Merge branch 'cw-994b' into 'dev'

Fix slow snp:readStats

See merge request epi2melabs/workflows/wf-human-variation!11

CHANGELOG.md

@@ -4,10 +4,11 @@ All notable changes to this project will be documented in this file.
 The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/),
 and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
 
-## [v0.2.1]
+## [v0.2.2]
 ### Fixed
 * "No such property" when using the `minimap2_ubam` alignment step
-* Slow performance on `minimap2_ubam` step when providing uCRAM
+* Slow performance on `minimap2_ubam` step when providing CRAM as `--ubam`
+* Slow performance on `snp:readStats` process
 ### Removed
 * "Missing reference index" warning was unnecessary
 

modules/local/wf-human-snp.nf

@@ -495,12 +495,16 @@ process readStats {
     cpus 1
     input:
         tuple path(reads), path(reads_index)
+        tuple path(ref), path(ref_idx), path(ref_cache)
     output:
         path "readstats.txt", emit: stats
-    """
-    # using multithreading inside docker container does strange things
-    bamstats --threads 2 ${reads} > readstats.txt
-    """
+    script:
+        def ref_path = "${ref_cache}/%2s/%2s/%s:" + System.getenv("REF_PATH")
+        """
+        export REF_PATH=${ref_path}
+        # using multithreading inside docker container does strange things
+        bamstats --threads 2 ${reads} > readstats.txt
+        """
 }
 
 process getVersions {

modules/local/wf-human-sv.nf

@@ -1,5 +1,6 @@
 import groovy.json.JsonBuilder
 
+// TODO bam2fq_ref is probably a bit silly here, we should just prevent minimap2_ubam working with referenced CRAM
 process minimap2_ubam {
     label "wf_human_sv"
     cpus {params.ubam_map_threads + params.ubam_sort_threads + params.ubam_bam2fq_threads}

nextflow.config

@@ -21,7 +21,7 @@ params {
     ubam_sort_threads = 3
     ubam_bam2fq_threads = 1
 
-    wfversion = "v0.2.1" // specifies the container image version, not the workflow version
+    wfversion = "v0.2.2" // specifies the container image version, not the workflow version
 
     aws_image_prefix = null
     aws_queue = null
@@ -116,7 +116,7 @@ manifest {
     description     = 'consolidated human variation calling pipeline for ONT data'
     mainScript      = 'main.nf'
     nextflowVersion = '>=21.05.0'
-    version         = '0.2.1'
+    version         = '0.2.2'
 }
 
 executor {

nextflow_schema.json

@@ -300,7 +300,7 @@
         },
         "wfversion": {
             "type": "string",
-            "default": "v0.2.1",
+            "default": "v0.2.2",
             "hidden": true
         },
         "monochrome_logs": {

workflows/wf-human-snp.nf

@@ -155,7 +155,7 @@ workflow snp {
             make_chunks.out.contigs_file)
 
         // reporting
-        read_stats = readStats(bam)
+        read_stats = readStats(bam, ref)
         software_versions = getVersions()
         workflow_params = getParams()
         vcf_stats = vcfStats(clair_final.final_vcf)