Merge pull request #241 from uclahs-cds/yashpatel-use-bzip2-directly

Use `bzip2` directly

CHANGELOG.md

@@ -6,6 +6,11 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 ## [Unreleased]
 
+## [7.0.0] - 2023-10-18
+
+### Changed
+- Use `bzip2` directly for compression
+
 ## [7.0.0-rc.2] - 2023-10-05
 
 ### Added

config/default.config

@@ -10,6 +10,9 @@ params {
     max_cpus   = SysHelper.getAvailCpus()
     max_memory = SysHelper.getAvailMemory()
 
+    min_cpus = 1
+    min_memory = 1.MB
+
     // default docker container registry
     docker_container_registry = "ghcr.io/uclahs-cds"
 
@@ -19,7 +22,7 @@ params {
     GATK_version = "4.4.0.0"
     somaticsniper_version = "1.0.5.0"
     bam_readcount_version = "0.8.0"
-    blarchive_version = "2.0.0"
+    ubuntu_version = "20.04"
     strelka2_version = "2.9.10"
     manta_version = "1.6.0"
     MuSE_version = "2.0.3"
@@ -31,7 +34,7 @@ params {
     docker_image_GATK = "broadinstitute/gatk:${params.GATK_version}"
     docker_image_somaticsniper = "${-> params.docker_container_registry}/somaticsniper:${params.somaticsniper_version}"
     docker_image_bam_readcount = "${-> params.docker_container_registry}/bam-readcount:${params.bam_readcount_version}"
-    docker_image_blarchive = "${-> params.docker_container_registry}/blarchive:${params.blarchive_version}"
+    docker_image_ubuntu = "ubuntu:${params.ubuntu_version}"
     docker_image_strelka2 = "${-> params.docker_container_registry}/strelka2:${params.strelka2_version}"
     docker_image_manta = "${-> params.docker_container_registry}/manta:${params.manta_version}"
     docker_image_MuSE = "${-> params.docker_container_registry}/muse:${params.MuSE_version}"

module/common.nf

@@ -5,7 +5,7 @@ log.info """\
 Docker Images:
 - docker_image_BCFtools: ${params.docker_image_BCFtools}
 - docker_image_validate_params: ${params.docker_image_validate_params}
-- docker_image_blarchive: ${params.docker_image_blarchive}
+- docker_image_ubuntu: ${params.docker_image_ubuntu}
 """
 
 process filter_VCF_BCFtools {
@@ -90,12 +90,12 @@ process rename_samples_BCFtools {
     """
     }
 
-process compress_file_blarchive {
-    container params.docker_image_blarchive
-    publishDir path: params.blarchive_publishDir,
+process compress_file_bzip2 {
+    container params.docker_image_ubuntu
+    publishDir path: params.compress_publishdir,
         mode: "copy",
         pattern: "*.bz2",
-        enabled: params.blarchive_enabled
+        enabled: params.compress_enabled
     publishDir path: "${params.workflow_log_output_dir}",
         mode: "copy",
         pattern: ".command.*",
@@ -112,8 +112,7 @@ process compress_file_blarchive {
     """
     set -euo pipefail
     dereferenced_file=\$(readlink -f ${file_to_compress})
-    blarchive compress_files --input \$dereferenced_file \
-        --log ./
+    bzip2 \$dereferenced_file
     ln -s \${dereferenced_file}.bz2 ${file_to_compress}.bz2
     """
     }

module/intersect.nf

@@ -1,7 +1,7 @@
 include { generate_sha512sum } from './common'
-include { compress_file_blarchive} from './common'  addParams(
-    blarchive_publishDir : "${params.workflow_output_dir}/output",
-    blarchive_enabled : true
+include { compress_file_bzip2} from './common'  addParams(
+    compress_publishdir : "${params.workflow_output_dir}/output",
+    compress_enabled : true
     )
 include { reorder_samples_BCFtools; intersect_VCFs_BCFtools; plot_VennDiagram_R; concat_VCFs_BCFtools ; convert_VCF_vcf2maf } from './intersect-processes.nf'
 include { compress_index_VCF as compress_index_VCF_reordered } from '../external/pipeline-Nextflow-module/modules/common/index_VCF_tabix/main.nf' addParams(
@@ -85,7 +85,7 @@ workflow intersect {
         compress_index_VCF_concat(concat_VCFs_BCFtools.out.vcf
             .map{ it -> ['SNV', it]}
             )
-        compress_file_blarchive(convert_VCF_vcf2maf.out.maf
+        compress_file_bzip2(convert_VCF_vcf2maf.out.maf
             .map{ it -> ['MAF', it]}
             )
         file_for_sha512 = intersect_VCFs_BCFtools.out.gzvcf
@@ -101,7 +101,7 @@ workflow intersect {
             .mix(compress_index_VCF_concat.out.index_out
                 .map{ it -> ["concat-${it[0]}-index", it[2]] }
                 )
-            .mix(compress_file_blarchive.out.compressed_file
+            .mix(compress_file_bzip2.out.compressed_file
                 .map{ it -> ["concat-${it[0]}", it[1]]}
                 )
         generate_sha512sum(file_for_sha512)

module/somaticsniper.nf

@@ -15,9 +15,9 @@ include { compress_index_VCF as compress_index_VCF_fix } from '../external/pipel
         bgzip_extra_args: params.bgzip_extra_args,
         tabix_extra_args: params.tabix_extra_args
         ])
-include { compress_file_blarchive} from './common'   addParams(
-    blarchive_publishDir : "${params.workflow_output_dir}/intermediate/generate_ReadCount_bam_readcount",
-    blarchive_enabled : params.save_intermediate_files
+include { compress_file_bzip2} from './common'   addParams(
+    compress_publishdir : "${params.workflow_output_dir}/intermediate/generate_ReadCount_bam_readcount",
+    compress_enabled : params.save_intermediate_files
     ) 
 
 workflow somaticsniper {
@@ -56,7 +56,7 @@ workflow somaticsniper {
         filter_FalsePositive_SomaticSniper(apply_TumorIndelFilter_SomaticSniper.out.vcf_tumor, generate_ReadCount_bam_readcount.out.readcount)
         call_HighConfidenceSNV_SomaticSniper(filter_FalsePositive_SomaticSniper.out.fp_pass)
         // combining to delay compression until after filtering step
-        compress_file_blarchive(
+        compress_file_bzip2(
             generate_ReadCount_bam_readcount.out.readcount
                 .combine(filter_FalsePositive_SomaticSniper.out.fp_pass.collect())
                 .map{ it -> ['readcount', it[0]] }

nextflow.config

@@ -9,6 +9,6 @@ manifest {
     nextflowVersion = '>=20.07.1'
     author = 'Yuan Zhe (Caden) Bugh, Mao Tian, Sorel Fitz-Gibbon'
     homePage = 'https://github.com/uclahs-cds/pipeline-call-sSNV'
-    version = '7.0.0-rc.2'
+    version = '7.0.0'
     name = 'call-sSNV'
 }