diff --git a/.gitattributes b/.gitattributes index c1c17000..7a2dabc2 100644 --- a/.gitattributes +++ b/.gitattributes @@ -1,5 +1,4 @@ *.config linguist-language=nextflow *.nf.test linguist-language=nextflow -tests/**/*nf.test.snap linguist-generated modules/nf-core/** linguist-generated subworkflows/nf-core/** linguist-generated diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml index 451613fb..5bef3edd 100644 --- a/.github/workflows/ci.yml +++ b/.github/workflows/ci.yml @@ -1,61 +1,31 @@ -# This workflow runs the pipeline with the minimal test dataset to check that it completes without any syntax errors name: nf-core CI +# This workflow runs the pipeline with the minimal test dataset to check that it completes without any syntax errors on: push: branches: - dev pull_request: - branches: - - dev - - master release: - types: - - "published" + types: [published] env: NXF_ANSI_LOG: false - NFTEST_VER: "0.7.3" concurrency: group: "${{ github.workflow }}-${{ github.event.pull_request.number || github.ref }}" cancel-in-progress: true jobs: - define_nxf_versions: - name: Choose nextflow versions to test against depending on target branch - runs-on: ubuntu-latest - outputs: - matrix: ${{ steps.nxf_versions.outputs.matrix }} - steps: - - id: nxf_versions - run: | - if [[ "${{ github.event_name }}" == "pull_request" && "${{ github.base_ref }}" == "dev" && "${{ matrix.NXF_VER }}" != "latest-everything" ]]; then - echo matrix='["latest-everything"]' | tee -a $GITHUB_OUTPUT - else - echo matrix='["latest-everything", "22.10.1"]' | tee -a $GITHUB_OUTPUT - fi - test: name: Run pipeline with test data - needs: define_nxf_versions + # Only run on push if this is the nf-core dev branch (merged PRs) + if: "${{ github.event_name != 'push' || (github.event_name == 'push' && github.repository == 'nf-core/fetchngs') }}" runs-on: ubuntu-latest strategy: - fail-fast: false matrix: - NXF_VER: ${{ fromJson(needs.define_nxf_versions.outputs.matrix) }} - test_tags: - - "modules_local" - - "sra_default_parameters" - - "sra_custom_ena_metadata_fields" - - "sra_force_sratools_download" - - "sra_nf_core_pipeline_atacseq" - - "sra_nf_core_pipeline_rnaseq" - - "sra_nf_core_pipeline_taxprofiler" - - "sra_nf_core_pipeline_viralrecon" - - "sra_skip_fastq_download" - profile: - - "docker" - + NXF_VER: + - "22.10.1" + - "latest-everything" steps: - name: Check out pipeline code uses: actions/checkout@v3 @@ -65,23 +35,29 @@ jobs: with: version: "${{ matrix.NXF_VER }}" - - name: Install nf-test + - name: Run pipeline with test data run: | - wget -qO- https://code.askimed.com/install/nf-test | bash -s $NFTEST_VER - sudo mv nf-test /usr/local/bin/ + nextflow run ${GITHUB_WORKSPACE} -profile test,docker --outdir ./results - - name: Run nf-test - run: | - nf-test test --tag ${{ matrix.test_tags }} --profile "test,${{ matrix.profile }}" --junitxml=test.xml + parameters: + name: Test workflow parameters + if: ${{ github.event_name != 'push' || (github.event_name == 'push' && github.repository == 'nf-core/fetchngs') }} + runs-on: ubuntu-latest + strategy: + matrix: + parameters: + - "--nf_core_pipeline rnaseq" + - "--ena_metadata_fields run_accession,experiment_accession,library_layout,fastq_ftp,fastq_md5 --sample_mapping_fields run_accession,library_layout" + - "--skip_fastq_download" + - "--force_sratools_download" + steps: + - name: Check out pipeline code + uses: actions/checkout@v2 - - name: Output log on failure - if: failure() + - name: Install Nextflow run: | - sudo apt install bat > /dev/null - batcat --decorations=always --color=always ${{ github.workspace }}/.nf-test/tests/*/output/pipeline_info/software_versions.yml - - - name: Publish Test Report - uses: mikepenz/action-junit-report@v3 - if: always() # always run even if the previous step fails - with: - report_paths: test.xml + wget -qO- get.nextflow.io | bash + sudo mv nextflow /usr/local/bin/ + - name: Run pipeline with various parameters + run: | + nextflow run ${GITHUB_WORKSPACE} -profile test,docker --outdir ./results ${{ matrix.parameters }} diff --git a/.gitignore b/.gitignore index 935326a7..5124c9ac 100644 --- a/.gitignore +++ b/.gitignore @@ -6,5 +6,3 @@ results/ testing/ testing* *.pyc -.nf-test/ -nf-test diff --git a/.nf-core.yml b/.nf-core.yml index 253f86e2..cafd671c 100644 --- a/.nf-core.yml +++ b/.nf-core.yml @@ -1,15 +1,5 @@ repository_type: pipeline lint: files_unchanged: - - .github/CONTRIBUTING.md - - .github/ISSUE_TEMPLATE/bug_report.yml - - assets/nf-core-fetchngs_logo_light.png - assets/sendmail_template.txt - lib/NfcoreTemplate.groovy - - .gitattributes - actions_ci: false - multiqc_config: false - nextflow_config: - - "params.validationShowHiddenParams" - - "params.validationSchemaIgnoreParams" - schema_params: false diff --git a/CHANGELOG.md b/CHANGELOG.md index 146b93b6..12ef2d50 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -3,22 +3,6 @@ The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/) and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html). -## [[1.10.1](https://github.com/nf-core/fetchngs/releases/tag/1.10.1)] - 2023-06-29 - -### Credits - -Special thanks to the following for their contributions to the release: - -- [Sateesh Peri](https://github.com/sateeshperi) -- [Edmund Miller](https://github.com/Emiller88) -- [Maxime Garcia](https://github.com/maxulysse) - -Thank you to everyone else that has contributed by reporting bugs, enhancements or in any other way, shape or form. - -### Enhancements & fixes - -- [#166](https://github.com/nf-core/fetchngs/issues/175) - Add NF-TEST pipeline end-to-end tests for existing CI tests - ## [[1.10.0](https://github.com/nf-core/fetchngs/releases/tag/1.10.0)] - 2023-05-16 ### Credits diff --git a/bin/sra_runinfo_to_ftp.py b/bin/sra_runinfo_to_ftp.py index c220f74e..ef80ec80 100755 --- a/bin/sra_runinfo_to_ftp.py +++ b/bin/sra_runinfo_to_ftp.py @@ -61,8 +61,7 @@ def parse_sra_runinfo(file_in): with open(file_in, "r", newline="") as fin: reader = csv.DictReader(fin, delimiter="\t", skipinitialspace=True) header = list(reader.fieldnames) - missing = frozenset(columns).difference(frozenset(header)) - if missing: + if missing := frozenset(columns).difference(frozenset(header)): logger.critical(f"The following expected columns are missing from {file_in}: " f"{', '.join(missing)}.") sys.exit(1) for row in reader: diff --git a/conf/test.config b/conf/test.config index 0bc98595..3c58e9cf 100644 --- a/conf/test.config +++ b/conf/test.config @@ -22,6 +22,3 @@ params { // Input data input = 'https://raw.githubusercontent.com/nf-core/test-datasets/fetchngs/sra_ids_test.csv' } - -// Load test_data.config for nf-tests -includeConfig 'test_data.config' diff --git a/conf/test_data.config b/conf/test_data.config deleted file mode 100644 index 42d3d818..00000000 --- a/conf/test_data.config +++ /dev/null @@ -1,36 +0,0 @@ -params { - // Base directory for test data - test_data_base = "https://raw.githubusercontent.com/nf-core/test-datasets/fetchngs" - - merge_samplesheet_ids = [ "DRX024467_DRR026872", "SRX11047067_SRR14709033", "SRX9504942_SRR13055517", "DRX026011_DRR028935", "SRX17709227_SRR21711856", "SRX9504942_SRR13055518", "ERX1188904_ERR1109373", "SRX17709228_SRR21711855", "SRX9504942_SRR13055519", "ERX1234253_ERR1160846", "SRX6725035_SRR9984183", "SRX9504942_SRR13055520", "SRX10940790_SRR14593545", "SRX9315476_SRR12848126", "SRX9626017_SRR13191702" ] - - def merge_samplesheet_url = "${params.test_data_base}/modules/local/sra_merge_samplesheet/samplesheets/" - def merge_mappings_url = "${params.test_data_base}/modules/local/sra_merge_samplesheet/mappings/" - def merge_samplesheet_urls = [] - def merge_mappings_urls = [] - - merge_samplesheet_ids.each { id -> - merge_samplesheet_urls += "${merge_samplesheet_url}${id}.samplesheet.csv" - merge_mappings_urls += "${merge_mappings_url}/${id}.mappings.csv" - } - - fastq_ftp_ids = ["SRR13191702"] - def fastq_ftp_url = "ftp.sra.ebi.ac.uk/vol1/fastq/SRR131/002/SRR13191702/" - def fastq_ftp_urls = [] - - fastq_ftp_ids.each { id -> - fastq_ftp_urls += "${fastq_ftp_url}${id}_1.fastq.gz" - fastq_ftp_urls += "${fastq_ftp_url}${id}_2.fastq.gz" - } - - test_data { - 'modules_local' { - multiqc_mappings_config = "${params.test_data_base}/modules/local/multiqc_mappings_config/SRX9626017_SRR13191702.mappings.csv" - sra_merge_samplesheet_samplesheets = merge_samplesheet_urls - sra_merge_samplesheet_mappings = merge_mappings_urls - sra_to_samplesheet = "${params.test_data_base}/modules/local/sra_to_samplesheet/SRX9626017_SRR13191702.mappings.csv" - sra_fastq_ftp = fastq_ftp_urls - sra_runinfo_to_ftp = "${params.test_data_base}/modules/local/sra_runinfo_to_ftp/SRR13191702.runinfo.tsv" - } - } -} diff --git a/docs/usage.md b/docs/usage.md index b2cd7b50..0720a680 100644 --- a/docs/usage.md +++ b/docs/usage.md @@ -70,12 +70,6 @@ From v1.9 of this pipeline the default `strandedness` in the output samplesheet If FTP connections are blocked on your network use the [`--force_sratools_download`](https://nf-co.re/fetchngs/parameters#force_sratools_download) parameter to force the pipeline to download data using sra-tools instead of the ENA FTP. -### Downloading 10X Genomics Data - -As of v1.10.0, this pipeline now supports downloading of 10X Genomics data. For 10X data sets, the output needs to be split into three fastq files, consisting of the feature barcode+UMI, cDNA sequence reads, and sample index. Adding the `--force_sratools_download` parameter will cause the pipeline to use the sra-tools fasterq-dump program with appropriate setting to ensure that all three files are generated. - -Please note that in our experience the downloaded R1, R2, and R3 fastq files do not always correspond to the same data types across different submissions. In many cases, R1 will be the cell barcode + UMI, R2 is the cDNA sequence, and R3 is the sample index. However, this is not alway the case. Users are strongly encouraged to verify their data before proceeding with downstream analysis. - ### Downloading dbGAP data with JWT As of v1.10.0, the SRA Toolkit used in this pipeline can be configured to access protected data from dbGAP using a [JWT cart file](https://www.ncbi.nlm.nih.gov/sra/docs/sra-dbGAP-cloud-download/) on a supported cloud computing environment (Amazon Web Services or Google Cloud