map_reads process fails due to SAM/BAM mismatch when using :dev Docker container

[jeremy-at-asimov]

Running with default :dev errors out as follows:

nextflow run formbio/laava -c nextflow.config -profile local -params-file my_params.json

ERROR ~ Error executing process > 'laava:map_reads (1)'

Caused by:
  Missing output file(s) `my_filename.sort_by_name.bam` expected by process `laava:map_reads (1)`

Command executed:

  map_reads.sh my_filename "my_filename.bam" \
      "pAI-15796.fasta" "packaging.fa" "hg38.fa" \
      "pAI_16625" "pAI_14833" "Lambda"

Running with :latest is fine

nextflow run formbio/laava -c nextflow.config -profile local -params-file my_params.json --container_version ':latest'

[46/65640e] process > laava:map_reads (1)   [100%] 1 of 1 ✔
[1d/384cdb] process > laava:make_report (1) [100%] 1 of 1 ✔

This was also noted in issue #96 and it prevents the pipeline from functioning without debugging. Seems like it just needs a tweak to output a bam file instead of a sam file at that intermediate step