From 3261675376d0011015373d86068182ac6ce6a3e5 Mon Sep 17 00:00:00 2001
From: Matt Parker <matt.parker@nanoporetech.com>
Date: Tue, 15 Aug 2023 12:16:54 +0000
Subject: [PATCH] Rename medaka process & tag

---
 .gitlab-ci.yml  | 8 ++++----
 CHANGELOG.md    | 2 +-
 main.nf         | 4 ++--
 nextflow.config | 2 +-
 4 files changed, 8 insertions(+), 8 deletions(-)

diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml
index 0ec1ac3..b892761 100644
--- 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
index a77e67d..f28ad03 100644
--- 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
index 825c56b..11d564e 100644
--- 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
index efe144a..3c59a40 100644
--- 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 {