Platform). The JWT cart file can be specified with `--dbgap_key /path/to/cart.jwt`. diff --git a/lib/NftestUtils.groovy b/lib/NftestUtils.groovy deleted file mode 100644 index ce6fc8b4..00000000 --- a/lib/NftestUtils.groovy +++ /dev/null @@ -1,38 +0,0 @@ -// Helper functions for pipeline tests - -class NftestUtils { - - // Function to remove Nextflow version from software_versions.yml - public static String removeNextflowVersion(outputDir) { - def softwareVersions = path("$outputDir/pipeline_info/software_versions.yml").yaml - if (softwareVersions.containsKey("Workflow")) { - softwareVersions.Workflow.remove("Nextflow") - } - return softwareVersions - } - - // Function to filter lines from a file and return a new file - public static File filterLines(String inFilePath, int linesToSkip) { - if (linesToSkip >= 0) { - File inputFile = new File(inFilePath) - File outputFile = new File(inFilePath + ".filtered") - def lineCount = 0 - inputFile.eachLine { line -> - lineCount++ - if (lineCount > linesToSkip) { - outputFile.append(line + '\n') - } - } - return outputFile - } else { - File inputFile = new File(inFilePath) - File outputFile = new File(inFilePath + ".filtered") - def lines = inputFile.readLines() - def totalLines = lines.size() - lines.take(totalLines + linesToSkip).each { line -> - outputFile.append(line + '\n') - } - return outputFile - } - } -} diff --git a/modules.json b/modules.json index 2244addd..3137b88b 100644 --- a/modules.json +++ b/modules.json @@ -8,8 +8,7 @@ "custom/dumpsoftwareversions": { "branch": "master", "git_sha": "911696ea0b62df80e900ef244d7867d177971f73", - "installed_by": ["modules"], - "patch": "modules/nf-core/custom/dumpsoftwareversions/custom-dumpsoftwareversions.diff" + "installed_by": ["modules"] }, "custom/sratoolsncbisettings": { "branch": "master", diff --git a/modules/local/multiqc_mappings_config/main.nf b/modules/local/multiqc_mappings_config.nf similarity index 100% rename from modules/local/multiqc_mappings_config/main.nf rename to modules/local/multiqc_mappings_config.nf diff --git a/modules/local/multiqc_mappings_config/tests/main.nf.test b/modules/local/multiqc_mappings_config/tests/main.nf.test deleted file mode 100644 index 3bf79537..00000000 --- a/modules/local/multiqc_mappings_config/tests/main.nf.test +++ /dev/null @@ -1,31 +0,0 @@ -nextflow_process { - - name "Test process: MULTIQC_MAPPINGS_CONFIG" - script "modules/local/multiqc_mappings_config/main.nf" - process "MULTIQC_MAPPINGS_CONFIG" - tag "modules" - tag "modules_local" - tag "multiqc_mappings_config" - - test("Should run without failures") { - - when { - params { - outdir = "$outputDir" - } - - process { - """ - input[0] = file(params.test_data['modules_local']['multiqc_mappings_config'], checkIfExists: true) - """ - } - } - - then { - assertAll( - { assert process.success }, - { assert snapshot(process.out).match() } - ) - } - } -} diff --git a/modules/local/multiqc_mappings_config/tests/main.nf.test.snap b/modules/local/multiqc_mappings_config/tests/main.nf.test.snap deleted file mode 100644 index 9cf7fb38..00000000 --- a/modules/local/multiqc_mappings_config/tests/main.nf.test.snap +++ /dev/null @@ -1,52 +0,0 @@ -{ - "SRX9626017_SRR13191702": { - "content": [ - { - "0": [ - [ - "multiqc_config.yml:md5,7f3cb10fff83ba9eb3e8fa6862d1290a", - "versions.yml:md5,dd4c66f0551d15510b36bb2e2b2fdd73" - ] - ], - "1": [ - "versions.yml:md5,dd4c66f0551d15510b36bb2e2b2fdd73" - ], - "versions": [ - "versions.yml:md5,dd4c66f0551d15510b36bb2e2b2fdd73" - ], - "yml": [ - [ - "multiqc_config.yml:md5,7f3cb10fff83ba9eb3e8fa6862d1290a", - "versions.yml:md5,dd4c66f0551d15510b36bb2e2b2fdd73" - ] - ] - } - ], - "timestamp": "2023-08-17T12:02:35+0000" - }, - "Should run without failures": { - "content": [ - { - "0": [ - [ - "multiqc_config.yml:md5,7f3cb10fff83ba9eb3e8fa6862d1290a", - "versions.yml:md5,dd4c66f0551d15510b36bb2e2b2fdd73" - ] - ], - "1": [ - "versions.yml:md5,dd4c66f0551d15510b36bb2e2b2fdd73" - ], - "versions": [ - "versions.yml:md5,dd4c66f0551d15510b36bb2e2b2fdd73" - ], - "yml": [ - [ - "multiqc_config.yml:md5,7f3cb10fff83ba9eb3e8fa6862d1290a", - "versions.yml:md5,dd4c66f0551d15510b36bb2e2b2fdd73" - ] - ] - } - ], - "timestamp": "2023-08-17T12:02:35+0000" - } -} \ No newline at end of file diff --git a/modules/local/sra_fastq_ftp/main.nf b/modules/local/sra_fastq_ftp.nf similarity index 100% rename from modules/local/sra_fastq_ftp/main.nf rename to modules/local/sra_fastq_ftp.nf diff --git a/modules/local/sra_fastq_ftp/tests/main.nf.test b/modules/local/sra_fastq_ftp/tests/main.nf.test deleted file mode 100644 index 7892d156..00000000 --- a/modules/local/sra_fastq_ftp/tests/main.nf.test +++ /dev/null @@ -1,34 +0,0 @@ -nextflow_process { - - name "Test process: SRA_FASTQ_FTP" - script "modules/local/sra_fastq_ftp/main.nf" - process "SRA_FASTQ_FTP" - tag "modules" - tag "modules_local" - tag "sra_fastq_ftp" - - test("Should run without failures") { - - when { - params { - outdir = "$outputDir" - } - - process { - """ - input[0] = [ - [ id:'SRX9626017_SRR13191702', single_end:false, md5_1: '89c5be920021a035084d8aeb74f32df7', md5_2: '56271be38a80db78ef3bdfc5d9909b98' ], // meta map - params.test_data['modules_local']['sra_fastq_ftp'] - ] - """ - } - } - - then { - assertAll( - { assert process.success }, - { assert snapshot(process.out).match() } - ) - } - } -} diff --git a/modules/local/sra_fastq_ftp/tests/main.nf.test.snap b/modules/local/sra_fastq_ftp/tests/main.nf.test.snap deleted file mode 100644 index c0d5ffdc..00000000 --- a/modules/local/sra_fastq_ftp/tests/main.nf.test.snap +++ /dev/null @@ -1,140 +0,0 @@ -{ - "SRX9626017_SRR13191702": { - "content": [ - { - "0": [ - [ - { - "id": "SRX9626017_SRR13191702", - "single_end": false, - "md5_1": "89c5be920021a035084d8aeb74f32df7", - "md5_2": "56271be38a80db78ef3bdfc5d9909b98" - }, - [ - "SRX9626017_SRR13191702_1.fastq.gz:md5,89c5be920021a035084d8aeb74f32df7", - "SRX9626017_SRR13191702_2.fastq.gz:md5,56271be38a80db78ef3bdfc5d9909b98" - ] - ] - ], - "1": [ - [ - { - "id": "SRX9626017_SRR13191702", - "single_end": false, - "md5_1": "89c5be920021a035084d8aeb74f32df7", - "md5_2": "56271be38a80db78ef3bdfc5d9909b98" - }, - [ - "SRX9626017_SRR13191702_1.fastq.gz.md5:md5,055a6916ec9ee478e453d50651f87997", - "SRX9626017_SRR13191702_2.fastq.gz.md5:md5,c30ac785f8d80ec563fabf604d8bf945" - ] - ] - ], - "2": [ - "versions.yml:md5,6b9d69dea1c1305f74a65197ee871f1b" - ], - "fastq": [ - [ - { - "id": "SRX9626017_SRR13191702", - "single_end": false, - "md5_1": "89c5be920021a035084d8aeb74f32df7", - "md5_2": "56271be38a80db78ef3bdfc5d9909b98" - }, - [ - "SRX9626017_SRR13191702_1.fastq.gz:md5,89c5be920021a035084d8aeb74f32df7", - "SRX9626017_SRR13191702_2.fastq.gz:md5,56271be38a80db78ef3bdfc5d9909b98" - ] - ] - ], - "md5": [ - [ - { - "id": "SRX9626017_SRR13191702", - "single_end": false, - "md5_1": "89c5be920021a035084d8aeb74f32df7", - "md5_2": "56271be38a80db78ef3bdfc5d9909b98" - }, - [ - "SRX9626017_SRR13191702_1.fastq.gz.md5:md5,055a6916ec9ee478e453d50651f87997", - "SRX9626017_SRR13191702_2.fastq.gz.md5:md5,c30ac785f8d80ec563fabf604d8bf945" - ] - ] - ], - "versions": [ - "versions.yml:md5,6b9d69dea1c1305f74a65197ee871f1b" - ] - } - ], - "timestamp": "2023-08-06T23:31:57+0000" - }, - "Should run without failures": { - "content": [ - { - "0": [ - [ - { - "id": "SRX9626017_SRR13191702", - "single_end": false, - "md5_1": "89c5be920021a035084d8aeb74f32df7", - "md5_2": "56271be38a80db78ef3bdfc5d9909b98" - }, - [ - "SRX9626017_SRR13191702_1.fastq.gz:md5,89c5be920021a035084d8aeb74f32df7", - "SRX9626017_SRR13191702_2.fastq.gz:md5,56271be38a80db78ef3bdfc5d9909b98" - ] - ] - ], - "1": [ - [ - { - "id": "SRX9626017_SRR13191702", - "single_end": false, - "md5_1": "89c5be920021a035084d8aeb74f32df7", - "md5_2": "56271be38a80db78ef3bdfc5d9909b98" - }, - [ - "SRX9626017_SRR13191702_1.fastq.gz.md5:md5,055a6916ec9ee478e453d50651f87997", - "SRX9626017_SRR13191702_2.fastq.gz.md5:md5,c30ac785f8d80ec563fabf604d8bf945" - ] - ] - ], - "2": [ - "versions.yml:md5,6b9d69dea1c1305f74a65197ee871f1b" - ], - "fastq": [ - [ - { - "id": "SRX9626017_SRR13191702", - "single_end": false, - "md5_1": "89c5be920021a035084d8aeb74f32df7", - "md5_2": "56271be38a80db78ef3bdfc5d9909b98" - }, - [ - "SRX9626017_SRR13191702_1.fastq.gz:md5,89c5be920021a035084d8aeb74f32df7", - "SRX9626017_SRR13191702_2.fastq.gz:md5,56271be38a80db78ef3bdfc5d9909b98" - ] - ] - ], - "md5": [ - [ - { - "id": "SRX9626017_SRR13191702", - "single_end": false, - "md5_1": "89c5be920021a035084d8aeb74f32df7", - "md5_2": "56271be38a80db78ef3bdfc5d9909b98" - }, - [ - "SRX9626017_SRR13191702_1.fastq.gz.md5:md5,055a6916ec9ee478e453d50651f87997", - "SRX9626017_SRR13191702_2.fastq.gz.md5:md5,c30ac785f8d80ec563fabf604d8bf945" - ] - ] - ], - "versions": [ - "versions.yml:md5,6b9d69dea1c1305f74a65197ee871f1b" - ] - } - ], - "timestamp": "2023-08-06T23:31:57+0000" - } -} \ No newline at end of file diff --git a/modules/local/sra_ids_to_runinfo/main.nf b/modules/local/sra_ids_to_runinfo.nf similarity index 100% rename from modules/local/sra_ids_to_runinfo/main.nf rename to modules/local/sra_ids_to_runinfo.nf diff --git a/modules/local/sra_ids_to_runinfo/tests/main.nf.test b/modules/local/sra_ids_to_runinfo/tests/main.nf.test deleted file mode 100644 index f8a44086..00000000 --- a/modules/local/sra_ids_to_runinfo/tests/main.nf.test +++ /dev/null @@ -1,32 +0,0 @@ -nextflow_process { - - name "Test process: SRA_IDS_TO_RUNINFO" - script "modules/local/sra_ids_to_runinfo/main.nf" - process "SRA_IDS_TO_RUNINFO" - tag "modules" - tag "modules_local" - tag "sra_ids_to_runinfo" - - test("Should run without failures") { - - when { - params { - outdir = "$outputDir" - } - - process { - """ - input[0] = 'SRR13191702' - input[1] = '' - """ - } - } - - then { - assertAll( - { assert process.success }, - { assert snapshot(process.out).match() } - ) - } - } -} diff --git a/modules/local/sra_ids_to_runinfo/tests/main.nf.test.snap b/modules/local/sra_ids_to_runinfo/tests/main.nf.test.snap deleted file mode 100644 index dbca931f..00000000 --- a/modules/local/sra_ids_to_runinfo/tests/main.nf.test.snap +++ /dev/null @@ -1,21 +0,0 @@ -{ - "Should run without failures": { - "content": [ - { - "0": [ - "SRR13191702.runinfo.tsv:md5,3a1be35781ca6e8a28d8fd4d2f3bbe85" - ], - "1": [ - "versions.yml:md5,1c14442e9b494b586eafe41e77300fae" - ], - "tsv": [ - "SRR13191702.runinfo.tsv:md5,3a1be35781ca6e8a28d8fd4d2f3bbe85" - ], - "versions": [ - "versions.yml:md5,1c14442e9b494b586eafe41e77300fae" - ] - } - ], - "timestamp": "2023-08-06T23:30:51+0000" - } -} \ No newline at end of file diff --git a/modules/local/sra_merge_samplesheet/main.nf b/modules/local/sra_merge_samplesheet.nf similarity index 100% rename from modules/local/sra_merge_samplesheet/main.nf rename to modules/local/sra_merge_samplesheet.nf diff --git a/modules/local/sra_merge_samplesheet/tests/main.nf.test b/modules/local/sra_merge_samplesheet/tests/main.nf.test deleted file mode 100644 index e37039bd..00000000 --- a/modules/local/sra_merge_samplesheet/tests/main.nf.test +++ /dev/null @@ -1,32 +0,0 @@ -nextflow_process { - - name "Test process: SRA_MERGE_SAMPLESHEET" - script "modules/local/sra_merge_samplesheet/main.nf" - process "SRA_MERGE_SAMPLESHEET" - tag "modules" - tag "modules_local" - tag "sra_merge_samplesheet" - - test("Should run without failures") { - - when { - params { - outdir = "$outputDir" - } - - process { - """ - input[0] = params.test_data['modules_local']['sra_merge_samplesheet_samplesheets'].collect { file(it, checkIfExists: true) } - input[1] = params.test_data['modules_local']['sra_merge_samplesheet_mappings'].collect { file(it, checkIfExists: true) } - """ - } - } - - then { - assertAll( - { assert process.success }, - { assert snapshot(process.out).match() } - ) - } - } -} diff --git a/modules/local/sra_merge_samplesheet/tests/main.nf.test.snap b/modules/local/sra_merge_samplesheet/tests/main.nf.test.snap deleted file mode 100644 index c5f06aac..00000000 --- a/modules/local/sra_merge_samplesheet/tests/main.nf.test.snap +++ /dev/null @@ -1,27 +0,0 @@ -{ - "Should run without failures": { - "content": [ - { - "0": [ - "samplesheet.csv:md5,ef756557b0735becd2574c2a3f5840b2" - ], - "1": [ - "id_mappings.csv:md5,07262807636ce4b50102308eabdcf253" - ], - "2": [ - "versions.yml:md5,410006679d5e496d8c55e58e78ca6b34" - ], - "mappings": [ - "id_mappings.csv:md5,07262807636ce4b50102308eabdcf253" - ], - "samplesheet": [ - "samplesheet.csv:md5,ef756557b0735becd2574c2a3f5840b2" - ], - "versions": [ - "versions.yml:md5,410006679d5e496d8c55e58e78ca6b34" - ] - } - ], - "timestamp": "2023-07-06T13:16:36+0000" - } -} \ No newline at end of file diff --git a/modules/local/sra_runinfo_to_ftp/main.nf b/modules/local/sra_runinfo_to_ftp.nf similarity index 100% rename from modules/local/sra_runinfo_to_ftp/main.nf rename to modules/local/sra_runinfo_to_ftp.nf diff --git a/modules/local/sra_runinfo_to_ftp/tests/main.nf.test b/modules/local/sra_runinfo_to_ftp/tests/main.nf.test deleted file mode 100644 index 1558ff39..00000000 --- a/modules/local/sra_runinfo_to_ftp/tests/main.nf.test +++ /dev/null @@ -1,31 +0,0 @@ -nextflow_process { - - name "Test process: SRA_RUNINFO_TO_FTP" - script "modules/local/sra_runinfo_to_ftp/main.nf" - process "SRA_RUNINFO_TO_FTP" - tag "modules" - tag "modules_local" - tag "sra_runinfo_to_ftp" - - test("Should run without failures") { - - when { - params { - outdir = "$outputDir" - } - - process { - """ - input[0] = file(params.test_data['modules_local']['sra_runinfo_to_ftp'], checkIfExists: true) - """ - } - } - - then { - assertAll( - { assert process.success }, - { assert snapshot(process.out).match() } - ) - } - } -} diff --git a/modules/local/sra_runinfo_to_ftp/tests/main.nf.test.snap b/modules/local/sra_runinfo_to_ftp/tests/main.nf.test.snap deleted file mode 100644 index 71a25f99..00000000 --- a/modules/local/sra_runinfo_to_ftp/tests/main.nf.test.snap +++ /dev/null @@ -1,21 +0,0 @@ -{ - "Should run without failures": { - "content": [ - { - "0": [ - "SRR13191702.runinfo_ftp.tsv:md5,94378c448c044b3e20e5c54e442ab62e" - ], - "1": [ - "versions.yml:md5,e95f8185f665127a73622a19d321bcca" - ], - "tsv": [ - "SRR13191702.runinfo_ftp.tsv:md5,94378c448c044b3e20e5c54e442ab62e" - ], - "versions": [ - "versions.yml:md5,e95f8185f665127a73622a19d321bcca" - ] - } - ], - "timestamp": "2023-08-06T23:13:20+0000" - } -} \ No newline at end of file diff --git a/modules/local/sra_to_samplesheet/main.nf b/modules/local/sra_to_samplesheet.nf similarity index 100% rename from modules/local/sra_to_samplesheet/main.nf rename to modules/local/sra_to_samplesheet.nf diff --git a/modules/local/sra_to_samplesheet/tests/main.nf.test b/modules/local/sra_to_samplesheet/tests/main.nf.test deleted file mode 100644 index b2ec5b11..00000000 --- a/modules/local/sra_to_samplesheet/tests/main.nf.test +++ /dev/null @@ -1,34 +0,0 @@ -nextflow_process { - - name "Test process: SRA_TO_SAMPLESHEET" - script "modules/local/sra_to_samplesheet/main.nf" - process "SRA_TO_SAMPLESHEET" - tag "modules" - tag "modules_local" - tag "sra_to_samplesheet" - - test("Should run without failures") { - - when { - params { - outdir = "$outputDir" - } - - process { - """ - input[0] = [id:'ERX1188904_ERR1109373', run_accession:'ERR1109373', experiment_accession:'ERX1188904', sample_accession:'SAMEA3643867', experiment_alias:'ena-EXPERIMENT-CAM-03-11-2015-17:01:52:847-7', run_alias:'ena-RUN-CAM-03-11-2015-17:01:52:847-7', sample_alias:'sample_56', study_alias:'ena-STUDY-CAM-02-11-2015-17:42:24:189-13', library_layout:'PAIRED', experiment_title:'Illumina HiSeq 2500 paired end sequencing', sample_title:'RNA-Seq reads mapped onto L. Boulardi Toti-like virus genome', sample_description:'RNA-Seq reads mapped onto L. Boulardi Toti-like virus genome', fastq_md5:'8d7d7b854d0207d1226477a30103fade;9fd57225d6c07a31843276d6df9b15c0;5a62e8f785687dce890cfb4fe3e607f9', fastq_ftp:'ftp.sra.ebi.ac.uk/vol1/fastq/ERR110/003/ERR1109373/ERR1109373.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/ERR110/003/ERR1109373/ERR1109373_1.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/ERR110/003/ERR1109373/ERR1109373_2.fastq.gz', fastq_1:'./results/fastq/ERX1188904_ERR1109373_1.fastq.gz', fastq_2:'./results/fastq/ERX1188904_ERR1109373_2.fastq.gz', md5_1:'9fd57225d6c07a31843276d6df9b15c0', md5_2:'5a62e8f785687dce890cfb4fe3e607f9', single_end:false] - input[1] = 'rnaseq' - input[2] = 'auto' - input[3] = 'experiment_accession,run_accession,sample_accession,experiment_alias,run_alias,sample_alias,experiment_title,sample_title,sample_description' - """ - } - } - - then { - assertAll( - { assert process.success }, - { assert snapshot(process.out).match() } - ) - } - } -} diff --git a/modules/local/sra_to_samplesheet/tests/main.nf.test.snap b/modules/local/sra_to_samplesheet/tests/main.nf.test.snap deleted file mode 100644 index 8b5f4947..00000000 --- a/modules/local/sra_to_samplesheet/tests/main.nf.test.snap +++ /dev/null @@ -1,113 +0,0 @@ -{ - "Should run without failures": { - "content": [ - { - "0": [ - [ - { - "id": "ERX1188904_ERR1109373", - "run_accession": "ERR1109373", - "experiment_accession": "ERX1188904", - "sample_accession": "SAMEA3643867", - "experiment_alias": "ena-EXPERIMENT-CAM-03-11-2015-17:01:52:847-7", - "run_alias": "ena-RUN-CAM-03-11-2015-17:01:52:847-7", - "sample_alias": "sample_56", - "study_alias": "ena-STUDY-CAM-02-11-2015-17:42:24:189-13", - "library_layout": "PAIRED", - "experiment_title": "Illumina HiSeq 2500 paired end sequencing", - "sample_title": "RNA-Seq reads mapped onto L. Boulardi Toti-like virus genome", - "sample_description": "RNA-Seq reads mapped onto L. Boulardi Toti-like virus genome", - "fastq_md5": "8d7d7b854d0207d1226477a30103fade;9fd57225d6c07a31843276d6df9b15c0;5a62e8f785687dce890cfb4fe3e607f9", - "fastq_ftp": "ftp.sra.ebi.ac.uk/vol1/fastq/ERR110/003/ERR1109373/ERR1109373.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/ERR110/003/ERR1109373/ERR1109373_1.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/ERR110/003/ERR1109373/ERR1109373_2.fastq.gz", - "fastq_1": "ERX1188904_ERR1109373_1.fastq.gz:md5,9fd57225d6c07a31843276d6df9b15c0", - "fastq_2": "ERX1188904_ERR1109373_2.fastq.gz:md5,5a62e8f785687dce890cfb4fe3e607f9", - "md5_1": "9fd57225d6c07a31843276d6df9b15c0", - "md5_2": "5a62e8f785687dce890cfb4fe3e607f9", - "single_end": false - }, - "ERX1188904_ERR1109373.samplesheet.csv:md5,e7898191d57258e049ee7129d36f5c08" - ] - ], - "1": [ - [ - { - "id": "ERX1188904_ERR1109373", - "run_accession": "ERR1109373", - "experiment_accession": "ERX1188904", - "sample_accession": "SAMEA3643867", - "experiment_alias": "ena-EXPERIMENT-CAM-03-11-2015-17:01:52:847-7", - "run_alias": "ena-RUN-CAM-03-11-2015-17:01:52:847-7", - "sample_alias": "sample_56", - "study_alias": "ena-STUDY-CAM-02-11-2015-17:42:24:189-13", - "library_layout": "PAIRED", - "experiment_title": "Illumina HiSeq 2500 paired end sequencing", - "sample_title": "RNA-Seq reads mapped onto L. Boulardi Toti-like virus genome", - "sample_description": "RNA-Seq reads mapped onto L. Boulardi Toti-like virus genome", - "fastq_md5": "8d7d7b854d0207d1226477a30103fade;9fd57225d6c07a31843276d6df9b15c0;5a62e8f785687dce890cfb4fe3e607f9", - "fastq_ftp": "ftp.sra.ebi.ac.uk/vol1/fastq/ERR110/003/ERR1109373/ERR1109373.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/ERR110/003/ERR1109373/ERR1109373_1.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/ERR110/003/ERR1109373/ERR1109373_2.fastq.gz", - "fastq_1": "ERX1188904_ERR1109373_1.fastq.gz:md5,9fd57225d6c07a31843276d6df9b15c0", - "fastq_2": "ERX1188904_ERR1109373_2.fastq.gz:md5,5a62e8f785687dce890cfb4fe3e607f9", - "md5_1": "9fd57225d6c07a31843276d6df9b15c0", - "md5_2": "5a62e8f785687dce890cfb4fe3e607f9", - "single_end": false - }, - "ERX1188904_ERR1109373.mappings.csv:md5,d09ddb4f0709675e5dfe1eadf12c608f" - ] - ], - "mappings": [ - [ - { - "id": "ERX1188904_ERR1109373", - "run_accession": "ERR1109373", - "experiment_accession": "ERX1188904", - "sample_accession": "SAMEA3643867", - "experiment_alias": "ena-EXPERIMENT-CAM-03-11-2015-17:01:52:847-7", - "run_alias": "ena-RUN-CAM-03-11-2015-17:01:52:847-7", - "sample_alias": "sample_56", - "study_alias": "ena-STUDY-CAM-02-11-2015-17:42:24:189-13", - "library_layout": "PAIRED", - "experiment_title": "Illumina HiSeq 2500 paired end sequencing", - "sample_title": "RNA-Seq reads mapped onto L. Boulardi Toti-like virus genome", - "sample_description": "RNA-Seq reads mapped onto L. Boulardi Toti-like virus genome", - "fastq_md5": "8d7d7b854d0207d1226477a30103fade;9fd57225d6c07a31843276d6df9b15c0;5a62e8f785687dce890cfb4fe3e607f9", - "fastq_ftp": "ftp.sra.ebi.ac.uk/vol1/fastq/ERR110/003/ERR1109373/ERR1109373.