Merge branch 'CW-3239' into 'dev'

fix medakaVariant using more CPU than allocated [CW-3239]

Closes CW-3239

See merge request epi2melabs/workflows/wf-amplicon!57

CHANGELOG.md

@@ -4,6 +4,10 @@ All notable changes to this project will be documented in this file.
 The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.1.0/),
 and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
 
+## [v1.0.2]
+### Fixed
+- Incorrect CPU use specification for the `medakaVariant` process.
+
 ## [v1.0.1]
 ### Changed
 - Default for `--reads_downsampling_size` to 1500 to limit memory usage.

lib/ingress.nf

@@ -149,28 +149,24 @@ def xam_ingress(Map arguments)
 
     def input = get_valid_inputs(margs, xam_extensions)
 
+    // check BAM headers to see if any samples are uBAM
     ch_result = input.dirs
     | map { meta, path -> [meta, get_target_files_in_dir(path, xam_extensions)] }
     | mix(input.files)
-
-    ch_is_unaligned = ch_result
     | checkBamHeaders
-    | map { meta, is_unaligned_env, mixed_headers_env ->
+    | map { meta, paths, is_unaligned_env, mixed_headers_env ->
         // convert the env. variables from strings ('0' or '1') into bools
         boolean is_unaligned = is_unaligned_env as int as boolean
         boolean mixed_headers = mixed_headers_env as int as boolean
         // throw an error if there was a sample with mixed headers
         if (mixed_headers) {
             error "Found mixed headers in (u)BAM files of sample '${meta.alias}'."
         }
-        [meta, is_unaligned]
+        // add `is_unaligned` to the metamap (note the use of `+` to create a copy of
+        // `meta` to avoid modifying every item in the channel;
+        // https://github.com/nextflow-io/nextflow/issues/2660)
+        [meta + [is_unaligned: is_unaligned], paths]
     }
-
-    ch_result = ch_result | join(ch_is_unaligned)
-    // add `is_unaligned` to the metamap (note the use of `+` to create a copy of `meta`
-    // to avoid modifying every item in the channel;
-    // https://github.com/nextflow-io/nextflow/issues/2660)
-    | map { meta, paths, is_unaligned -> [meta + [is_unaligned: is_unaligned], paths] }
     | branch { meta, paths ->
         // set `paths` to `null` for uBAM samples if unallowed (they will be added to
         // the results channel in shape of `[meta, null]` at the end of the function
@@ -245,7 +241,12 @@ process checkBamHeaders {
     output:
         // set the two env variables by `eval`-ing the output of the python script
         // checking the XAM headers
-        tuple val(meta), env(IS_UNALIGNED), env(MIXED_HEADERS)
+        tuple(
+            val(meta),
+            path("input_dir/reads*.bam", includeInputs: true),
+            env(IS_UNALIGNED),
+            env(MIXED_HEADERS),
+        )
     script:
     """
     workflow-glue check_bam_headers_in_dir input_dir > env.vars

modules/local/variant-calling.nf

@@ -73,7 +73,7 @@ process medakaConsensus {
 
 process medakaVariant {
     label "medaka"
-    cpus 1
+    cpus 2
     memory "8 GB"
     input:
         tuple val(meta),

nextflow.config

@@ -76,7 +76,7 @@ manifest {
     description     = 'Amplicon workflow'
     mainScript      = 'main.nf'
     nextflowVersion = '>=23.04.2'
-    version         = 'v1.0.1'
+    version         = 'v1.0.2'
 }
 
 epi2melabs {