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Rename medaka process & tag
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mattdmem committed Aug 15, 2023
1 parent f90d53e commit 3261675
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Showing 4 changed files with 8 additions and 8 deletions.
8 changes: 4 additions & 4 deletions .gitlab-ci.yml
Original file line number Diff line number Diff line change
Expand Up @@ -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"
Expand All @@ -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 \
Expand All @@ -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"
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2 changes: 1 addition & 1 deletion CHANGELOG.md
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Expand Up @@ -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
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4 changes: 2 additions & 2 deletions main.nf
Original file line number Diff line number Diff line change
Expand Up @@ -153,7 +153,7 @@ process medakaNetwork {
}


process medakaVariantConsensus {
process medakaVariantHdf {
// run medaka consensus for each region

label "medaka"
Expand Down Expand Up @@ -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
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2 changes: 1 addition & 1 deletion nextflow.config
Original file line number Diff line number Diff line change
Expand Up @@ -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 {
Expand Down

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