tools: update default dockerImage to use umitools v1.1.1
+ UMI-tools dedup: Add tempdir
+ Update BCFTOOLS view: add options for filtering (include, exclude, excludeUncalled).
+ Duphold: add duphold.wdl.
+ Add new wdl file prepareShiny.wdl for creating input files for shiny app.
......
......@@ -31,7 +31,7 @@ task Extract {
Boolean threePrime = false
Int timeMinutes = 1 + ceil(size([read1, read2], "G") * 2)
String dockerImage = "quay.io/biocontainers/mulled-v2-509311a44630c01d9cb7d2ac5727725f51ea43af:6089936aca6219b5bb5f54210ac5eb456c7503f2-0"
String dockerImage = "quay.io/biocontainers/mulled-v2-509311a44630c01d9cb7d2ac5727725f51ea43af:f9d5e41daab14b273ff04f257621890af6f82b93-0"
}
command {
......@@ -87,7 +87,7 @@ task Dedup {
String memory = "25G"
Int timeMinutes = 30 + ceil(size(inputBam, "G") * 30)
String dockerImage = "quay.io/biocontainers/umi_tools:1.1.1--py38h0213d0e_1"
String dockerImage = "quay.io/biocontainers/mulled-v2-509311a44630c01d9cb7d2ac5727725f51ea43af:f9d5e41daab14b273ff04f257621890af6f82b93-0"
}
String outputBamIndex = sub(outputBamPath, "\.bam$", ".bai")
......@@ -102,10 +102,12 @@ task Dedup {
~{"--umi-separator=" + umiSeparator} \
~{true="--paired" false="" paired} \
--temp-dir=~{tmpDir}
samtools index ~{outputBamPath} ~{outputBamIndex}
}
output {
File deduppedBam = outputBamPath
File deduppedBamIndex = outputBamIndex
File? editDistance = "~{statsPrefix}_edit_distance.tsv"
File? umiStats = "~{statsPrefix}_per_umi.tsv"
File? positionStats = "~{statsPrefix}_per_umi_per_position.tsv"
......@@ -132,6 +134,7 @@ task Dedup {
# outputs
deduppedBam: {description: "Deduplicated BAM file."}
deduppedBamIndex: {description: "Index of the deduplicated BAM file."}
editDistance: {description: "Report of the (binned) average edit distance between the UMIs at each position."}
umiStats: {description: "UMI-level summary statistics."}
positionStats: {description: "The counts for unique combinations of UMI and position."}
......
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