From 5c6c2205def46754827603e66c59846d91252357 Mon Sep 17 00:00:00 2001 From: nf-core-bot Date: Tue, 15 Mar 2022 20:58:29 +0000 Subject: [PATCH 1/3] Template update for nf-core/tools version 2.3 --- .github/ISSUE_TEMPLATE/bug_report.yml | 1 - .github/PULL_REQUEST_TEMPLATE.md | 2 +- .github/workflows/awsfulltest.yml | 6 +- .github/workflows/awstest.yml | 6 +- .github/workflows/ci.yml | 4 +- .github/workflows/linting.yml | 28 +-- .gitpod.yml | 14 ++ .nf-core.yml | 1 + .yamllint.yml | 6 + CHANGELOG.md | 2 +- README.md | 6 +- assets/nf-core-mag_logo_light.png | Bin 288 -> 9354 bytes bin/check_samplesheet.py | 346 +++++++++++++++++--------- conf/base.config | 4 +- conf/igenomes.config | 80 +++--- conf/modules.config | 18 +- conf/test.config | 6 +- conf/test_full.config | 6 +- docs/images/nf-core-mag_logo_dark.png | Bin 428 -> 64856 bytes docs/usage.md | 21 +- lib/NfcoreSchema.groovy | 4 +- lib/Utils.groovy | 4 +- lib/WorkflowMag.groovy | 4 +- main.nf | 24 +- nextflow.config | 20 +- nextflow_schema.json | 23 +- subworkflows/local/input_check.nf | 18 +- workflows/mag.nf | 28 +-- 28 files changed, 421 insertions(+), 261 deletions(-) create mode 100644 .gitpod.yml create mode 100644 .nf-core.yml create mode 100644 .yamllint.yml diff --git a/.github/ISSUE_TEMPLATE/bug_report.yml b/.github/ISSUE_TEMPLATE/bug_report.yml index 8af04d7f..a9dff0f9 100644 --- a/.github/ISSUE_TEMPLATE/bug_report.yml +++ b/.github/ISSUE_TEMPLATE/bug_report.yml @@ -1,4 +1,3 @@ - name: Bug report description: Report something that is broken or incorrect labels: bug diff --git a/.github/PULL_REQUEST_TEMPLATE.md b/.github/PULL_REQUEST_TEMPLATE.md index d832fa1d..39b8c44a 100644 --- a/.github/PULL_REQUEST_TEMPLATE.md +++ b/.github/PULL_REQUEST_TEMPLATE.md @@ -19,7 +19,7 @@ Learn more about contributing: [CONTRIBUTING.md](https://github.com/nf-core/mag/ - [ ] If you've added a new tool - have you followed the pipeline conventions in the [contribution docs](https://github.com/nf-core/mag/tree/master/.github/CONTRIBUTING.md) - [ ] If necessary, also make a PR on the nf-core/mag _branch_ on the [nf-core/test-datasets](https://github.com/nf-core/test-datasets) repository. - [ ] Make sure your code lints (`nf-core lint`). -- [ ] Ensure the test suite passes (`nextflow run . -profile test,docker`). +- [ ] Ensure the test suite passes (`nextflow run . -profile test,docker` --outdir `). - [ ] Usage Documentation in `docs/usage.md` is updated. - [ ] Output Documentation in `docs/output.md` is updated. - [ ] `CHANGELOG.md` is updated. diff --git a/.github/workflows/awsfulltest.yml b/.github/workflows/awsfulltest.yml index 150acfbf..0a02db8f 100644 --- a/.github/workflows/awsfulltest.yml +++ b/.github/workflows/awsfulltest.yml @@ -14,7 +14,7 @@ jobs: runs-on: ubuntu-latest steps: - name: Launch workflow via tower - uses: nf-core/tower-action@v2 + uses: nf-core/tower-action@v3 # TODO nf-core: You can customise AWS full pipeline tests as required # Add full size test data (but still relatively small datasets for few samples) # on the `test_full.config` test runs with only one set of parameters @@ -31,4 +31,6 @@ jobs: "outdir": "s3://${{ secrets.AWS_S3_BUCKET }}/mag/results-${{ github.sha }}" } profiles: test_full,aws_tower - pre_run_script: 'export NXF_VER=21.10.3' + nextflow_config: | + process.errorStrategy = 'retry' + process.maxRetries = 3 diff --git a/.github/workflows/awstest.yml b/.github/workflows/awstest.yml index f42d2878..6e009f41 100644 --- a/.github/workflows/awstest.yml +++ b/.github/workflows/awstest.yml @@ -11,7 +11,7 @@ jobs: runs-on: ubuntu-latest steps: - name: Launch workflow via tower - uses: nf-core/tower-action@v2 + uses: nf-core/tower-action@v3 with: workspace_id: ${{ secrets.TOWER_WORKSPACE_ID }} @@ -25,4 +25,6 @@ jobs: "outdir": "s3://${{ secrets.AWS_S3_BUCKET }}/mag/results-test-${{ github.sha }}" } profiles: test,aws_tower - pre_run_script: 'export NXF_VER=21.10.3' + nextflow_config: | + process.errorStrategy = 'retry' + process.maxRetries = 3 diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml index 59ec52ae..b1c578c1 100644 --- a/.github/workflows/ci.yml +++ b/.github/workflows/ci.yml @@ -14,7 +14,7 @@ env: jobs: test: - name: Run workflow tests + name: Run pipeline with test data # 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/mag') }} runs-on: ubuntu-latest @@ -47,4 +47,4 @@ jobs: # For example: adding multiple test runs with different parameters # Remember that you can parallelise this by using strategy.matrix run: | - nextflow run ${GITHUB_WORKSPACE} -profile test,docker + nextflow run ${GITHUB_WORKSPACE} -profile test,docker --outdir ./results diff --git a/.github/workflows/linting.yml b/.github/workflows/linting.yml index 3b448773..fda934c0 100644 --- a/.github/workflows/linting.yml +++ b/.github/workflows/linting.yml @@ -12,9 +12,7 @@ jobs: runs-on: ubuntu-latest steps: - uses: actions/checkout@v2 - - uses: actions/setup-node@v1 - with: - node-version: '10' + - uses: actions/setup-node@v2 - name: Install markdownlint run: npm install -g markdownlint-cli - name: Run Markdownlint @@ -51,9 +49,7 @@ jobs: steps: - uses: actions/checkout@v2 - - uses: actions/setup-node@v1 - with: - node-version: '10' + - uses: actions/setup-node@v2 - name: Install editorconfig-checker run: npm install -g editorconfig-checker @@ -64,14 +60,13 @@ jobs: YAML: runs-on: ubuntu-latest steps: - - uses: actions/checkout@v1 - - uses: actions/setup-node@v1 + - name: Checkout + uses: actions/checkout@master + - name: 'Yamllint' + uses: karancode/yamllint-github-action@master with: - node-version: '10' - - name: Install yaml-lint - run: npm install -g yaml-lint - - name: Run yaml-lint - run: yamllint $(find ${GITHUB_WORKSPACE} -type f -name "*.yml" -o -name "*.yaml") + yamllint_file_or_dir: '.' + yamllint_config_filepath: '.yamllint.yml' # If the above check failed, post a comment on the PR explaining the failure - name: Post PR comment @@ -84,10 +79,11 @@ jobs: To keep the code consistent with lots of contributors, we run automated code consistency checks. To fix this CI test, please run: - * Install `yaml-lint` - * [Install `npm`](https://www.npmjs.com/get-npm) then [install `yaml-lint`](https://www.npmjs.com/package/yaml-lint) (`npm install -g yaml-lint`) + * Install `yamllint` + * Install `yamllint` following [this](https://yamllint.readthedocs.io/en/stable/quickstart.html#installing-yamllint) + instructions or alternative install it in your [conda environment](https://anaconda.org/conda-forge/yamllint) * Fix the markdown errors - * Run the test locally: `yamllint $(find . -type f -name "*.yml" -o -name "*.yaml")` + * Run the test locally: `yamllint $(find . -type f -name "*.yml" -o -name "*.yaml") -c ./.yamllint.yml` * Fix any reported errors in your YAML files Once you push these changes the test should pass, and you can hide this comment :+1: diff --git a/.gitpod.yml b/.gitpod.yml new file mode 100644 index 00000000..b7d4cee1 --- /dev/null +++ b/.gitpod.yml @@ -0,0 +1,14 @@ +image: