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Merge pull request #35 from phac-nml/dev
Release 0.3.0: Added database incorporation
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1,6 +1,6 @@ | ||
| name: nf-core linting | ||
| # This workflow is triggered on pushes and PRs to the repository. | ||
| # It runs the `nf-core lint` and markdown lint tests to ensure | ||
| # It runs the `nf-core pipelines lint` and markdown lint tests to ensure | ||
| # that the code meets the nf-core guidelines. | ||
| on: | ||
| push: | ||
|
|
@@ -41,17 +41,32 @@ jobs: | |
| python-version: "3.12" | ||
| architecture: "x64" | ||
|
|
||
| - name: read .nf-core.yml | ||
| uses: pietrobolcato/[email protected] | ||
| id: read_yml | ||
| with: | ||
| config: ${{ github.workspace }}/.nf-core.yml | ||
|
|
||
| - name: Install dependencies | ||
| run: | | ||
| python -m pip install --upgrade pip | ||
| pip install nf-core | ||
| pip install nf-core==${{ steps.read_yml.outputs['nf_core_version'] }} | ||
| - name: Run nf-core pipelines lint | ||
| if: ${{ github.base_ref != 'master' }} | ||
| env: | ||
| GITHUB_COMMENTS_URL: ${{ github.event.pull_request.comments_url }} | ||
| GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} | ||
| GITHUB_PR_COMMIT: ${{ github.event.pull_request.head.sha }} | ||
| run: nf-core -l lint_log.txt pipelines lint --dir ${GITHUB_WORKSPACE} --markdown lint_results.md | ||
|
|
||
| - name: Run nf-core lint | ||
| - name: Run nf-core pipelines lint --release | ||
| if: ${{ github.base_ref == 'master' }} | ||
| env: | ||
| GITHUB_COMMENTS_URL: ${{ github.event.pull_request.comments_url }} | ||
| GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} | ||
| GITHUB_PR_COMMIT: ${{ github.event.pull_request.head.sha }} | ||
| run: nf-core -l lint_log.txt lint --dir ${GITHUB_WORKSPACE} --markdown lint_results.md | ||
| run: nf-core -l lint_log.txt pipelines lint --release --dir ${GITHUB_WORKSPACE} --markdown lint_results.md | ||
|
|
||
| - name: Save PR number | ||
| if: ${{ always() }} | ||
|
|
||
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
|
|
@@ -10,3 +10,4 @@ testing/ | |
| testing* | ||
| *.pyc | ||
| bin/ | ||
| tests/data/irida/sample_name_add_iridanext.output.json | ||
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,51 @@ | ||
| process APPEND_CLUSTERS { | ||
| tag "Append additional clusters from database" | ||
| label 'process_single' | ||
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||
| container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? | ||
| 'https://depot.galaxyproject.org/singularity/csvtk:0.22.0--h9ee0642_1' : | ||
| 'biocontainers/csvtk:0.22.0--h9ee0642_1' }" | ||
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| input: | ||
| path(initial_clusters) | ||
| path(additional_clusters) | ||
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| output: | ||
| path("reference_clusters.tsv") | ||
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| script: | ||
| """ | ||
| # Function to get the first address line from the files, handling gzipped files | ||
| get_address() { | ||
| if [[ "\${1##*.}" == "gz" ]]; then | ||
| zcat "\$1" | awk 'NR>1 {print \$2}' | head -n 1 | ||
| else | ||
| awk 'NR>1 {print \$2}' "\$1" | head -n 1 | ||
| fi | ||
| } | ||
| # Check if two files have consistent delimeter splits in the address column | ||
| init_splits=\$(get_address "${initial_clusters}" | awk -F '${params.gm_delimiter}' '{print NF}') | ||
| add_splits=\$(get_address "${additional_clusters}" | awk -F '${params.gm_delimiter}' '{print NF}') | ||
| if [ "\$init_splits" != "\$add_splits" ]; then | ||
| echo "Error: Address levels do not match between initial_clusters and --db_clusters." | ||
| exit 1 | ||
| fi | ||
| # Add a "source" column to differentiate the reference profiles and additional profiles | ||
| csvtk mutate2 -t -n source -e " 'ref' " ${initial_clusters} > reference_clusters_source.tsv | ||
| csvtk mutate2 -t -n source -e " 'db' " ${additional_clusters} > additional_clusters_source.tsv | ||
| # Combine profiles from both the reference and database into a single file | ||
| csvtk concat -t reference_clusters_source.tsv additional_clusters_source.tsv | csvtk sort -t -k id > combined_profiles.tsv | ||
| # Calculate the frequency of each sample_id across both sources | ||
| csvtk freq -t -f id combined_profiles.tsv > sample_counts.tsv | ||
| # For any sample_id that appears in both the reference and database, add a 'db_' prefix to the sample_id from the database | ||
| csvtk join -t -f id combined_profiles.tsv sample_counts.tsv | \ | ||
| csvtk mutate2 -t -n id -e '(\$source == "db" && \$frequency > 1) ? "db_" + \$id : \$id' | \ | ||
| csvtk cut -t -f id,address > reference_clusters.tsv | ||
| """ | ||
| } |
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