Merge pull request #27 from uclahs-cds/cz-update-bwa-mem2-2.1

update to bwa-mem2 v2.1

Author: Chenghao Zhu

docker/bwa-and-samtools/Dockerfile

@@ -5,7 +5,7 @@ LABEL maintainer="Ben Carlin <bcarlin@mednet.ucla.edu>"
 # add channels in correct order to avoid missing libcrypto dependency
 # https://github.com/bioconda/bioconda-recipes/issues/12100
 RUN conda update -n base -c defaults conda && \
-    conda install -q -y -c bioconda bwa-mem2=2.0 && \
+    conda install -q -y -c bioconda bwa-mem2=2.1 && \
     conda clean --all -y 
 
 CMD ["bwa-mem2"]

pipeline/align-DNA.nf

@@ -6,7 +6,7 @@
       - NEEDS LOGGING UPDATE FOR OUTPUS, LOGS AND REPORTS
 */
 
-def docker_image_BWA_and_SAMTools = "blcdsdockerregistry/align-dna:bwa-mem2-2.0_samtools-1.10"
+def docker_image_BWA_and_SAMTools = "blcdsdockerregistry/align-dna:bwa-mem2-2.1_samtools-1.10"
 def docker_image_PicardTools = "blcdsdockerregistry/align-dna:picardtools-2.23.3"
 def docker_image_sha512sum = "blcdsdockerregistry/align-dna:sha512sum-1.0"
 def docker_image_validate_params = "blcdsdockerregistry/align-dna:sha512sum-1.0"
@@ -33,13 +33,11 @@ params.mem_command_build_bam_index = "4g"
 // The memory requied by bwa-mem2 increases along with the threads. Here we ensure that each cpu has
 // at least 2.5 GB of memory, to avoid out-of-memory failure, unless the number of cpu is defined in
 // config.
-if (params.containsKey("bwa_mem_number_of_cpus")) {
-   bwa_mem_number_of_cpus = params.bwa_mem_number_of_cpus
-} else {
+if (!params.containsKey("bwa_mem_number_of_cpus")) {
    amount_of_memory_int = amount_of_memory.replace(" GB", "") as Integer
-   bwa_mem_number_of_cpus = (int) Math.min(number_of_cpus, Math.floor(amount_of_memory_int / 2.5))
-   if (bwa_mem_number_of_cpus < 1) {
-      bwa_mem_number_of_cpus  = 1
+   params.bwa_mem_number_of_cpus = (int) Math.min(number_of_cpus, Math.floor(amount_of_memory_int / 2.5))
+   if (params.bwa_mem_number_of_cpus < 1) {
+      params.bwa_mem_number_of_cpus  = 1
    }
 }
 
@@ -66,6 +64,7 @@ log.info """\
       save_intermediate_files = ${params.save_intermediate_files}
       cache_intermediate_pipeline_steps = ${params.cache_intermediate_pipeline_steps}
       max_number_of_parallel_jobs = ${params.max_number_of_parallel_jobs}
+      bwa_mem_number_of_cpus = ${params.bwa_mem_number_of_cpus}
 
    Tools Used:
    - BWA-MEM2 and SAMtools: ${docker_image_BWA_and_SAMTools}
@@ -161,7 +160,7 @@ process BWA_mem_SAMTools_Convert_Sam_to_Bam {
    publishDir path: params.output_dir, enabled: params.save_intermediate_files, mode: 'copy'
 
    memory amount_of_memory
-   cpus bwa_mem_number_of_cpus
+   cpus params.bwa_mem_number_of_cpus
 
    when:
       number_of_invalid_inputs == 0