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Fixed WDL of task assemble for the trinity-spades case. Removed workaround for a now-fixed Cromwell issue. #952

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May 26, 2019
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Fixed WDL of task assemble for the trinity-spades case. Removed workaround for a now-fixed Cromwell issue. #952

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9 changes: 4 additions & 5 deletions pipes/WDL/workflows/tasks/tasks_assembly.wdl
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Original file line number Diff line number Diff line change
Expand Up @@ -9,7 +9,6 @@ task assemble {
String? assembler="trinity" # trinity, spades, or trinity-spades
Boolean? always_succeed=false

String cleaned_assembler = select_first([assembler, ""]) # workaround for https://gatkforums.broadinstitute.org/wdl/discussion/10462/string-type-in-output-section
# do this in two steps in case the input doesn't actually have "taxfilt" in the name
String sample_name = basename(basename(reads_unmapped_bam, ".bam"), ".taxfilt")

Expand All @@ -25,7 +24,7 @@ task assemble {
assembly.py assemble_trinity \
${reads_unmapped_bam} \
${trim_clip_db} \
${sample_name}.assembly1-trinity.fasta \
${sample_name}.assembly1-${assembler}.fasta \
${'--n_reads=' + trinity_n_reads} \
${true='--alwaysSucceed' false="" always_succeed} \
--JVMmemory "$mem_in_mb"m \
Expand All @@ -36,7 +35,7 @@ task assemble {
assembly.py assemble_spades \
${reads_unmapped_bam} \
${trim_clip_db} \
${sample_name}.assembly1-spades.fasta \
${sample_name}.assembly1-${assembler}.fasta \
${'--nReads=' + spades_n_reads} \
${true="--alwaysSucceed" false="" always_succeed} \
${'--minContigLen=' + spades_min_contig_len} \
Expand All @@ -57,7 +56,7 @@ task assemble {
assembly.py assemble_spades \
${reads_unmapped_bam} \
${trim_clip_db} \
${sample_name}.assembly1-spades.fasta \
${sample_name}.assembly1-${assembler}.fasta \
--contigsUntrusted=${sample_name}.assembly1-trinity.fasta \
${'--nReads=' + spades_n_reads} \
${true='--alwaysSucceed' false='' always_succeed} \
Expand All @@ -74,7 +73,7 @@ task assemble {
}

output {
File contigs_fasta = "${sample_name}.assembly1-${cleaned_assembler}.fasta"
File contigs_fasta = "${sample_name}.assembly1-${assembler}.fasta"
File subsampBam = "${sample_name}.subsamp.bam"
Int subsample_read_count = read_int("subsample_read_count")
String viralngs_version = "viral-ngs_version_unknown"
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