diff --git a/.github/workflows/prek.yml b/.github/workflows/prek.yml new file mode 100644 index 0000000..ffeeb0a --- /dev/null +++ b/.github/workflows/prek.yml @@ -0,0 +1,12 @@ +name: Lint code +on: + push: + pull_request: + +jobs: + prek: + runs-on: ubuntu-latest + steps: + - uses: actions/checkout@v3 + - uses: actions/setup-python@v3 + - uses: pre-commit/action@v3.0.0 diff --git a/.gitignore b/.gitignore index b5c4c82..09ca261 100644 --- a/.gitignore +++ b/.gitignore @@ -13,6 +13,7 @@ results *.yml !src/main/resources/**/*.yml !src/main/resources/**/*.yaml +!.github/workflows/**.yml DONE !tests/*/*.yaml .nf-test* diff --git a/src/main/resources/worksheets/nfcmgg_preprocessing.yml b/src/main/resources/worksheets/nfcmgg_preprocessing.yml index dba03e1..f1f4bfa 100644 --- a/src/main/resources/worksheets/nfcmgg_preprocessing.yml +++ b/src/main/resources/worksheets/nfcmgg_preprocessing.yml @@ -78,12 +78,12 @@ output: # - id: The name of the field in the matched file that should be used as the identifier for the metric. # - field: The name of the field in the matched file that should be used as the value for the metric. metrics: - yield: + clusters: pattern: ".*_SAV_data$" subpath: "multiqc_bclconvert_bysample.txt" filetype: tsv id: Sample - field: yield_ + field: clusters # Define which samplesheets that should be generated and what their content is. # This is structured as a list of maps, where each map contains the following keys: # - name: The name of the YAML samplesheet to generate @@ -126,14 +126,14 @@ samplesheets: && data.tag?.toLowerCase() == 'rnaseqmdg' && data.fastq_1 != null filter_func: | - data.yield?.toLong() >= 1000000L + data.clusters?.toLong() >= 1000000L fields: sample: fastq_1: fastq_2: strandedness: reads: - source: yield + source: clusters - name: nfcmgg_vivar_samplesheet.yaml description: The samplesheet for the nf-cmgg/vivar pipeline include_func: | diff --git a/tests/preprocessing_mock/main.nf b/tests/preprocessing_mock/main.nf index bac3cf0..a79c64d 100644 --- a/tests/preprocessing_mock/main.nf +++ b/tests/preprocessing_mock/main.nf @@ -74,7 +74,7 @@ process MOCK_OUTPUT { # Creating SAV data mkdir multiqc_SAV_data - echo "Sample\tyield_" > multiqc_SAV_data/multiqc_bclconvert_bysample.txt + echo "Sample\tclusters" > multiqc_SAV_data/multiqc_bclconvert_bysample.txt ${sav_data} """ } \ No newline at end of file