nfcore/gitpod:latest + +vscode: + extensions: # based on nf-core.nf-core-extensionpack + - codezombiech.gitignore # Language support for .gitignore files + # - cssho.vscode-svgviewer # SVG viewer + - davidanson.vscode-markdownlint # Markdown/CommonMark linting and style checking for Visual Studio Code + - eamodio.gitlens # Quickly glimpse into whom, why, and when a line or code block was changed + - EditorConfig.EditorConfig # override user/workspace settings with settings found in .editorconfig files + - Gruntfuggly.todo-tree # Display TODO and FIXME in a tree view in the activity bar + - mechatroner.rainbow-csv # Highlight columns in csv files in different colors + # - nextflow.nextflow # Nextflow syntax highlighting + - oderwat.indent-rainbow # Highlight indentation level + - streetsidesoftware.code-spell-checker # Spelling checker for source code diff --git a/.nf-core.yml b/.nf-core.yml new file mode 100644 index 00000000..3805dc81 --- /dev/null +++ b/.nf-core.yml @@ -0,0 +1 @@ +repository_type: pipeline diff --git a/.yamllint.yml b/.yamllint.yml new file mode 100644 index 00000000..d466deec --- /dev/null +++ b/.yamllint.yml @@ -0,0 +1,6 @@ +extends: default + +rules: + document-start: disable + line-length: disable + truthy: disable diff --git a/CHANGELOG.md b/CHANGELOG.md index 2854a2b3..0803027f 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -3,7 +3,7 @@ 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). -## v2.1.1 - [date] +## v2.2.0dev - [date] Initial release of nf-core/mag, created with the [nf-core](https://nf-co.re/) template. diff --git a/README.md b/README.md index 7cbbd4d4..39f3d98e 100644 --- a/README.md +++ b/README.md @@ -40,14 +40,14 @@ On release, automated continuous integration tests run the pipeline on a full-si 3. Download the pipeline and test it on a minimal dataset with a single command: ```console - nextflow run nf-core/mag -profile test,YOURPROFILE + nextflow run nf-core/mag -profile test,YOURPROFILE --outdir ``` Note that some form of configuration will be needed so that Nextflow knows how to fetch the required software. This is usually done in the form of a config profile (`YOURPROFILE` in the example command above). You can chain multiple config profiles in a comma-separated string. > * The pipeline comes with config profiles called `docker`, `singularity`, `podman`, `shifter`, `charliecloud` and `conda` which instruct the pipeline to use the named tool for software management. For example, `-profile test,docker`. > * Please check [nf-core/configs](https://github.com/nf-core/configs#documentation) to see if a custom config file to run nf-core pipelines already exists for your Institute. If so, you can simply use `-profile ` in your command. This will enable either `docker` or `singularity` and set the appropriate execution settings for your local compute environment. - > * If you are using `singularity` and are persistently observing issues downloading Singularity images directly due to timeout or network issues, then you can use the `--singularity_pull_docker_container` parameter to pull and convert the Docker image instead. Alternatively, you can use the [`nf-core download`](https://nf-co.re/tools/#downloading-pipelines-for-offline-use) command to download images first, before running the pipeline. Setting the [`NXF_SINGULARITY_CACHEDIR` or `singularity.cacheDir`](https://www.nextflow.io/docs/latest/singularity.html?