Merge branch 'CW-2475-tag' into 'dev'

Rename medaka process & tag Closes CW-2475 See merge request epi2melabs/workflows/wf-bacterial-genomes!85
epi2me-labs · Aug 15, 2023 · 9ab3396 · 9ab3396
2 parents f90d53e + 3261675
commit 9ab3396
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Showing 4 changed files with 8 additions and 8 deletions.
diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml
@@ -26,7 +26,7 @@ docker-run:
           variables:
               NF_WORKFLOW_OPTS: "-executor.\\$$local.memory 16GB \
                   --fastq test_data/fastq --threads 3 --chunk_size 100000"
-              NF_IGNORE_PROCESSES: "medakaVariant,medakaVariantConsensus,makePerSampleReports"
+              NF_IGNORE_PROCESSES: "medakaVariant,medakaVariantHdf,makePerSampleReports"
         - if: $MATRIX_NAME == "reference-based"
           variables:
               NF_WORKFLOW_OPTS: "--fastq test_data/fastq --reference_based_assembly --reference test_data/ref/reference.subseq.fa.gz --threads 4 --chunk_size 100000"
@@ -40,7 +40,7 @@ docker-run:
           variables:
               NF_WORKFLOW_OPTS: "-executor.\\$$local.memory 16GB \
                   --fastq s3://ont-exd-int-s3-euwst1-epi2me-labs/wf-bacterial-genomes/test_data/isolates_fastq --sample_sheet test_data/isolates_sample_sheet.csv --threads 3 --chunk_size 100000 --isolates"
-              NF_IGNORE_PROCESSES: "runProkka,medakaVariant,medakaVariantConsensus,makePerSampleReports"
+              NF_IGNORE_PROCESSES: "runProkka,medakaVariant,medakaVariantHdf,makePerSampleReports"
         - if: $MATRIX_NAME == "sample-sheet"
           variables:
               NF_WORKFLOW_OPTS: "--fastq test_data/fastq --reference_based_assembly --reference test_data/ref/reference.subseq.fa.gz --threads 4 --chunk_size 100000 \
@@ -52,12 +52,12 @@ docker-run:
               NF_WORKFLOW_OPTS: "--fastq s3://ont-exd-int-s3-euwst1-epi2me-labs/wf-bacterial-genomes/test_data/isolates_fastq/barcode04 \
                   --threads 3 --chunk_size 100000"
               NF_IGNORE_PROCESSES: "alignReads,readStats,coverStats,splitRegions,\
-                  medakaConsensus,medakaNetwork,medakaVariant,medakaVariantConsensus,makeReport,runProkka,makePerSampleReports"
+                  medakaConsensus,medakaNetwork,medakaVariant,medakaVariantHdf,makeReport,runProkka,makePerSampleReports"
         - if: $MATRIX_NAME == "mixed-species"
           variables:
               NF_WORKFLOW_OPTS: "-executor.\\$$local.memory 16GB \
               --fastq s3://ont-exd-int-s3-euwst1-epi2me-labs/wf-bacterial-genomes/test_data/isolates_fastq/ --sample_sheet test_data/isolates_mixed_sample_sheet.csv --threads 3 --chunk_size 100000 --isolates"
-              NF_IGNORE_PROCESSES: "runProkka,medakaVariant,medakaVariantConsensus"
+              NF_IGNORE_PROCESSES: "runProkka,medakaVariant,medakaVariantHdf"
         - if: $MATRIX_NAME == "reference-iso"
           variables:
               NF_WORKFLOW_OPTS: "--fastq test_data/fastq --reference_based_assembly --reference test_data/ref/reference.subseq.fa.gz --threads 4 --chunk_size 100000 --isolates"

diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -4,7 +4,7 @@ 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).
 
-## [unreleased]
+## [v0.3.2]
 ### Fixed
 - Edge case where medaka variant output is unsorted and causes medaka annotate to exit
 ### Changed

diff --git a/main.nf b/main.nf
@@ -153,7 +153,7 @@ process medakaNetwork {
 }
 
 
-process medakaVariantConsensus {
+process medakaVariantHdf {
     // run medaka consensus for each region
 
     label "medaka"
@@ -521,7 +521,7 @@ workflow calling_pipeline {
         // medaka variants
         if (params.reference_based_assembly){
             bam_model = regions_bams.combine(medaka_variant_model)
-            hdfs_variant = medakaVariantConsensus(bam_model)
+            hdfs_variant = medakaVariantHdf(bam_model)
             hdfs_grouped = hdfs_variant.groupTuple().combine(alignments, by: [0]).join(named_refs)
             variant = medakaVariant(hdfs_grouped)
             variants = variant.variant_stats

diff --git a/nextflow.config b/nextflow.config
@@ -56,7 +56,7 @@ manifest {
     description     = 'Assembly, variant calling, and annotation of bacterial genomes.'
     mainScript      = 'main.nf'
     nextflowVersion = '>=23.04.2'
-    version         = 'v0.3.1'
+    version         = 'v0.3.2'
 }
 
 epi2melabs {