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update WDL comments to reflect minimap2 option #110

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merged 2 commits into from
Jun 10, 2020
Merged

update WDL comments to reflect minimap2 option #110

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update WDL comments to reflect minimap2 option
dpark01 Jun 8, 2020
2108857
Merge branch 'master' into dp-mm2
dpark01 Jun 10, 2020
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6 changes: 3 additions & 3 deletions pipes/WDL/tasks/tasks_assembly.wdl
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Original file line number Diff line number Diff line change
Expand Up @@ -242,7 +242,7 @@ task ivar_trim {

task align_reads {
meta {
description: "Align unmapped reads to a reference genome, either using novoalign (default) or bwa. Produces an aligned bam file (including all unmapped reads), an aligned-only bam file, both sorted and indexed, along with samtools flagstat output, fastqc stats (on mapped only reads), and some basic figures of merit."
description: "Align unmapped reads to a reference genome, either using novoalign (default), minimap2, or bwa. Produces an aligned bam file (including all unmapped reads), an aligned-only bam file, both sorted and indexed, along with samtools flagstat output, fastqc stats (on mapped only reads), and some basic figures of merit."
}

input {
Expand All @@ -251,7 +251,7 @@ task align_reads {

File? novocraft_license

String? aligner="novoalign" # novoalign or bwa
String? aligner="novoalign"
String? aligner_options
Boolean? skip_mark_dupes=false

Expand All @@ -261,7 +261,7 @@ task align_reads {
}

parameter_meta {
aligner: { description: "Short read aligner to use: novoalign or bwa. (Default: novoalign)" }
aligner: { description: "Short read aligner to use: novoalign, minimap2, or bwa. (Default: novoalign)" }
}

command {
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