#singularity-docker-hub) Nextflow options enables you to store and re-use the images from a central location for future pipeline runs. + > * If you are using `singularity`, please use the [`nf-core download`](https://nf-co.re/tools/#downloading-pipelines-for-offline-use) command to download images first, before running the pipeline. Setting the [`NXF_SINGULARITY_CACHEDIR` or `singularity.cacheDir`](https://www.nextflow.io/docs/latest/singularity.html?#singularity-docker-hub) Nextflow options enables you to store and re-use the images from a central location for future pipeline runs. > * If you are using `conda`, it is highly recommended to use the [`NXF_CONDA_CACHEDIR` or `conda.cacheDir`](https://www.nextflow.io/docs/latest/conda.html) settings to store the environments in a central location for future pipeline runs. 4. Start running your own analysis! @@ -55,7 +55,7 @@ On release, automated continuous integration tests run the pipeline on a full-si ```console - nextflow run nf-core/mag -profile --input samplesheet.csv --genome GRCh37 + nextflow run nf-core/mag --input samplesheet.csv --outdir --genome GRCh37 -profile ``` ## Documentation diff --git a/assets/nf-core-mag_logo_light.png b/assets/nf-core-mag_logo_light.png index dee3db82069b61e9a5380d940355f47ff565057c..26d7ed5d17ce0345f80ad676dc7da7e928f44ef4 100644 GIT binary patch literal 9354 zcmbt)Wmr^Q)bg&G)oPC#y4Fuu_X{$dp4KLVViORJ$>&71WXLQdLYVTJn`TnkC z_O2;wZ3#4_rEP#?HUrpbG>D8|yu=2|4IQaQMEreMXQrNJek&N%NB)AnzcPWn+9HCM zmPVMdTFJTQy?>2wjVttxxWaf>+~r*JjHjsg?S zEMpy^vj59zQF!iv_)ggmm-^^oUU>LD#{4`z!3xHdfiJ7wQEiZcmPfuGLAyI8V0ED~ z)#m8o55JL}@cZ$6@s-Z8HiSjQb0Ac8j935JTw8stK_?p^5dGA#K+3ub$l?a;i$DbBa_gGc3jH{Bz zYzE&TFbxc!L7)BiP1tm{wwb`Fynd4S32?C;{zsDPuJsc0|8{2M4q^f?!BI7U2wP8- zdpUnW+(2z%i(P{j(B#@IWBo>8RMh862(W=A@L|;Aa;f3K(h8_7>#fQv)tK6rlwdFx z^uJx{ZRf@L@BL`uc<2E#(y0`*=y92%aFB0ob=Hrvo?-phomXe@2tV>aFL;xGtoVr6+c=vg=Zg53;D|ggl4N9 zfFrGc6ljh~-!LvMzGR#RIq_tUCcN@5dY;8I^do#ENlz62GCFJ`VBXini(n|wA-?aZ zM_l{|ZA!D&XlA&tuLij%s1o=_RAYpWoeSd`G`04y%uA<2k^0;)Ta8m|&NMh-3i-rC z@XfwzErf-?UXLVWYdZ#MP-@=Np6M?o4L5a&V z$=`j*G(FdjWOr!2i2Ge>eZ$CgF?Tcef|9W>g-aek^*S!%tSl&VLciE*cX8^?uqzkn zfY@&$47W#hgz|ujxEence51s5E_iy%{}--yyrRT0b@;f7LvQDxE?r4-WP!LV+~MP7 zPH%~x=q^YLyn<{%@>Wr_2wWNqomRL%@8;-yzTy;T?o)c}Flu;N^@iNtOh=#7Ul!|% zc?)R8p=95mh?3jYC2(N?Sz`KKyG{f0!dSZ0WOWKD_KCeQ(BUIC`EiSTmUfmr+h+m` zs|oq_*oNHIj!$yZy-L?@=40;RR_2XoO=p(W1$l=D3lA6bdoJM4jo=L|5bfsmAov&*zJ?rR+$DqkZ!9L=`CWhKf)ls2WF3Y{dO| zE^Ss7s!%7mGZ(~;nw_8vc^Spn_|8zsOcT1P?|SpNZnIjWHO`kbDE?ZiQBKZlRSlx% z={O^`n#kc7vFwKV`ouFV5m_iG;y+!jX(s$GNG|*lwxQ?8`m@9o#K0?~pWLo?59SY& zvPvv1oOAv5nsT1oXCEG1C_A=lRVE7-90`+*%8G+D;cq|sf? 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The order of rows is maintained. + """ -def print_error(error, context="Line", context_str=""): - error_str = "ERROR: Please check samplesheet -> {}".format(error) - if context != "" and context_str != "": - error_str = "ERROR: Please check samplesheet -> {}\n{}: '{}'".format( - error, context.strip(), context_str.strip() + VALID_FORMATS = ( + ".fq.gz", + ".fastq.gz", + ) + + def __init__( + self, + sample_col="sample", + first_col="fastq_1", + second_col="fastq_2", + single_col="single_end", + **kwargs, + ): + """ + Initialize the row checker with the expected column names. + + Args: + sample_col (str): The name of the column that contains the sample name + (default "sample"). + first_col (str): The name of the column that contains the first (or only) + FASTQ file path (default "fastq_1"). + second_col (str): The name of the column that contains the second (if any) + FASTQ file path (default "fastq_2"). + single_col (str): The name of the new column that will be inserted and + records whether the sample contains single- or paired-end sequencing + reads (default "single_end"). + + """ + super().