diff --git a/.github/ISSUE_TEMPLATE/bug_report.yml b/.github/ISSUE_TEMPLATE/bug_report.yml index d8f9579..f2c8a55 100644 --- a/.github/ISSUE_TEMPLATE/bug_report.yml +++ b/.github/ISSUE_TEMPLATE/bug_report.yml @@ -122,3 +122,22 @@ body: render: shell validations: required: false + - type: dropdown + id: run-demo + attributes: + label: Were you able to successfully run the latest version of the workflow with the demo data? + description: For CLI execution, were you able to successfully run the workflow using the demo data available in the [Install and run](./README.md#install-and-run) section of the `README.md`? For execution in the EPI2ME application, were you able to successfully run the workflow via the "Use demo data" button? + options: + - yes + - no + - other (please describe below) + validations: + required: true + - type: textarea + id: demo-other + attributes: + label: Other demo data information + render: shell + validations: + required: false + diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml index 8134142..2ca2e89 100644 --- a/.pre-commit-config.yaml +++ b/.pre-commit-config.yaml @@ -3,12 +3,12 @@ repos: hooks: - id: docs_readme name: docs_readme - entry: parse_docs -p docs -e .md -s 01_brief_description 02_introduction 03_compute_requirements 04_install_and_run 05_related_protocols 06_inputs 07_outputs 08_pipeline_overview 09_troubleshooting 10_FAQ 11_other -ot README.md -od output_definition.json -ns nextflow_schema.json + entry: parse_docs -p docs -e .md -s 01_brief_description 02_introduction 03_compute_requirements 04_install_and_run 05_related_protocols 06_input_example 06_input_parameters 07_outputs 08_pipeline_overview 09_troubleshooting 10_FAQ 11_other -ot README.md -od output_definition.json -ns nextflow_schema.json language: python always_run: true pass_filenames: false additional_dependencies: - - epi2melabs>=0.0.50 + - epi2melabs>=0.0.51 - id: build_models name: build_models entry: datamodel-codegen --strict-nullable --base-class workflow_glue.results_schema_helpers.BaseModel --use-schema-description --disable-timestamp --input results_schema.yml --input-file-type openapi --output bin/workflow_glue/results_schema.py diff --git a/README.md b/README.md index c527339..a3dd7eb 100644 --- a/README.md +++ b/README.md @@ -83,7 +83,31 @@ Find related protocols in the [Nanopore community](https://community.nanoporetec -## Inputs +## Input example + + +This workflow accepts FASTQ files as input. + +The FASTQ input parameters for this workflow accept one of three cases: (i) the path to a single FASTQ file; (ii) the path to a top-level directory containing FASTQ files; (iii) the path to a directory containing one level of sub-directories which in turn contain FASTQ files. In the first and second cases (i and ii), a sample name can be supplied with `--sample`. In the last case (iii), the data is assumed to be multiplexed with the names of the sub-directories as barcodes. In this case, a sample sheet can be provided with `--sample_sheet`. If you are using the workflow for differential expression analysis the last case(iii) will be expected with a minimum of 4 samples (at least 2 replicates of each sample to compare) but we recommend 6 samples (three replicates). + +``` +(i) (ii) (iii) +input_reads.fastq ─── input_directory ─── input_directory + ├── reads0.fastq ├── barcode01 + └── reads1.fastq │ ├── reads0.fastq + │ └── reads1.fastq + ├── barcode02 + │ ├── reads0.fastq + │ ├── reads1.fastq + │ └── reads2.fastq + └── barcode03 + └── reads0.fastq +``` + + + + +## Input parameters ### Input Options @@ -163,7 +187,7 @@ Find related protocols in the [Nanopore community](https://community.nanoporetec ## Outputs -Outputs files may be aggregated including information for all samples or provided per sample. Per-sample files will be prefixed with respective aliases and represented below as {{ alias }}. +Output files may be aggregated including information for all samples or provided per sample. Per-sample files will be prefixed with respective aliases and represented below as {{ alias }}. | Title | File path | Description | Per sample or aggregated | |-------|-----------|-------------|--------------------------| diff --git a/bin/workflow_glue/check_sample_sheet.py b/bin/workflow_glue/check_sample_sheet.py index fe4fc37..62e3483 100755 --- a/bin/workflow_glue/check_sample_sheet.py +++ b/bin/workflow_glue/check_sample_sheet.py @@ -43,7 +43,7 @@ def main(args): ] if not os.path.exists(args.sample_sheet) or not os.path.isfile(args.sample_sheet): - sys.stdout.write(f"Could not open sample sheet '{args.sample_sheet}'.") + sys.stdout.write("Could not open sample sheet file.") sys.exit() try: diff --git a/docs/06_input_example.md b/docs/06_input_example.md new file mode 100644 index 0000000..45ef56d --- /dev/null +++ b/docs/06_input_example.md @@ -0,0 +1,18 @@ + +This workflow accepts FASTQ files as input. + +The FASTQ input parameters for this workflow accept one of three cases: (i) the path to a single FASTQ file; (ii) the path to a top-level directory containing FASTQ files; (iii) the path to a directory containing one level of sub-directories which in turn contain FASTQ files. In the first and second cases (i and ii), a sample name can be supplied with `--sample`. In the last case (iii), the data is assumed to be multiplexed with the names of the sub-directories as barcodes. In this case, a sample sheet can be provided with `--sample_sheet`. If you are using the workflow for differential expression analysis the last case(iii) will be expected with a minimum of 4 samples (at least 2 replicates of each sample to compare) but we recommend 6 samples (three replicates). + +``` +(i) (ii) (iii) +input_reads.fastq ─── input_directory ─── input_directory + ├── reads0.fastq ├── barcode01 + └── reads1.fastq │ ├── reads0.fastq + │ └── reads1.fastq + ├── barcode02 + │ ├── reads0.fastq + │ ├── reads1.fastq + │ └── reads2.fastq + └── barcode03 + └── reads0.fastq +``` diff --git a/docs/06_inputs.md b/docs/06_input_parameters.md similarity index 100% rename from docs/06_inputs.md rename to docs/06_input_parameters.md diff --git a/docs/07_outputs.md b/docs/07_outputs.md index 1368f96..1a30f9a 100644 --- a/docs/07_outputs.md +++ b/docs/07_outputs.md @@ -1,4 +1,4 @@ -Outputs files may be aggregated including information for all samples or provided per sample. Per-sample files will be prefixed with respective aliases and represented below as {{ alias }}. +Output files may be aggregated including information for all samples or provided per sample. Per-sample files will be prefixed with respective aliases and represented below as {{ alias }}. | Title | File path | Description | Per sample or aggregated | |-------|-----------|-------------|--------------------------| diff --git a/nextflow.config b/nextflow.config index fd003fa..f738b1c 100644 --- a/nextflow.config +++ b/nextflow.config @@ -105,7 +105,7 @@ params { ] agent = null container_sha = "shae7c9f184996a384e99be68e790f0612f0c732867" - common_sha = "sha399b89c275a4d8eac477a415691cb93180661be6" + common_sha = "sha1c5febff9f75143710826498b093d9769a5edbb9" } }