Merge branch 'CW-3104/NCM' into 'dev'

Resolve CW-3104 "/ncm"

Closes CW-3104

See merge request epi2melabs/workflows/wf-bacterial-genomes!99

.gitlab-ci.yml

@@ -34,11 +34,13 @@ docker-run:
               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"
+              NF_WORKFLOW_OPTS: "-executor.\\$$local.memory 8GB \
+              --fastq test_data/fastq --reference_based_assembly --reference test_data/ref/reference.subseq.fa.gz --threads 4 --chunk_size 100000"
               NF_IGNORE_PROCESSES: "deNovo,assemblyStats,runProkka,makePerSampleReports"
         - if: $MATRIX_NAME == "check-model"
           variables:
-              NF_WORKFLOW_OPTS: "--fastq test_data/fastq --reference_based_assembly --reference test_data/ref/reference.subseq.fa.gz --threads 4 --chunk_size 100000 \
+              NF_WORKFLOW_OPTS: "-executor.\\$$local.memory 8GB \
+              --fastq test_data/fastq --reference_based_assembly --reference test_data/ref/reference.subseq.fa.gz --threads 4 --chunk_size 100000 \
                   --basecaller_cfg dna_r10.4.1_e8.2_400bps_hac@v3.5.2"
               NF_IGNORE_PROCESSES: "deNovo,assemblyStats,runProkka,makePerSampleReports"
         - if: $MATRIX_NAME == "amr"
@@ -48,13 +50,15 @@ docker-run:
               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 \
+              NF_WORKFLOW_OPTS: "-executor.\\$$local.memory 16GB \
+              --fastq test_data/fastq --reference_based_assembly --reference test_data/ref/reference.subseq.fa.gz --threads 4 --chunk_size 100000 \
                   --basecaller_cfg dna_r10.4.1_e8.2_400bps_hac@v3.5.2 --sample_sheet test_data/sample_sheet.csv"
               NF_IGNORE_PROCESSES: "deNovo,assemblyStats,runProkka,makePerSampleReports"
         - if: $MATRIX_NAME == "barcode04"
           # isolates barcode04 only has 4 reads and flye will fail due to low coverage
           variables:
-              NF_WORKFLOW_OPTS: "--fastq s3://ont-exd-int-s3-euwst1-epi2me-labs/wf-bacterial-genomes/test_data/isolates_fastq/barcode04 \
+              NF_WORKFLOW_OPTS: "-executor.\\$$local.memory 16GB \
+              --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,medakaVariantHdf,makeReport,runProkka,makePerSampleReports"
@@ -65,7 +69,8 @@ docker-run:
               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"
+              NF_WORKFLOW_OPTS: "-executor.\\$$local.memory 8GB \
+              --fastq test_data/fastq --reference_based_assembly --reference test_data/ref/reference.subseq.fa.gz --threads 4 --chunk_size 100000 --isolates"
               NF_IGNORE_PROCESSES: "deNovo,runProkka"
 # reminder: update AUX_IMAGE_TAG if the aux container package versions are changed
 release-prokka:

.pre-commit-config.yaml

@@ -1,22 +1,14 @@
 repos:
   - repo: local
     hooks:
-      - id: docs_schema
-        name: docs_schema
-        entry: parse_docs -p docs -e .md -s intro links -oj nextflow_schema.json
-        language: python
-        always_run: true
-        pass_filenames: false
-        additional_dependencies:
-          - epi2melabs
       - id: docs_readme
         name: docs_readme
-        entry: parse_docs -p docs -e .md -s header intro quickstart links -ot README.md
+        entry: parse_docs -p docs -e .md -s 01_brief_description 02_introduction 03_compute_requirements 04_install_and_run 05_related_protocols 06_inputs 07_outputs 08_pipeline_overview 09_troubleshooting 10_FAQ 11_other -ot README.md -od output_definition.json -ns nextflow_schema.json
         language: python
         always_run: true
         pass_filenames: false
         additional_dependencies:
-          - epi2melabs
+          - epi2melabs>=0.0.50
       - id: build_models
         name: build_models
         entry: datamodel-codegen --strict-nullable --base-class workflow_glue.results_schema_helpers.BaseModel --use-schema-description --disable-timestamp --input results_schema.yml --input-file-type openapi --output bin/workflow_glue/results_schema.py

CHANGELOG.md

@@ -4,6 +4,12 @@ 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).
 
+## [v1.0.0]
+### Added
+- Cloud support for the workflow within the EPI2ME Application.
+### Changed
+- Documentation
+
 ## [v0.4.0]
 ### Added
 - MacOS ARM64 support