schedule-pipelines

GASNomenclature

nextflow run phac-nml/gasnomenclature -r 0.2.2 --input https://raw.githubusercontent.com/phac-nml/schedule-pipelines/refs/heads/main/test/data/samplesheet_gasnomeclasture.csv -w /tmp/gasnomenclature/work -profile docker -params-file https://raw.githubusercontent.com/phac-nml/schedule-pipelines/refs/heads/main/config/gasnomenclature-listeria.json -queue-size 4 --outdir /tmp/gasnomenclature/output

• --input: path to the input sample sheet
• -w: path to the work directory
• -params-file: parameters / config file for species / run
• queue-size: number of Nextflow jobs to run simultaneously
• outdir: the output directory

Update Samplesheet

python scripts/update-samplesheet.py --json /tmp/gasnomenclature/output/iridanext.output.json.gz --samplesheet test/data/samplesheet_arborator.csv --output /tmp/updated_samplesheet.csv

• json: path to JSON file output by the previous step (GASNomenclature)
• samplesheet: path to Arborator sample sheet to update
• output: the output directory

Arborator

nextflow run phac-nml/arboratornf -r 0.2.0 --input /tmp/updated_samplesheet.csv -w /tmp/arborator_detection/work -profile docker -params-file https://raw.githubusercontent.com/phac-nml/schedule-pipelines/refs/heads/main/config/arboratornf-detection-listeria.json -queue-size 4 --outdir /tmp/arborator_detection/output

• --input: path to the input sample sheet
• -w: path to the work directory
• -params-file: parameters / config file for species / run
• queue-size: number of Nextflow jobs to run simultaneously
• outdir: the output directory

Post-Processing

python scripts/post-processing.py --gasnomenclature /tmp/gasnomenclature/output/ --arborator /tmp/arborator/output/ --output /tmp/post/

• gasnomenclature: GASNomenclature output directory (from the GASNomenclature step above)
• arborator: Arborator output directory (from the Arborator step above)

Outputs

arborator_2024-10-03_13-42-34.iridanext.output.json.zip
arborator_2024-10-03_13-42-34.zip
gasnomenclature_2024-10-03_13-42-34.iridanext.output.json.zip
gasnomenclature_2024-10-03_13-42-34.zip

Legal

Copyright Government of Canada 2024

Written by: National Microbiology Laboratory, Public Health Agency of Canada

Licensed under the Apache License, Version 2.0 (the "License"); you may not use this work except in compliance with the License. You may obtain a copy of the License at:

http://www.apache.org/licenses/LICENSE-2.0

Unless required by applicable law or agreed to in writing, software distributed under the License is distributed on an "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. See the License for the specific language governing permissions and limitations under the License.