Merge branch 'develop' into BIOWDL-532

CHANGELOG.md

@@ -12,13 +12,16 @@ version 5.0.0-dev
 ---------------------------
 + mergePacBio: Rename `mergedReport` to `outputPathMergedReport`.
 + Lima: Fix copy commands & return to `fl` naming.
++ Fixed the `size` call in the default for gffread's timeMinutes, to retrieve
+  GBs instead of bytes.
++ Update stringtie to version 1.3.6.
 + 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.
++ ~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`.

gffread.wdl

@@ -32,7 +32,7 @@ task GffRead {
         String? proteinFastaPath
         String? filteredGffPath
 
-        Int timeMinutes = 1 + ceil(size(inputGff) * 10)
+        Int timeMinutes = 1 + ceil(size(inputGff, "G") * 10)
         String dockerImage = "quay.io/biocontainers/gffread:0.9.12--0"
     }
 

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:2.1.4--h7e0af3c_0"
+        String dockerImage = "quay.io/biocontainers/stringtie:1.3.6--h92e31bf_0"
     }
 
     command {