Fixed WDL of task assemble for the trinity-spades case. Removed worka…

…round for a now-fixed Cromwell issue. (#952)

pipes/WDL/workflows/tasks/tasks_assembly.wdl

@@ -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")
 
@@ -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 \
@@ -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} \
@@ -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} \
@@ -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"