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/ERR110/003/ERR1109373/ERR1109373_1.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/ERR110/003/ERR1109373/ERR1109373_2.fastq.gz", - "fastq_1": "ERX1188904_ERR1109373_1.fastq.gz:md5,9fd57225d6c07a31843276d6df9b15c0", - "fastq_2": "ERX1188904_ERR1109373_2.fastq.gz:md5,5a62e8f785687dce890cfb4fe3e607f9", - "md5_1": "9fd57225d6c07a31843276d6df9b15c0", - "md5_2": "5a62e8f785687dce890cfb4fe3e607f9", - "single_end": false - }, - "ERX1188904_ERR1109373.mappings.csv:md5,d09ddb4f0709675e5dfe1eadf12c608f" - ] - ], - "samplesheet": [ - [ - { - "id": "ERX1188904_ERR1109373", - "run_accession": "ERR1109373", - "experiment_accession": "ERX1188904", - "sample_accession": "SAMEA3643867", - "experiment_alias": "ena-EXPERIMENT-CAM-03-11-2015-17:01:52:847-7", - "run_alias": "ena-RUN-CAM-03-11-2015-17:01:52:847-7", - "sample_alias": "sample_56", - "study_alias": "ena-STUDY-CAM-02-11-2015-17:42:24:189-13", - "library_layout": "PAIRED", - "experiment_title": "Illumina HiSeq 2500 paired end sequencing", - "sample_title": "RNA-Seq reads mapped onto L. Boulardi Toti-like virus genome", - "sample_description": "RNA-Seq reads mapped onto L. Boulardi Toti-like virus genome", - "fastq_md5": "8d7d7b854d0207d1226477a30103fade;9fd57225d6c07a31843276d6df9b15c0;5a62e8f785687dce890cfb4fe3e607f9", - "fastq_ftp": "ftp.sra.ebi.ac.uk/vol1/fastq/ERR110/003/ERR1109373/ERR1109373.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/ERR110/003/ERR1109373/ERR1109373_1.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/ERR110/003/ERR1109373/ERR1109373_2.fastq.gz", - "fastq_1": "ERX1188904_ERR1109373_1.fastq.gz:md5,9fd57225d6c07a31843276d6df9b15c0", - "fastq_2": "ERX1188904_ERR1109373_2.fastq.gz:md5,5a62e8f785687dce890cfb4fe3e607f9", - "md5_1": "9fd57225d6c07a31843276d6df9b15c0", - "md5_2": "5a62e8f785687dce890cfb4fe3e607f9", - "single_end": false - }, - "ERX1188904_ERR1109373.samplesheet.csv:md5,e7898191d57258e049ee7129d36f5c08" - ] - ] - } - ], - "timestamp": "2023-08-17T10:55:52+0000" - } -} \ No newline at end of file diff --git a/modules/local/synapse_get/main.nf b/modules/local/synapse_get.nf similarity index 100% rename from modules/local/synapse_get/main.nf rename to modules/local/synapse_get.nf diff --git a/modules/local/synapse_list/main.nf b/modules/local/synapse_list.nf similarity index 100% rename from modules/local/synapse_list/main.nf rename to modules/local/synapse_list.nf diff --git a/modules/local/synapse_merge_samplesheet/main.nf b/modules/local/synapse_merge_samplesheet.nf similarity index 100% rename from modules/local/synapse_merge_samplesheet/main.nf rename to modules/local/synapse_merge_samplesheet.nf diff --git a/modules/local/synapse_show/main.nf b/modules/local/synapse_show.nf similarity index 100% rename from modules/local/synapse_show/main.nf rename to modules/local/synapse_show.nf diff --git a/modules/local/synapse_to_samplesheet/main.nf b/modules/local/synapse_to_samplesheet.nf similarity index 100% rename from modules/local/synapse_to_samplesheet/main.nf rename to modules/local/synapse_to_samplesheet.nf diff --git a/modules/nf-core/custom/dumpsoftwareversions/custom-dumpsoftwareversions.diff b/modules/nf-core/custom/dumpsoftwareversions/custom-dumpsoftwareversions.diff deleted file mode 100644 index a7893b24..00000000 --- a/modules/nf-core/custom/dumpsoftwareversions/custom-dumpsoftwareversions.diff +++ /dev/null @@ -1,13 +0,0 @@ -Changes in module 'nf-core/custom/dumpsoftwareversions' ---- modules/nf-core/custom/dumpsoftwareversions/templates/dumpsoftwareversions.py -+++ modules/nf-core/custom/dumpsoftwareversions/templates/dumpsoftwareversions.py -@@ -75,7 +75,6 @@ - versions_by_module[module] = process_versions - - versions_by_module["Workflow"] = { -- "Nextflow": "$workflow.nextflow.version", - "$workflow.manifest.name": "$workflow.manifest.version", - } - - -************************************************************ diff --git a/modules/nf-core/custom/dumpsoftwareversions/templates/dumpsoftwareversions.py b/modules/nf-core/custom/dumpsoftwareversions/templates/dumpsoftwareversions.py index 33d127f8..da033408 100755 --- a/modules/nf-core/custom/dumpsoftwareversions/templates/dumpsoftwareversions.py +++ b/modules/nf-core/custom/dumpsoftwareversions/templates/dumpsoftwareversions.py @@ -75,6 +75,7 @@ def main(): versions_by_module[module] = process_versions versions_by_module["Workflow"] = { + "Nextflow": "$workflow.nextflow.version", "$workflow.manifest.name": "$workflow.manifest.version", } diff --git a/nextflow.config b/nextflow.config index 6eb5c18d..1e9aaed0 100644 --- a/nextflow.config +++ b/nextflow.config @@ -212,7 +212,7 @@ manifest { description = """Pipeline to fetch metadata and raw FastQ files from public databases""" mainScript = 'main.nf' nextflowVersion = '!>=22.10.1' - version = '1.10.1' + version = '1.10.0' doi = 'https://doi.org/10.5281/zenodo.5070524' } diff --git a/nf-test.config b/nf-test.config deleted file mode 100644 index 0799cb40..00000000 --- a/nf-test.config +++ /dev/null @@ -1,16 +0,0 @@ -config { - // location for all nf-tests - testsDir "." - - // nf-test directory including temporary files for each test - workDir ".nf-test" - - // location of library folder that is added automatically to the classpath - libDir "lib/" - - // location of an optional nextflow.config file specific for executing tests - configFile "nextflow.config" - - // run all test with the defined docker profile from the main nextflow.config - profile "" -} diff --git a/workflows/sra/main.nf b/workflows/sra.nf similarity index 89% rename from workflows/sra/main.nf rename to workflows/sra.nf index 512a73d4..44ff8346 100644 --- a/workflows/sra/main.nf +++ b/workflows/sra.nf @@ -19,12 +19,12 @@ WorkflowSra.initialise(params, valid_params) ======================================================================================== */ -include { SRA_IDS_TO_RUNINFO } from '../../modules/local/sra_ids_to_runinfo' -include { SRA_RUNINFO_TO_FTP } from '../../modules/local/sra_runinfo_to_ftp' -include { SRA_FASTQ_FTP } from '../../modules/local/sra_fastq_ftp' -include { SRA_TO_SAMPLESHEET } from '../../modules/local/sra_to_samplesheet' -include { SRA_MERGE_SAMPLESHEET } from '../../modules/local/sra_merge_samplesheet' -include { MULTIQC_MAPPINGS_CONFIG } from '../../modules/local/multiqc_mappings_config' +include { SRA_IDS_TO_RUNINFO } from '../modules/local/sra_ids_to_runinfo' +include { SRA_RUNINFO_TO_FTP } from '../modules/local/sra_runinfo_to_ftp' +include { SRA_FASTQ_FTP } from '../modules/local/sra_fastq_ftp' +include { SRA_TO_SAMPLESHEET } from '../modules/local/sra_to_samplesheet' +include { SRA_MERGE_SAMPLESHEET } from '../modules/local/sra_merge_samplesheet' +include { MULTIQC_MAPPINGS_CONFIG } from '../modules/local/multiqc_mappings_config' /* ======================================================================================== @@ -32,9 +32,9 @@ include { MULTIQC_MAPPINGS_CONFIG } from '../../modules/local/multiqc_mappings_c ======================================================================================== */ -include { CUSTOM_DUMPSOFTWAREVERSIONS } from '../../modules/nf-core/custom/dumpsoftwareversions' +include { CUSTOM_DUMPSOFTWAREVERSIONS } from '../modules/nf-core/custom/dumpsoftwareversions/main' -include { FASTQ_DOWNLOAD_PREFETCH_FASTERQDUMP_SRATOOLS } from '../../subworkflows/nf-core/fastq_download_prefetch_fasterqdump_sratools' +include { FASTQ_DOWNLOAD_PREFETCH_FASTERQDUMP_SRATOOLS } from '../subworkflows/nf-core/fastq_download_prefetch_fasterqdump_sratools/main' /* ======================================================================================== diff --git a/workflows/sra/tests/main.nf.test b/workflows/sra/tests/main.nf.test deleted file mode 100644 index 39a5cc3f..00000000 --- a/workflows/sra/tests/main.nf.test +++ /dev/null @@ -1,24 +0,0 @@ -nextflow_pipeline { - - name "Test workflow: sra.nf" - script "main.nf" - tag "workflows" - tag "workflows_sra" - tag "sra_default_parameters" - - test("Parameters: default") { - - when { - params { - outdir = "$outputDir" - } - } - - then { - assertAll( - { assert workflow.success }, - { assert snapshot(process.out).match() } - ) - } - } -} diff --git a/workflows/sra/tests/main.nf.test.snap b/workflows/sra/tests/main.nf.test.snap deleted file mode 100644 index 88ea9654..00000000 --- a/workflows/sra/tests/main.nf.test.snap +++ /dev/null @@ -1,88 +0,0 @@ -{ - "Parameters: default": { - "content": [ - { - - } - ], - "timestamp": "2023-08-17T12:09:45+0000" - }, - "metadata": { - "content": [ - "DRR026872.runinfo_ftp.tsv:md5,73606f6a05c45b077809da43ca638b5f", - "DRR028935.runinfo_ftp.tsv:md5,f79eefcea5db346f76f76f87df7f8dd2", - "ERR1109373.runinfo_ftp.tsv:md5,d1717cb1638950b7af22ec1b976616a4", - "ERR1160846.runinfo_ftp.tsv:md5,1b2dc1a64117de20b2164724836da345", - "GSE214215.runinfo_ftp.tsv:md5,23a580c89ee7bf681ca3ffa26aa1837f", - "SRR12848126.runinfo_ftp.tsv:md5,5d1e6bfd3d4077d1e66378c58e44975d", - "SRR13191702.runinfo_ftp.tsv:md5,409e262bb41bb6103315126db4d0dd1d", - "SRR14593545.runinfo_ftp.tsv:md5,62015706ac156693ba3d86ed050cab54", - "SRR14709033.runinfo_ftp.tsv:md5,975dd9b32bdbd78b5da3cd88a5f705c1", - "SRR9984183.runinfo_ftp.tsv:md5,53ab34ff3612b0e2c7d60476822787be" - ], - "timestamp": "2023-08-17T12:09:45+0000" - }, - "samplesheet": { - "content": [ - "id_mappings.csv:md5,3e287081f1e9349921fa8c709a874565", - "multiqc_config.yml:md5,a97047e12b0ea3f46d285629e4053548" - ], - "timestamp": "2023-08-17T12:09:45+0000" - }, - "software_versions": { - "content": [ - "{CUSTOM_DUMPSOFTWAREVERSIONS={python=3.11.0, yaml=6.0}, CUSTOM_SRATOOLSNCBISETTINGS={sratools=2.11.0}, MULTIQC_MAPPINGS_CONFIG={python=3.9.5}, SRA_FASTQ_FTP={curl=7.81.0}, SRA_IDS_TO_RUNINFO={python=3.9.5}, SRA_MERGE_SAMPLESHEET={sed=4.7}, SRA_RUNINFO_TO_FTP={python=3.9.5}, Workflow={nf-core/fetchngs=1.10.1}}" - ], - "timestamp": "2023-08-17T12:09:45+0000" - }, - "fastq": { - "content": [ - "DRX024467_DRR026872.fastq.gz:md5,515e5448c55e054113c4a22df5f62791", - "DRX026011_DRR028935_1.fastq.gz:md5,cc01df82a9354bb6b3be93483b20c35a", - "DRX026011_DRR028935_2.fastq.gz:md5,941c9998d746416dad53c94c480ddf30", - "ERX1188904_ERR1109373_1.fastq.gz:md5,9fd57225d6c07a31843276d6df9b15c0", - "ERX1188904_ERR1109373_2.fastq.gz:md5,5a62e8f785687dce890cfb4fe3e607f9", - "ERX1234253_ERR1160846.fastq.gz:md5,5924f20ef547ebdfed7cad795bbab6e6", - "SRX10940790_SRR14593545_1.fastq.gz:md5,6a4762cf0f1f9f5544d3735e2e07c5d3", - "SRX10940790_SRR14593545_2.fastq.gz:md5,cbd30715fdef457d7aa24a12f19eedf2", - "SRX11047067_SRR14709033.fastq.gz:md5,79140dd1cb3fd1c5e02d88e01f7c3eda", - "SRX17709227_SRR21711856.fastq.gz:md5,7cd1402155befc87be338132d1f31f64", - "SRX17709228_SRR21711855.fastq.gz:md5,cbe4e9f967a71593f9ec3c6edaf11c83", - "SRX6725035_SRR9984183.fastq.gz:md5,0b512d2dc31685983456bd56fd836544", - "SRX9315476_SRR12848126_1.fastq.gz:md5,03f5a34586aef9cd61f54eb26831a665", - "SRX9315476_SRR12848126_2.fastq.gz:md5,97701c5d884af8d96ba95d7237f3bf79", - "SRX9504942_SRR13055517_1.fastq.gz:md5,dcf4438c0b682242ee90c5f3a803fb40", - "SRX9504942_SRR13055517_2.fastq.gz:md5,18dbe96e7f58b63406d9058938df1962", - "SRX9504942_SRR13055518_1.fastq.gz:md5,5ec894d863fcefe394470a0925aefde4", - "SRX9504942_SRR13055518_2.fastq.gz:md5,aead170df9851773d5202b5760c76d76", - "SRX9504942_SRR13055519_1.fastq.gz:md5,5ad51460c6c4a850dd37a206e2c441c1", - "SRX9504942_SRR13055519_2.fastq.gz:md5,a977367bf41dacf4c21bc0c8201b8b88", - "SRX9504942_SRR13055520_1.fastq.gz:md5,795d460abff6009c7f5ff7c14b773fbe", - "SRX9504942_SRR13055520_2.fastq.gz:md5,c3f34379356b28d6dac7212abc1a0a04", - "SRX9626017_SRR13191702_1.fastq.gz:md5,89c5be920021a035084d8aeb74f32df7", - "SRX9626017_SRR13191702_2.fastq.gz:md5,56271be38a80db78ef3bdfc5d9909b98", - [ - "DRX024467_DRR026872.fastq.gz.md5:md5,dacaeba3498fb8f405411a22cdb4b40d", - "DRX026011_DRR028935_1.fastq.gz.md5:md5,a47018c5972ba4c11539d0d6bc25eda9", - "DRX026011_DRR028935_2.fastq.gz.md5:md5,f477bbef548fbed665734ebf084eea2f", - "ERX1188904_ERR1109373_1.fastq.gz.md5:md5,50c1c3108631dc32a3151b67e0260d86", - "ERX1188904_ERR1109373_2.fastq.gz.md5:md5,1f22463d410e91a288c83d43654b2499", - "ERX1234253_ERR1160846.fastq.gz.md5:md5,513a8437ad331fc512b088b3750aa1ff", - "SRX17709227_SRR21711856.fastq.gz.md5:md5,13a38fbef27c3e15867d80887145ae75", - "SRX17709228_SRR21711855.fastq.gz.md5:md5,1e871ddd9e92e1866e0c64d36eb5ec85", - "SRX6725035_SRR9984183.fastq.gz.md5:md5,84f59dbb76c9b5eab7e14d90ced352c4", - "SRX9504942_SRR13055517_1.fastq.gz.md5:md5,a03f7f374dc401047b6f6ccaec3885cc", - "SRX9504942_SRR13055517_2.fastq.gz.md5:md5,facaf207753e977327e7b7df7bb8ace0", - "SRX9504942_SRR13055518_1.fastq.gz.md5:md5,5cf412cd62aadaa4838d9eabb5b44368", - "SRX9504942_SRR13055518_2.fastq.gz.md5:md5,93292b826afc72b23be93df26dd710c8", - "SRX9504942_SRR13055519_1.fastq.gz.md5:md5,f6ad6e2610397147a0a55c651de3992f", - "SRX9504942_SRR13055519_2.fastq.gz.md5:md5,2fe7dd4bcc1e7e61c6f54ef50cf961f3", - "SRX9504942_SRR13055520_1.fastq.gz.md5:md5,ab195b37746a3424a1099d9f8cc58de8", - "SRX9504942_SRR13055520_2.fastq.gz.md5:md5,10c448e23f1f7e7af61ec1204f8fc882", - "SRX9626017_SRR13191702_1.fastq.gz.md5:md5,055a6916ec9ee478e453d50651f87997", - "SRX9626017_SRR13191702_2.fastq.gz.md5:md5,c30ac785f8d80ec563fabf604d8bf945" - ] - ], - "timestamp": "2023-08-17T12:09:45+0000" - } -} \ No newline at end of file diff --git a/workflows/sra/tests/sra_custom_ena_metadata_fields.nf.test b/workflows/sra/tests/sra_custom_ena_metadata_fields.nf.test deleted file mode 100644 index 6e27c4a9..00000000 --- a/workflows/sra/tests/sra_custom_ena_metadata_fields.nf.test +++ /dev/null @@ -1,27 +0,0 @@ -nextflow_pipeline { - - name "Test workflow: sra.nf" - script "main.nf" - tag "workflows" - tag "workflows_sra" - tag "sra_custom_ena_metadata_fields" - - test("Parameters: --nf_core_pipeline rnaseq --ena_metadata_fields ... --sample_mapping_fields ...") { - - when { - params { - outdir = "$outputDir" - nf_core_pipeline = "rnaseq" - ena_metadata_fields = "run_accession,experiment_accession,library_layout,fastq_ftp,fastq_md5" - sample_mapping_fields = "run_accession,library_layout" - } - } - - then { - assertAll( - { assert workflow.success }, - { assert snapshot(process.out).match() } - ) - } - } -} diff --git a/workflows/sra/tests/sra_custom_ena_metadata_fields.nf.test.snap b/workflows/sra/tests/sra_custom_ena_metadata_fields.nf.test.snap deleted file mode 100644 index 55c39d4f..00000000 --- a/workflows/sra/tests/sra_custom_ena_metadata_fields.nf.test.snap +++ /dev/null @@ -1,88 +0,0 @@ -{ - "metadata": { - "content": [ - "DRR026872.runinfo_ftp.tsv:md5,74a5f7058f27a565ce59db481355ca54", - "DRR028935.runinfo_ftp.tsv:md5,07a98fdcec207686a4ea2c9a3997edf3", - "ERR1109373.runinfo_ftp.tsv:md5,868897310855c50b1d5fc77d1195a1f9", - "ERR1160846.runinfo_ftp.tsv:md5,146d7f2ec778b32b7da7ad040e554114", - "GSE214215.runinfo_ftp.tsv:md5,adf62affe371dc9bad8e271450bdc2fe", - "SRR12848126.runinfo_ftp.tsv:md5,cf8827612a76645824e83418d7d76cbf", - "SRR13191702.runinfo_ftp.tsv:md5,2031ca9b7ab736dbde37d05b10cdb0ad", - "SRR14593545.runinfo_ftp.tsv:md5,3a1ac14d71744224a61ab542f869e180", - "SRR14709033.runinfo_ftp.tsv:md5,2385a9cc5e320e78b02743c45d1338f1", - "SRR9984183.runinfo_ftp.tsv:md5,f1ed9fc572d2e0d145be7f547f6d1236" - ], - "timestamp": "2023-08-17T12:11:42+0000" - }, - "samplesheet": { - "content": [ - "id_mappings.csv:md5,8473773df806859c6af7acafcfe5aa6f", - "multiqc_config.yml:md5,6f6189ee58855de81eaf82ad86e21040" - ], - "timestamp": "2023-08-17T12:11:42+0000" - }, - "software_versions": { - "content": [ - "{CUSTOM_DUMPSOFTWAREVERSIONS={python=3.11.0, yaml=6.0}, CUSTOM_SRATOOLSNCBISETTINGS={sratools=2.11.0}, MULTIQC_MAPPINGS_CONFIG={python=3.9.5}, SRA_FASTQ_FTP={curl=7.81.0}, SRA_IDS_TO_RUNINFO={python=3.9.5}, SRA_MERGE_SAMPLESHEET={sed=4.7}, SRA_RUNINFO_TO_FTP={python=3.9.5}, Workflow={nf-core/fetchngs=1.10.1}}" - ], - "timestamp": "2023-08-17T12:11:42+0000" - }, - "Parameters: '--nf_core_pipeline rnaseq --ena_metadata_fields ... --sample_mapping_fields ...'": { - "content": [ - { - - } - ], - "timestamp": "2023-08-17T12:11:42+0000" - }, - "fastq": { - "content": [ - "DRX024467_DRR026872.fastq.gz:md5,515e5448c55e054113c4a22df5f62791", - "DRX026011_DRR028935_1.fastq.gz:md5,cc01df82a9354bb6b3be93483b20c35a", - "DRX026011_DRR028935_2.fastq.gz:md5,941c9998d746416dad53c94c480ddf30", - "ERX1188904_ERR1109373_1.fastq.gz:md5,9fd57225d6c07a31843276d6df9b15c0", - "ERX1188904_ERR1109373_2.fastq.gz:md5,5a62e8f785687dce890cfb4fe3e607f9", - "ERX1234253_ERR1160846.fastq.gz:md5,5924f20ef547ebdfed7cad795bbab6e6", - "SRX10940790_SRR14593545_1.fastq.gz:md5,6a4762cf0f1f9f5544d3735e2e07c5d3", - "SRX10940790_SRR14593545_2.fastq.gz:md5,cbd30715fdef457d7aa24a12f19eedf2", - "SRX11047067_SRR14709033.fastq.gz:md5,79140dd1cb3fd1c5e02d88e01f7c3eda", - "SRX17709227_SRR21711856.fastq.gz:md5,7cd1402155befc87be338132d1f31f64", - "SRX17709228_SRR21711855.fastq.gz:md5,cbe4e9f967a71593f9ec3c6edaf11c83", - "SRX6725035_SRR9984183.fastq.gz:md5,0b512d2dc31685983456bd56fd836544", - "SRX9315476_SRR12848126_1.fastq.gz:md5,03f5a34586aef9cd61f54eb26831a665", - "SRX9315476_SRR12848126_2.fastq.gz:md5,97701c5d884af8d96ba95d7237f3bf79", - "SRX9504942_SRR13055517_1.fastq.gz:md5,dcf4438c0b682242ee90c5f3a803fb40", - "SRX9504942_SRR13055517_2.fastq.gz:md5,18dbe96e7f58b63406d9058938df1962", - "SRX9504942_SRR13055518_1.fastq.gz:md5,5ec894d863fcefe394470a0925aefde4", - "SRX9504942_SRR13055518_2.fastq.gz:md5,aead170df9851773d5202b5760c76d76", - "SRX9504942_SRR13055519_1.fastq.gz:md5,5ad51460c6c4a850dd37a206e2c441c1", - "SRX9504942_SRR13055519_2.fastq.gz:md5,a977367bf41dacf4c21bc0c8201b8b88", - "SRX9504942_SRR13055520_1.fastq.gz:md5,795d460abff6009c7f5ff7c14b773fbe", - "SRX9504942_SRR13055520_2.fastq.gz:md5,c3f34379356b28d6dac7212abc1a0a04", - "SRX9626017_SRR13191702_1.fastq.gz:md5,89c5be920021a035084d8aeb74f32df7", - "SRX9626017_SRR13191702_2.fastq.gz:md5,56271be38a80db78ef3bdfc5d9909b98", - [ - "DRX024467_DRR026872.fastq.gz.md5:md5,dacaeba3498fb8f405411a22cdb4b40d", - "DRX026011_DRR028935_1.fastq.gz.md5:md5,a47018c5972ba4c11539d0d6bc25eda9", - "DRX026011_DRR028935_2.fastq.gz.md5:md5,f477bbef548fbed665734ebf084eea2f", - "ERX1188904_ERR1109373_1.fastq.gz.md5:md5,50c1c3108631dc32a3151b67e0260d86", - "ERX1188904_ERR1109373_2.fastq.gz.md5:md5,1f22463d410e91a288c83d43654b2499", - "ERX1234253_ERR1160846.fastq.gz.md5:md5,513a8437ad331fc512b088b3750aa1ff", - "SRX17709227_SRR21711856.fastq.gz.md5:md5,13a38fbef27c3e15867d80887145ae75", - "SRX17709228_SRR21711855.fastq.gz.md5:md5,1e871ddd9e92e1866e0c64d36eb5ec85", - "SRX6725035_SRR9984183.fastq.gz.md5:md5,84f59dbb76c9b5eab7e14d90ced352c4", - "SRX9504942_SRR13055517_1.fastq.gz.md5:md5,a03f7f374dc401047b6f6ccaec3885cc", - "SRX9504942_SRR13055517_2.fastq.gz.md5:md5,facaf207753e977327e7b7df7bb8ace0", - "SRX9504942_SRR13055518_1.fastq.gz.md5:md5,5cf412cd62aadaa4838d9eabb5b44368", - "SRX9504942_SRR13055518_2.fastq.gz.md5:md5,93292b826afc72b23be93df26dd710c8", - "SRX9504942_SRR13055519_1.fastq.gz.md5:md5,f6ad6e2610397147a0a55c651de3992f", - "SRX9504942_SRR13055519_2.fastq.gz.md5:md5,2fe7dd4bcc1e7e61c6f54ef50cf961f3", - "SRX9504942_SRR13055520_1.fastq.gz.md5:md5,ab195b37746a3424a1099d9f8cc58de8", - "SRX9504942_SRR13055520_2.fastq.gz.md5:md5,10c448e23f1f7e7af61ec1204f8fc882", - "SRX9626017_SRR13191702_1.fastq.gz.md5:md5,055a6916ec9ee478e453d50651f87997", - "SRX9626017_SRR13191702_2.fastq.gz.md5:md5,c30ac785f8d80ec563fabf604d8bf945" - ] - ], - "timestamp": "2023-08-17T12:11:42+0000" - } -} \ No newline at end of file diff --git a/workflows/sra/tests/sra_force_sratools_download.nf.test b/workflows/sra/tests/sra_force_sratools_download.nf.test deleted file mode 100644 index 1b501975..00000000 --- a/workflows/sra/tests/sra_force_sratools_download.nf.test +++ /dev/null @@ -1,25 +0,0 @@ -nextflow_pipeline { - - name "Test workflow: sra.nf" - script "main.nf" - tag "workflows" - tag "workflows_sra" - tag "sra_force_sratools_download" - - test("Parameters: --force_sratools_download") { - - when { - params { - outdir = "$outputDir" - force_sratools_download = true - } - } - - then { - assertAll( - { assert workflow.success }, - { assert snapshot(process.out).match() } - ) - } - } -} diff --git a/workflows/sra/tests/sra_force_sratools_download.nf.test.snap b/workflows/sra/tests/sra_force_sratools_download.nf.test.snap deleted file mode 100644 index d5d694da..00000000 --- a/workflows/sra/tests/sra_force_sratools_download.nf.test.snap +++ /dev/null @@ -1,67 +0,0 @@ -{ - "Parameters: '--force_sratools_download'": { - "content": [ - { - - } - ], - "timestamp": "2023-08-17T12:15:55+0000" - }, - "metadata": { - "content": [ - "DRR026872.runinfo_ftp.tsv:md5,73606f6a05c45b077809da43ca638b5f", - "DRR028935.runinfo_ftp.tsv:md5,f79eefcea5db346f76f76f87df7f8dd2", - "ERR1109373.runinfo_ftp.tsv:md5,d1717cb1638950b7af22ec1b976616a4", - "ERR1160846.runinfo_ftp.tsv:md5,1b2dc1a64117de20b2164724836da345", - "GSE214215.runinfo_ftp.tsv:md5,23a580c89ee7bf681ca3ffa26aa1837f", - "SRR12848126.runinfo_ftp.tsv:md5,5d1e6bfd3d4077d1e66378c58e44975d", - "SRR13191702.runinfo_ftp.tsv:md5,409e262bb41bb6103315126db4d0dd1d", - "SRR14593545.runinfo_ftp.tsv:md5,62015706ac156693ba3d86ed050cab54", - "SRR14709033.runinfo_ftp.tsv:md5,975dd9b32bdbd78b5da3cd88a5f705c1", - "SRR9984183.runinfo_ftp.tsv:md5,53ab34ff3612b0e2c7d60476822787be" - ], - "timestamp": "2023-08-17T12:15:55+0000" - }, - "samplesheet": { - "content": [ - "id_mappings.csv:md5,3e287081f1e9349921fa8c709a874565", - "multiqc_config.yml:md5,a97047e12b0ea3f46d285629e4053548" - ], - "timestamp": "2023-08-17T12:15:55+0000" - }, - "software_versions": { - "content": [ - "{CUSTOM_DUMPSOFTWAREVERSIONS={python=3.11.0, yaml=6.0}, CUSTOM_SRATOOLSNCBISETTINGS={sratools=2.11.0}, MULTIQC_MAPPINGS_CONFIG={python=3.9.5}, SRA_IDS_TO_RUNINFO={python=3.9.5}, SRA_MERGE_SAMPLESHEET={sed=4.7}, SRA_RUNINFO_TO_FTP={python=3.9.5}, Workflow={nf-core/fetchngs=1.10.1}}" - ], - "timestamp": "2023-08-17T12:15:55+0000" - }, - "fastq": { - "content": [ - "DRX024467_DRR026872.fastq.gz:md5,bd3f113c3b06cf4499fa0e00c634ec85", - "DRX026011_DRR028935_1.fastq.gz:md5,0f96fb60e903c8cbd55a6977e66f7c93", - "DRX026011_DRR028935_2.fastq.gz:md5,b97b1e0e806bcae10a7443e2f22d6ca2", - "ERX1188904_ERR1109373_1.fastq.gz:md5,e7edae2715dfaf4c318d37959fd9ae22", - "ERX1188904_ERR1109373_2.fastq.gz:md5,34ab048c92201a5ec4ab36d8dc1c5732", - "ERX1234253_ERR1160846.fastq.gz:md5,22683b24b2467494e430643423f1e275", - "SRX10940790_SRR14593545_1.fastq.gz:md5,6a4762cf0f1f9f5544d3735e2e07c5d3", - "SRX10940790_SRR14593545_2.fastq.gz:md5,cbd30715fdef457d7aa24a12f19eedf2", - "SRX11047067_SRR14709033.fastq.gz:md5,79140dd1cb3fd1c5e02d88e01f7c3eda", - "SRX17709227_SRR21711856.fastq.gz:md5,eae43f1368d4568f415581394dc9726e", - "SRX17709228_SRR21711855.fastq.gz:md5,5194f8009b74552595c4ec5b7605d231", - "SRX6725035_SRR9984183.fastq.gz:md5,7a70e678c400366869601c8be41fe74b", - "SRX9315476_SRR12848126_1.fastq.gz:md5,03f5a34586aef9cd61f54eb26831a665", - "SRX9315476_SRR12848126_2.fastq.gz:md5,97701c5d884af8d96ba95d7237f3bf79", - "SRX9504942_SRR13055517_1.fastq.gz:md5,b6d912a73466c8f27b1d8021f80ec2bb", - "SRX9504942_SRR13055517_2.fastq.gz:md5,7c6e220694fa5d6d9124c739aa70ea92", - "SRX9504942_SRR13055518_1.fastq.gz:md5,ed29278c21a1bb2d8907a74be0dd4bc4", - "SRX9504942_SRR13055518_2.fastq.gz:md5,83785b728312deb81483fc1fd5b14264", - "SRX9504942_SRR13055519_1.fastq.gz:md5,28babc59a625b5161d97392efd4d0018", - "SRX9504942_SRR13055519_2.fastq.gz:md5,cf1eb4c61ab3522f4d473c86b2f696e1", - "SRX9504942_SRR13055520_1.fastq.gz:md5,cc75af896ec8a7cececb37851b0c6fcd", - "SRX9504942_SRR13055520_2.fastq.gz:md5,fe3e2bf9f738e4959243fad59e879eae", - "SRX9626017_SRR13191702_1.fastq.gz:md5,627a90afcd9f3cfc7f5f91074f9a2df7", - "SRX9626017_SRR13191702_2.fastq.gz:md5,3d9b2c68a8ad1547105b17de81b2d9af" - ], - "timestamp": "2023-08-17T12:15:55+0000" - } -} \ No newline at end of file diff --git a/workflows/sra/tests/sra_nf_core_pipeline_atacseq.nf.test b/workflows/sra/tests/sra_nf_core_pipeline_atacseq.nf.test deleted file mode 100644 index bda1d724..00000000 --- a/workflows/sra/tests/sra_nf_core_pipeline_atacseq.nf.test +++ /dev/null @@ -1,25 +0,0 @@ -nextflow_pipeline { - - name "Test workflow: sra.nf" - script "main.nf" - tag "workflows" - tag "workflows_sra" - tag "sra_nf_core_pipeline_atacseq" - - test("Parameters: --nf_core_pipeline atacseq") { - - when { - params { - outdir = "$outputDir" - nf_core_pipeline = "atacseq" - } - } - - then { - assertAll( - { assert workflow.success }, - { assert snapshot(process.out).match() } - ) - } - } -} diff --git a/workflows/sra/tests/sra_nf_core_pipeline_atacseq.nf.test.snap b/workflows/sra/tests/sra_nf_core_pipeline_atacseq.nf.test.snap deleted file mode 100644 index c99f258e..00000000 --- a/workflows/sra/tests/sra_nf_core_pipeline_atacseq.nf.test.snap +++ /dev/null @@ -1,88 +0,0 @@ -{ - "metadata": { - "content": [ - "DRR026872.runinfo_ftp.tsv:md5,73606f6a05c45b077809da43ca638b5f", - "DRR028935.runinfo_ftp.tsv:md5,f79eefcea5db346f76f76f87df7f8dd2", - "ERR1109373.runinfo_ftp.tsv:md5,d1717cb1638950b7af22ec1b976616a4", - "ERR1160846.runinfo_ftp.tsv:md5,1b2dc1a64117de20b2164724836da345", - "GSE214215.runinfo_ftp.tsv:md5,23a580c89ee7bf681ca3ffa26aa1837f", - "SRR12848126.runinfo_ftp.tsv:md5,5d1e6bfd3d4077d1e66378c58e44975d", - "SRR13191702.runinfo_ftp.tsv:md5,409e262bb41bb6103315126db4d0dd1d", - "SRR14593545.runinfo_ftp.tsv:md5,62015706ac156693ba3d86ed050cab54", - "SRR14709033.runinfo_ftp.tsv:md5,975dd9b32bdbd78b5da3cd88a5f705c1", - "SRR9984183.runinfo_ftp.tsv:md5,53ab34ff3612b0e2c7d60476822787be" - ], - "timestamp": "2023-08-17T12:21:36+0000" - }, - "samplesheet": { - "content": [ - "id_mappings.csv:md5,3e287081f1e9349921fa8c709a874565", - "multiqc_config.yml:md5,a97047e12b0ea3f46d285629e4053548" - ], - "timestamp": "2023-08-17T12:21:36+0000" - }, - "software_versions": { - "content": [ - "{CUSTOM_DUMPSOFTWAREVERSIONS={python=3.11.0, yaml=6.0}, CUSTOM_SRATOOLSNCBISETTINGS={sratools=2.11.0}, MULTIQC_MAPPINGS_CONFIG={python=3.9.5}, SRA_FASTQ_FTP={curl=7.81.0}, SRA_IDS_TO_RUNINFO={python=3.9.5}, SRA_MERGE_SAMPLESHEET={sed=4.7}, SRA_RUNINFO_TO_FTP={python=3.9.5}, Workflow={nf-core/fetchngs=1.10.1}}" - ], - "timestamp": "2023-08-17T12:21:36+0000" - }, - "Parameters: '--nf_core_pipeline atacseq'": { - "content": [ - { - - } - ], - "timestamp": "2023-08-17T12:21:36+0000" - }, - "fastq": { - "content": [ - "DRX024467_DRR026872.fastq.gz:md5,515e5448c55e054113c4a22df5f62791", - "DRX026011_DRR028935_1.fastq.gz:md5,cc01df82a9354bb6b3be93483b20c35a", - "DRX026011_DRR028935_2.fastq.gz:md5,941c9998d746416dad53c94c480ddf30", - "ERX1188904_ERR1109373_1.fastq.gz:md5,9fd57225d6c07a31843276d6df9b15c0", - "ERX1188904_ERR1109373_2.fastq.gz:md5,5a62e8f785687dce890cfb4fe3e607f9", - "ERX1234253_ERR1160846.fastq.gz:md5,5924f20ef547ebdfed7cad795bbab6e6", - "SRX10940790_SRR14593545_1.fastq.gz:md5,6a4762cf0f1f9f5544d3735e2e07c5d3", - 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"SRX9504942_SRR13055520_2.fastq.gz:md5,c3f34379356b28d6dac7212abc1a0a04", - "SRX9626017_SRR13191702_1.fastq.gz:md5,89c5be920021a035084d8aeb74f32df7", - "SRX9626017_SRR13191702_2.fastq.gz:md5,56271be38a80db78ef3bdfc5d9909b98", - [ - "DRX024467_DRR026872.fastq.gz.md5:md5,dacaeba3498fb8f405411a22cdb4b40d", - "DRX026011_DRR028935_1.fastq.gz.md5:md5,a47018c5972ba4c11539d0d6bc25eda9", - "DRX026011_DRR028935_2.fastq.gz.md5:md5,f477bbef548fbed665734ebf084eea2f", - "ERX1188904_ERR1109373_1.fastq.gz.md5:md5,50c1c3108631dc32a3151b67e0260d86", - "ERX1188904_ERR1109373_2.fastq.gz.md5:md5,1f22463d410e91a288c83d43654b2499", - "ERX1234253_ERR1160846.fastq.gz.md5:md5,513a8437ad331fc512b088b3750aa1ff", - "SRX17709227_SRR21711856.fastq.gz.md5:md5,13a38fbef27c3e15867d80887145ae75", - "SRX17709228_SRR21711855.fastq.gz.md5:md5,1e871ddd9e92e1866e0c64d36eb5ec85", - "SRX6725035_SRR9984183.fastq.gz.md5:md5,84f59dbb76c9b5eab7e14d90ced352c4", - "SRX9504942_SRR13055517_1.fastq.gz.md5:md5,a03f7f374dc401047b6f6ccaec3885cc", - "SRX9504942_SRR13055517_2.fastq.gz.md5:md5,facaf207753e977327e7b7df7bb8ace0", - "SRX9504942_SRR13055518_1.fastq.gz.md5:md5,5cf412cd62aadaa4838d9eabb5b44368", - "SRX9504942_SRR13055518_2.fastq.gz.md5:md5,93292b826afc72b23be93df26dd710c8", - "SRX9504942_SRR13055519_1.fastq.gz.md5:md5,f6ad6e2610397147a0a55c651de3992f", - "SRX9504942_SRR13055519_2.fastq.gz.md5:md5,2fe7dd4bcc1e7e61c6f54ef50cf961f3", - "SRX9504942_SRR13055520_1.fastq.gz.md5:md5,ab195b37746a3424a1099d9f8cc58de8", - "SRX9504942_SRR13055520_2.fastq.gz.md5:md5,10c448e23f1f7e7af61ec1204f8fc882", - "SRX9626017_SRR13191702_1.fastq.gz.md5:md5,055a6916ec9ee478e453d50651f87997", - "SRX9626017_SRR13191702_2.fastq.gz.md5:md5,c30ac785f8d80ec563fabf604d8bf945" - ] - ], - "timestamp": "2023-08-17T12:21:36+0000" - } -} \ No newline at end of file diff --git a/workflows/sra/tests/sra_nf_core_pipeline_rnaseq.nf.test b/workflows/sra/tests/sra_nf_core_pipeline_rnaseq.nf.test deleted file mode 100644 index 438b7f55..00000000 --- a/workflows/sra/tests/sra_nf_core_pipeline_rnaseq.nf.test +++ /dev/null @@ -1,25 +0,0 @@ -nextflow_pipeline { - - name "Test workflow: sra.nf" - script "main.nf" - tag "workflows" - tag "workflows_sra" - tag "sra_nf_core_pipeline_rnaseq" - - test("Parameters: --nf_core_pipeline rnaseq") { - - when { - params { - outdir = "$outputDir" - nf_core_pipeline = "rnaseq" - } - } - - then { - assertAll( - { assert workflow.success }, - { assert snapshot(process.out).match() } - ) - } - } -} diff --git a/workflows/sra/tests/sra_nf_core_pipeline_rnaseq.nf.test.snap b/workflows/sra/tests/sra_nf_core_pipeline_rnaseq.nf.test.snap deleted file mode 100644 index 1da0381a..00000000 --- a/workflows/sra/tests/sra_nf_core_pipeline_rnaseq.nf.test.snap +++ /dev/null @@ -1,88 +0,0 @@ -{ - "metadata": { - "content": [ - "DRR026872.runinfo_ftp.tsv:md5,73606f6a05c45b077809da43ca638b5f", - "DRR028935.runinfo_ftp.tsv:md5,f79eefcea5db346f76f76f87df7f8dd2", - "ERR1109373.runinfo_ftp.tsv:md5,d1717cb1638950b7af22ec1b976616a4", - "ERR1160846.runinfo_ftp.tsv:md5,1b2dc1a64117de20b2164724836da345", - "GSE214215.runinfo_ftp.tsv:md5,23a580c89ee7bf681ca3ffa26aa1837f", - "SRR12848126.runinfo_ftp.tsv:md5,5d1e6bfd3d4077d1e66378c58e44975d", - "SRR13191702.runinfo_ftp.tsv:md5,409e262bb41bb6103315126db4d0dd1d", - "SRR14593545.runinfo_ftp.tsv:md5,62015706ac156693ba3d86ed050cab54", - "SRR14709033.runinfo_ftp.tsv:md5,975dd9b32bdbd78b5da3cd88a5f705c1", - "SRR9984183.runinfo_ftp.tsv:md5,53ab34ff3612b0e2c7d60476822787be" - ], - "timestamp": "2023-08-17T12:19:51+0000" - }, - "samplesheet": { - "content": [ - "id_mappings.csv:md5,3e287081f1e9349921fa8c709a874565", - "multiqc_config.yml:md5,a97047e12b0ea3f46d285629e4053548" - ], - "timestamp": "2023-08-17T12:19:51+0000" - }, - "software_versions": { - "content": [ - "{CUSTOM_DUMPSOFTWAREVERSIONS={python=3.11.0, yaml=6.0}, CUSTOM_SRATOOLSNCBISETTINGS={sratools=2.11.0}, MULTIQC_MAPPINGS_CONFIG={python=3.9.5}, SRA_FASTQ_FTP={curl=7.81.0}, SRA_IDS_TO_RUNINFO={python=3.9.5}, SRA_MERGE_SAMPLESHEET={sed=4.7}, SRA_RUNINFO_TO_FTP={python=3.9.5}, Workflow={nf-core/fetchngs=1.10.1}}" - ], - "timestamp": "2023-08-17T12:19:51+0000" - }, - "Parameters: '--nf_core_pipeline rnaseq'": { - "content": [ - { - - } - ], - "timestamp": "2023-08-17T12:19:51+0000" - }, - "fastq": { - "content": [ - "DRX024467_DRR026872.fastq.gz:md5,515e5448c55e054113c4a22df5f62791", - "DRX026011_DRR028935_1.fastq.gz:md5,cc01df82a9354bb6b3be93483b20c35a", - "DRX026011_DRR028935_2.fastq.gz:md5,941c9998d746416dad53c94c480ddf30", - "ERX1188904_ERR1109373_1.fastq.gz:md5,9fd57225d6c07a31843276d6df9b15c0", - "ERX1188904_ERR1109373_2.fastq.gz:md5,5a62e8f785687dce890cfb4fe3e607f9", - "ERX1234253_ERR1160846.fastq.gz:md5,5924f20ef547ebdfed7cad795bbab6e6", - "SRX10940790_SRR14593545_1.fastq.gz:md5,6a4762cf0f1f9f5544d3735e2e07c5d3", - "SRX10940790_SRR14593545_2.fastq.gz:md5,cbd30715fdef457d7aa24a12f19eedf2", - "SRX11047067_SRR14709033.fastq.gz:md5,79140dd1cb3fd1c5e02d88e01f7c3eda", - "SRX17709227_SRR21711856.fastq.gz:md5,7cd1402155befc87be338132d1f31f64", - "SRX17709228_SRR21711855.fastq.gz:md5,cbe4e9f967a71593f9ec3c6edaf11c83", - "SRX6725035_SRR9984183.fastq.gz:md5,0b512d2dc31685983456bd56fd836544", - "SRX9315476_SRR12848126_1.fastq.gz:md5,03f5a34586aef9cd61f54eb26831a665", - "SRX9315476_SRR12848126_2.fastq.gz:md5,97701c5d884af8d96ba95d7237f3bf79", - "SRX9504942_SRR13055517_1.fastq.gz:md5,dcf4438c0b682242ee90c5f3a803fb40", - "SRX9504942_SRR13055517_2.fastq.gz:md5,18dbe96e7f58b63406d9058938df1962", - "SRX9504942_SRR13055518_1.fastq.gz:md5,5ec894d863fcefe394470a0925aefde4", - "SRX9504942_SRR13055518_2.fastq.gz:md5,aead170df9851773d5202b5760c76d76", - "SRX9504942_SRR13055519_1.fastq.gz:md5,5ad51460c6c4a850dd37a206e2c441c1", - "SRX9504942_SRR13055519_2.fastq.gz:md5,a977367bf41dacf4c21bc0c8201b8b88", - "SRX9504942_SRR13055520_1.fastq.gz:md5,795d460abff6009c7f5ff7c14b773fbe", - "SRX9504942_SRR13055520_2.fastq.gz:md5,c3f34379356b28d6dac7212abc1a0a04", - "SRX9626017_SRR13191702_1.fastq.gz:md5,89c5be920021a035084d8aeb74f32df7", - "SRX9626017_SRR13191702_2.fastq.gz:md5,56271be38a80db78ef3bdfc5d9909b98", - [ - "DRX024467_DRR026872.fastq.gz.md5:md5,dacaeba3498fb8f405411a22cdb4b40d", - "DRX026011_DRR028935_1.fastq.gz.md5:md5,a47018c5972ba4c11539d0d6bc25eda9", - "DRX026011_DRR028935_2.fastq.gz.md5:md5,f477bbef548fbed665734ebf084eea2f", - "ERX1188904_ERR1109373_1.fastq.gz.md5:md5,50c1c3108631dc32a3151b67e0260d86", - "ERX1188904_ERR1109373_2.fastq.gz.md5:md5,1f22463d410e91a288c83d43654b2499", - "ERX1234253_ERR1160846.fastq.gz.md5:md5,513a8437ad331fc512b088b3750aa1ff", - "SRX17709227_SRR21711856.fastq.gz.md5:md5,13a38fbef27c3e15867d80887145ae75", - "SRX17709228_SRR21711855.fastq.gz.md5:md5,1e871ddd9e92e1866e0c64d36eb5ec85", - "SRX6725035_SRR9984183.fastq.gz.md5:md5,84f59dbb76c9b5eab7e14d90ced352c4", - "SRX9504942_SRR13055517_1.fastq.gz.md5:md5,a03f7f374dc401047b6f6ccaec3885cc", - "SRX9504942_SRR13055517_2.fastq.gz.md5:md5,facaf207753e977327e7b7df7bb8ace0", - "SRX9504942_SRR13055518_1.fastq.gz.md5:md5,5cf412cd62aadaa4838d9eabb5b44368", - "SRX9504942_SRR13055518_2.fastq.gz.md5:md5,93292b826afc72b23be93df26dd710c8", - "SRX9504942_SRR13055519_1.fastq.gz.md5:md5,f6ad6e2610397147a0a55c651de3992f", - "SRX9504942_SRR13055519_2.fastq.gz.md5:md5,2fe7dd4bcc1e7e61c6f54ef50cf961f3", - "SRX9504942_SRR13055520_1.fastq.gz.md5:md5,ab195b37746a3424a1099d9f8cc58de8", - "SRX9504942_SRR13055520_2.fastq.gz.md5:md5,10c448e23f1f7e7af61ec1204f8fc882", - "SRX9626017_SRR13191702_1.fastq.gz.md5:md5,055a6916ec9ee478e453d50651f87997", - "SRX9626017_SRR13191702_2.fastq.gz.md5:md5,c30ac785f8d80ec563fabf604d8bf945" - ] - ], - "timestamp": "2023-08-17T12:19:51+0000" - } -} \ No newline at end of file diff --git a/workflows/sra/tests/sra_nf_core_pipeline_taxprofiler.nf.test b/workflows/sra/tests/sra_nf_core_pipeline_taxprofiler.nf.test deleted file mode 100644 index 301938c4..00000000 --- a/workflows/sra/tests/sra_nf_core_pipeline_taxprofiler.nf.test +++ /dev/null @@ -1,25 +0,0 @@ -nextflow_pipeline { - - name "Test workflow: sra.nf" - script "main.nf" - tag "workflows" - tag "workflows_sra" - tag "sra_nf_core_pipeline_taxprofiler" - - test("Parameters: --nf_core_pipeline taxprofiler") { - - when { - params { - outdir = "$outputDir" - nf_core_pipeline = "taxprofiler" - } - } - - then { - assertAll( - { assert workflow.success }, - { assert snapshot(process.out).match() } - ) - } - } -} diff --git a/workflows/sra/tests/sra_nf_core_pipeline_taxprofiler.nf.test.snap b/workflows/sra/tests/sra_nf_core_pipeline_taxprofiler.nf.test.snap deleted file mode 100644 index 85f3957b..00000000 --- a/workflows/sra/tests/sra_nf_core_pipeline_taxprofiler.nf.test.snap +++ /dev/null @@ -1,88 +0,0 @@ -{ - "metadata": { - "content": [ - "DRR026872.runinfo_ftp.tsv:md5,73606f6a05c45b077809da43ca638b5f", - "DRR028935.runinfo_ftp.tsv:md5,f79eefcea5db346f76f76f87df7f8dd2", - "ERR1109373.runinfo_ftp.tsv:md5,d1717cb1638950b7af22ec1b976616a4", - "ERR1160846.runinfo_ftp.tsv:md5,1b2dc1a64117de20b2164724836da345", - "GSE214215.runinfo_ftp.tsv:md5,23a580c89ee7bf681ca3ffa26aa1837f", - "SRR12848126.runinfo_ftp.tsv:md5,5d1e6bfd3d4077d1e66378c58e44975d", - "SRR13191702.runinfo_ftp.tsv:md5,409e262bb41bb6103315126db4d0dd1d", - "SRR14593545.runinfo_ftp.tsv:md5,62015706ac156693ba3d86ed050cab54", - "SRR14709033.runinfo_ftp.tsv:md5,975dd9b32bdbd78b5da3cd88a5f705c1", - "SRR9984183.runinfo_ftp.tsv:md5,53ab34ff3612b0e2c7d60476822787be" - ], - "timestamp": "2023-08-17T12:24:34+0000" - }, - "samplesheet": { - "content": [ - "id_mappings.csv:md5,3e287081f1e9349921fa8c709a874565", - "multiqc_config.yml:md5,a97047e12b0ea3f46d285629e4053548" - ], - "timestamp": "2023-08-17T12:24:34+0000" - }, - "software_versions": { - "content": [ - "{CUSTOM_DUMPSOFTWAREVERSIONS={python=3.11.0, yaml=6.0}, CUSTOM_SRATOOLSNCBISETTINGS={sratools=2.11.0}, MULTIQC_MAPPINGS_CONFIG={python=3.9.5}, SRA_FASTQ_FTP={curl=7.81.0}, SRA_IDS_TO_RUNINFO={python=3.9.5}, SRA_MERGE_SAMPLESHEET={sed=4.7}, SRA_RUNINFO_TO_FTP={python=3.9.5}, Workflow={nf-core/fetchngs=1.10.1}}" - ], - "timestamp": "2023-08-17T12:24:34+0000" - }, - "Parameters: --nf_core_pipeline taxprofiler": { - "content": [ - { - - } - ], - "timestamp": "2023-08-17T12:24:34+0000" - }, - "fastq": { - "content": [ - "DRX024467_DRR026872.fastq.gz:md5,515e5448c55e054113c4a22df5f62791", - "DRX026011_DRR028935_1.fastq.gz:md5,cc01df82a9354bb6b3be93483b20c35a", - "DRX026011_DRR028935_2.fastq.gz:md5,941c9998d746416dad53c94c480ddf30", - "ERX1188904_ERR1109373_1.fastq.gz:md5,9fd57225d6c07a31843276d6df9b15c0", - "ERX1188904_ERR1109373_2.fastq.gz:md5,5a62e8f785687dce890cfb4fe3e607f9", - "ERX1234253_ERR1160846.fastq.gz:md5,5924f20ef547ebdfed7cad795bbab6e6", - "SRX10940790_SRR14593545_1.fastq.gz:md5,6a4762cf0f1f9f5544d3735e2e07c5d3", - "SRX10940790_SRR14593545_2.fastq.gz:md5,cbd30715fdef457d7aa24a12f19eedf2", - "SRX11047067_SRR14709033.fastq.gz:md5,79140dd1cb3fd1c5e02d88e01f7c3eda", - "SRX17709227_SRR21711856.fastq.gz:md5,7cd1402155befc87be338132d1f31f64", - "SRX17709228_SRR21711855.fastq.gz:md5,cbe4e9f967a71593f9ec3c6edaf11c83", - "SRX6725035_SRR9984183.fastq.gz:md5,0b512d2dc31685983456bd56fd836544", - "SRX9315476_SRR12848126_1.fastq.gz:md5,03f5a34586aef9cd61f54eb26831a665", - "SRX9315476_SRR12848126_2.fastq.gz:md5,97701c5d884af8d96ba95d7237f3bf79", - "SRX9504942_SRR13055517_1.fastq.gz:md5,dcf4438c0b682242ee90c5f3a803fb40", - "SRX9504942_SRR13055517_2.fastq.gz:md5,18dbe96e7f58b63406d9058938df1962", - "SRX9504942_SRR13055518_1.fastq.gz:md5,5ec894d863fcefe394470a0925aefde4", - "SRX9504942_SRR13055518_2.fastq.gz:md5,aead170df9851773d5202b5760c76d76", - "SRX9504942_SRR13055519_1.fastq.gz:md5,5ad51460c6c4a850dd37a206e2c441c1", - "SRX9504942_SRR13055519_2.fastq.gz:md5,a977367bf41dacf4c21bc0c8201b8b88", - "SRX9504942_SRR13055520_1.fastq.gz:md5,795d460abff6009c7f5ff7c14b773fbe", - "SRX9504942_SRR13055520_2.fastq.gz:md5,c3f34379356b28d6dac7212abc1a0a04", - "SRX9626017_SRR13191702_1.fastq.gz:md5,89c5be920021a035084d8aeb74f32df7", - "SRX9626017_SRR13191702_2.fastq.gz:md5,56271be38a80db78ef3bdfc5d9909b98", - [ - "DRX024467_DRR026872.fastq.gz.md5:md5,dacaeba3498fb8f405411a22cdb4b40d", - "DRX026011_DRR028935_1.fastq.gz.md5:md5,a47018c5972ba4c11539d0d6bc25eda9", - "DRX026011_DRR028935_2.fastq.gz.md5:md5,f477bbef548fbed665734ebf084eea2f", - "ERX1188904_ERR1109373_1.fastq.gz.md5:md5,50c1c3108631dc32a3151b67e0260d86", - "ERX1188904_ERR1109373_2.fastq.gz.md5:md5,1f22463d410e91a288c83d43654b2499", - "ERX1234253_ERR1160846.fastq.gz.md5:md5,513a8437ad331fc512b088b3750aa1ff", - "SRX17709227_SRR21711856.fastq.gz.md5:md5,13a38fbef27c3e15867d80887145ae75", - "SRX17709228_SRR21711855.fastq.gz.md5:md5,1e871ddd9e92e1866e0c64d36eb5ec85", - "SRX6725035_SRR9984183.fastq.gz.md5:md5,84f59dbb76c9b5eab7e14d90ced352c4", - "SRX9504942_SRR13055517_1.fastq.gz.md5:md5,a03f7f374dc401047b6f6ccaec3885cc", - "SRX9504942_SRR13055517_2.fastq.gz.md5:md5,facaf207753e977327e7b7df7bb8ace0", - "SRX9504942_SRR13055518_1.fastq.gz.md5:md5,5cf412cd62aadaa4838d9eabb5b44368", - "SRX9504942_SRR13055518_2.fastq.gz.md5:md5,93292b826afc72b23be93df26dd710c8", - "SRX9504942_SRR13055519_1.fastq.gz.md5:md5,f6ad6e2610397147a0a55c651de3992f", - "SRX9504942_SRR13055519_2.fastq.gz.md5:md5,2fe7dd4bcc1e7e61c6f54ef50cf961f3", - "SRX9504942_SRR13055520_1.fastq.gz.md5:md5,ab195b37746a3424a1099d9f8cc58de8", - "SRX9504942_SRR13055520_2.fastq.gz.md5:md5,10c448e23f1f7e7af61ec1204f8fc882", - "SRX9626017_SRR13191702_1.fastq.gz.md5:md5,055a6916ec9ee478e453d50651f87997", - "SRX9626017_SRR13191702_2.fastq.gz.md5:md5,c30ac785f8d80ec563fabf604d8bf945" - ] - ], - "timestamp": "2023-08-17T12:24:34+0000" - } -} \ No newline at end of file diff --git a/workflows/sra/tests/sra_nf_core_pipeline_viralrecon.nf.test b/workflows/sra/tests/sra_nf_core_pipeline_viralrecon.nf.test deleted file mode 100644 index 892a7c3a..00000000 --- a/workflows/sra/tests/sra_nf_core_pipeline_viralrecon.nf.test +++ /dev/null @@ -1,25 +0,0 @@ -nextflow_pipeline { - - name "Test workflow: sra.nf" - script "main.nf" - tag "workflows" - tag "workflows_sra" - tag "sra_nf_core_pipeline_viralrecon" - - test("Parameters: --nf_core_pipeline viralrecon") { - - when { - params { - outdir = "$outputDir" - nf_core_pipeline = "viralrecon" - } - } - - then { - assertAll( - { assert workflow.success }, - { assert snapshot(process.out).match() } - ) - } - } -} diff --git a/workflows/sra/tests/sra_nf_core_pipeline_viralrecon.nf.test.snap b/workflows/sra/tests/sra_nf_core_pipeline_viralrecon.nf.test.snap deleted file mode 100644 index 13c59b5d..00000000 --- a/workflows/sra/tests/sra_nf_core_pipeline_viralrecon.nf.test.snap +++ /dev/null @@ -1,88 +0,0 @@ -{ - "metadata": { - "content": [ - "DRR026872.runinfo_ftp.tsv:md5,73606f6a05c45b077809da43ca638b5f", - "DRR028935.runinfo_ftp.tsv:md5,f79eefcea5db346f76f76f87df7f8dd2", - "ERR1109373.runinfo_ftp.tsv:md5,d1717cb1638950b7af22ec1b976616a4", - "ERR1160846.runinfo_ftp.tsv:md5,1b2dc1a64117de20b2164724836da345", - "GSE214215.runinfo_ftp.tsv:md5,23a580c89ee7bf681ca3ffa26aa1837f", - "SRR12848126.runinfo_ftp.tsv:md5,5d1e6bfd3d4077d1e66378c58e44975d", - "SRR13191702.runinfo_ftp.tsv:md5,409e262bb41bb6103315126db4d0dd1d", - "SRR14593545.runinfo_ftp.tsv:md5,62015706ac156693ba3d86ed050cab54", - "SRR14709033.runinfo_ftp.tsv:md5,975dd9b32bdbd78b5da3cd88a5f705c1", - "SRR9984183.runinfo_ftp.tsv:md5,53ab34ff3612b0e2c7d60476822787be" - ], - "timestamp": "2023-08-17T12:26:57+0000" - }, - "samplesheet": { - "content": [ - "id_mappings.csv:md5,3e287081f1e9349921fa8c709a874565", - "multiqc_config.yml:md5,a97047e12b0ea3f46d285629e4053548" - ], - "timestamp": "2023-08-17T12:26:57+0000" - }, - "Parameters: --nf_core_pipeline viralrecon": { - "content": [ - { - - } - ], - "timestamp": "2023-08-17T12:26:57+0000" - }, - "software_versions": { - "content": [ - "{CUSTOM_DUMPSOFTWAREVERSIONS={python=3.11.0, yaml=6.0}, CUSTOM_SRATOOLSNCBISETTINGS={sratools=2.11.0}, MULTIQC_MAPPINGS_CONFIG={python=3.9.5}, SRA_FASTQ_FTP={curl=7.81.0}, SRA_IDS_TO_RUNINFO={python=3.9.5}, SRA_MERGE_SAMPLESHEET={sed=4.7}, SRA_RUNINFO_TO_FTP={python=3.9.5}, Workflow={nf-core/fetchngs=1.10.1}}" - ], - "timestamp": "2023-08-17T12:26:57+0000" - }, - "fastq": { - "content": [ - "DRX024467_DRR026872.fastq.gz:md5,515e5448c55e054113c4a22df5f62791", - "DRX026011_DRR028935_1.fastq.gz:md5,cc01df82a9354bb6b3be93483b20c35a", - "DRX026011_DRR028935_2.fastq.gz:md5,941c9998d746416dad53c94c480ddf30", - "ERX1188904_ERR1109373_1.fastq.gz:md5,9fd57225d6c07a31843276d6df9b15c0", - "ERX1188904_ERR1109373_2.fastq.gz:md5,5a62e8f785687dce890cfb4fe3e607f9", - "ERX1234253_ERR1160846.fastq.gz:md5,5924f20ef547ebdfed7cad795bbab6e6", - "SRX10940790_SRR14593545_1.fastq.gz:md5,6a4762cf0f1f9f5544d3735e2e07c5d3", - "SRX10940790_SRR14593545_2.fastq.gz:md5,cbd30715fdef457d7aa24a12f19eedf2", - "SRX11047067_SRR14709033.fastq.gz:md5,79140dd1cb3fd1c5e02d88e01f7c3eda", - "SRX17709227_SRR21711856.fastq.gz:md5,7cd1402155befc87be338132d1f31f64", - "SRX17709228_SRR21711855.fastq.gz:md5,cbe4e9f967a71593f9ec3c6edaf11c83", - "SRX6725035_SRR9984183.fastq.gz:md5,0b512d2dc31685983456bd56fd836544", - "SRX9315476_SRR12848126_1.fastq.gz:md5,03f5a34586aef9cd61f54eb26831a665", - "SRX9315476_SRR12848126_2.fastq.gz:md5,97701c5d884af8d96ba95d7237f3bf79", - "SRX9504942_SRR13055517_1.fastq.gz:md5,dcf4438c0b682242ee90c5f3a803fb40", - "SRX9504942_SRR13055517_2.fastq.gz:md5,18dbe96e7f58b63406d9058938df1962", - "SRX9504942_SRR13055518_1.fastq.gz:md5,5ec894d863fcefe394470a0925aefde4", - "SRX9504942_SRR13055518_2.fastq.gz:md5,aead170df9851773d5202b5760c76d76", - "SRX9504942_SRR13055519_1.fastq.gz:md5,5ad51460c6c4a850dd37a206e2c441c1", - "SRX9504942_SRR13055519_2.fastq.gz:md5,a977367bf41dacf4c21bc0c8201b8b88", - "SRX9504942_SRR13055520_1.fastq.gz:md5,795d460abff6009c7f5ff7c14b773fbe", - "SRX9504942_SRR13055520_2.fastq.gz:md5,c3f34379356b28d6dac7212abc1a0a04", - "SRX9626017_SRR13191702_1.fastq.gz:md5,89c5be920021a035084d8aeb74f32df7", - "SRX9626017_SRR13191702_2.fastq.gz:md5,56271be38a80db78ef3bdfc5d9909b98", - [ - "DRX024467_DRR026872.fastq.gz.md5:md5,dacaeba3498fb8f405411a22cdb4b40d", - "DRX026011_DRR028935_1.fastq.gz.md5:md5,a47018c5972ba4c11539d0d6bc25eda9", - "DRX026011_DRR028935_2.fastq.gz.md5:md5,f477bbef548fbed665734ebf084eea2f", - "ERX1188904_ERR1109373_1.fastq.gz.md5:md5,50c1c3108631dc32a3151b67e0260d86", - "ERX1188904_ERR1109373_2.fastq.gz.md5:md5,1f22463d410e91a288c83d43654b2499", - "ERX1234253_ERR1160846.fastq.gz.md5:md5,513a8437ad331fc512b088b3750aa1ff", - "SRX17709227_SRR21711856.fastq.gz.md5:md5,13a38fbef27c3e15867d80887145ae75", - "SRX17709228_SRR21711855.fastq.gz.md5:md5,1e871ddd9e92e1866e0c64d36eb5ec85", - "SRX6725035_SRR9984183.fastq.gz.md5:md5,84f59dbb76c9b5eab7e14d90ced352c4", - "SRX9504942_SRR13055517_1.fastq.gz.md5:md5,a03f7f374dc401047b6f6ccaec3885cc", - "SRX9504942_SRR13055517_2.fastq.gz.md5:md5,facaf207753e977327e7b7df7bb8ace0", - "SRX9504942_SRR13055518_1.fastq.gz.md5:md5,5cf412cd62aadaa4838d9eabb5b44368", - "SRX9504942_SRR13055518_2.fastq.gz.md5:md5,93292b826afc72b23be93df26dd710c8", - "SRX9504942_SRR13055519_1.fastq.gz.md5:md5,f6ad6e2610397147a0a55c651de3992f", - "SRX9504942_SRR13055519_2.fastq.gz.md5:md5,2fe7dd4bcc1e7e61c6f54ef50cf961f3", - "SRX9504942_SRR13055520_1.fastq.gz.md5:md5,ab195b37746a3424a1099d9f8cc58de8", - "SRX9504942_SRR13055520_2.fastq.gz.md5:md5,10c448e23f1f7e7af61ec1204f8fc882", - "SRX9626017_SRR13191702_1.fastq.gz.md5:md5,055a6916ec9ee478e453d50651f87997", - "SRX9626017_SRR13191702_2.fastq.gz.md5:md5,c30ac785f8d80ec563fabf604d8bf945" - ] - ], - "timestamp": "2023-08-17T12:26:57+0000" - } -} \ No newline at end of file diff --git a/workflows/sra/tests/sra_skip_fastq_download.nf.test b/workflows/sra/tests/sra_skip_fastq_download.nf.test deleted file mode 100644 index 7d218cf7..00000000 --- a/workflows/sra/tests/sra_skip_fastq_download.nf.test +++ /dev/null @@ -1,25 +0,0 @@ -nextflow_pipeline { - - name "Test workflow: sra.nf" - script "main.nf" - tag "workflows" - tag "workflows_sra" - tag "sra_skip_fastq_download" - - test("Parameters: --skip_fastq_download") { - - when { - params { - outdir = "$outputDir" - skip_fastq_download = true - } - } - - then { - assertAll( - { assert workflow.success }, - { assert snapshot(process.out).match() } - ) - } - } -} diff --git a/workflows/sra/tests/sra_skip_fastq_download.nf.test.snap b/workflows/sra/tests/sra_skip_fastq_download.nf.test.snap deleted file mode 100644 index d004d5d2..00000000 --- a/workflows/sra/tests/sra_skip_fastq_download.nf.test.snap +++ /dev/null @@ -1,46 +0,0 @@ -{ - "Parameters: '--skip_fastq_download'": { - "content": [ - { - - } - ], - "timestamp": "2023-08-17T12:25:19+0000" - }, - "metadata": { - "content": [ - "DRR026872.runinfo_ftp.tsv:md5,73606f6a05c45b077809da43ca638b5f", - "DRR028935.runinfo_ftp.tsv:md5,f79eefcea5db346f76f76f87df7f8dd2", - "ERR1109373.runinfo_ftp.tsv:md5,d1717cb1638950b7af22ec1b976616a4", - "ERR1160846.runinfo_ftp.tsv:md5,1b2dc1a64117de20b2164724836da345", - "GSE214215.runinfo_ftp.tsv:md5,23a580c89ee7bf681ca3ffa26aa1837f", - "SRR12848126.runinfo_ftp.tsv:md5,5d1e6bfd3d4077d1e66378c58e44975d", - "SRR13191702.runinfo_ftp.tsv:md5,409e262bb41bb6103315126db4d0dd1d", - "SRR14593545.runinfo_ftp.tsv:md5,62015706ac156693ba3d86ed050cab54", - "SRR14709033.runinfo_ftp.tsv:md5,975dd9b32bdbd78b5da3cd88a5f705c1", - "SRR9984183.runinfo_ftp.tsv:md5,53ab34ff3612b0e2c7d60476822787be" - ], - "timestamp": "2023-08-17T12:25:19+0000" - }, - "samplesheet": { - "content": [ - "id_mappings.csv:md5,3e287081f1e9349921fa8c709a874565", - "multiqc_config.yml:md5,a97047e12b0ea3f46d285629e4053548" - ], - "timestamp": "2023-08-17T12:25:19+0000" - }, - "software_versions": { - "content": [ - "{CUSTOM_DUMPSOFTWAREVERSIONS={python=3.11.0, yaml=6.0}, MULTIQC_MAPPINGS_CONFIG={python=3.9.5}, SRA_IDS_TO_RUNINFO={python=3.9.5}, SRA_MERGE_SAMPLESHEET={sed=4.7}, SRA_RUNINFO_TO_FTP={python=3.9.5}, Workflow={nf-core/fetchngs=1.10.1}}" - ], - "timestamp": "2023-08-17T12:25:19+0000" - }, - "Parameters: --skip_fastq_download": { - "content": [ - { - - } - ], - "timestamp": "2023-08-17T12:25:19+0000" - } -} \ No newline at end of file diff --git a/workflows/synapse/main.nf b/workflows/synapse.nf similarity index 89% rename from workflows/synapse/main.nf rename to workflows/synapse.nf index f8cbeba1..f2138a60 100644 --- a/workflows/synapse/main.nf +++ b/workflows/synapse.nf @@ -19,11 +19,11 @@ if (params.synapse_config) { ======================================================================================== */ -include { SYNAPSE_LIST } from '../../modules/local/synapse_list' -include { SYNAPSE_SHOW } from '../../modules/local/synapse_show' -include { SYNAPSE_GET } from '../../modules/local/synapse_get' -include { SYNAPSE_TO_SAMPLESHEET } from '../../modules/local/synapse_to_samplesheet' -include { SYNAPSE_MERGE_SAMPLESHEET } from '../../modules/local/synapse_merge_samplesheet' +include { SYNAPSE_LIST } from '../modules/local/synapse_list' +include { SYNAPSE_SHOW } from '../modules/local/synapse_show' +include { SYNAPSE_GET } from '../modules/local/synapse_get' +include { SYNAPSE_TO_SAMPLESHEET } from '../modules/local/synapse_to_samplesheet' +include { SYNAPSE_MERGE_SAMPLESHEET } from '../modules/local/synapse_merge_samplesheet' /* ======================================================================================== @@ -31,7 +31,7 @@ include { SYNAPSE_MERGE_SAMPLESHEET } from '../../modules/local/synapse_merge_sa ======================================================================================== */ -include { CUSTOM_DUMPSOFTWAREVERSIONS } from '../../modules/nf-core/custom/dumpsoftwareversions' +include { CUSTOM_DUMPSOFTWAREVERSIONS } from '../modules/nf-core/custom/dumpsoftwareversions/main' /* ======================================================================================== diff --git a/workflows/synapse/tests/main.nf.test b/workflows/synapse/tests/main.nf.test deleted file mode 100644 index 7cbfed11..00000000 --- a/workflows/synapse/tests/main.nf.test +++ /dev/null @@ -1,28 +0,0 @@ -nextflow_pipeline { - - name "Test workflow: synapse.nf" - script "main.nf" - tag "workflows" - tag "synapse" - tag "synapse_default" - profile "test_synapse" - - test("Synapse Input Type") { - - when { - params { - outdir = "$outputDir" - } - } - - then { - assertAll( - { assert workflow.success }, - { assert snapshot(path("$outputDir/pipeline_info/software_versions.yml")).match("software_versions") }, - { assert snapshot(path("$outputDir/samplesheet/").list()).match("samplesheet") } - ) - } - - } - -}