__init__(**kwargs) + self._sample_col = sample_col + self._first_col = first_col + self._second_col = second_col + self._single_col = single_col + self._seen = set() + self.modified = [] + + def validate_and_transform(self, row): + """ + Perform all validations on the given row and insert the read pairing status. + + Args: + row (dict): A mapping from column headers (keys) to elements of that row + (values). + + """ + self._validate_sample(row) + self._validate_first(row) + self._validate_second(row) + self._validate_pair(row) + self._seen.add((row[self._sample_col], row[self._first_col])) + self.modified.append(row) + + def _validate_sample(self, row): + """Assert that the sample name exists and convert spaces to underscores.""" + assert len(row[self._sample_col]) > 0, "Sample input is required." + # Sanitize samples slightly. + row[self._sample_col] = row[self._sample_col].replace(" ", "_") + + def _validate_first(self, row): + """Assert that the first FASTQ entry is non-empty and has the right format.""" + assert len(row[self._first_col]) > 0, "At least the first FASTQ file is required." + self._validate_fastq_format(row[self._first_col]) + + def _validate_second(self, row): + """Assert that the second FASTQ entry has the right format if it exists.""" + if len(row[self._second_col]) > 0: + self._validate_fastq_format(row[self._second_col]) + + def _validate_pair(self, row): + """Assert that read pairs have the same file extension. Report pair status.""" + if row[self._first_col] and row[self._second_col]: + row[self._single_col] = False + assert ( + Path(row[self._first_col]).suffixes == Path(row[self._second_col]).suffixes + ), "FASTQ pairs must have the same file extensions." + else: + row[self._single_col] = True + + def _validate_fastq_format(self, filename): + """Assert that a given filename has one of the expected FASTQ extensions.""" + assert any(filename.endswith(extension) for extension in self.VALID_FORMATS), ( + f"The FASTQ file has an unrecognized extension: {filename}\n" + f"It should be one of: {', '.join(self.VALID_FORMATS)}" ) - print(error_str) - sys.exit(1) + def validate_unique_samples(self): + """ + Assert that the combination of sample name and FASTQ filename is unique. + + In addition to the validation, also rename the sample if more than one sample, + FASTQ file combination exists. + + """ + assert len(self._seen) == len(self.modified), "The pair of sample name and FASTQ must be unique." + if len({pair[0] for pair in self._seen}) < len(self._seen): + counts = Counter(pair[0] for pair in self._seen) + seen = Counter() + for row in self.modified: + sample = row[self._sample_col] + seen[sample] += 1 + if counts[sample] > 1: + row[self._sample_col] = f"{sample}_T{seen[sample]}" + + +def sniff_format(handle): + """ + Detect the tabular format. + + Args: + handle (text file): A handle to a `text file`_ object. The read position is + expected to be at the beginning (index 0). + + Returns: + csv.Dialect: The detected tabular format. + + .. _text file: + https://docs.python.org/3/glossary.html#term-text-file -# TODO nf-core: Update the check_samplesheet function -def check_samplesheet(file_in, file_out): """ - This function checks that the samplesheet follows the following structure: + peek = handle.read(2048) + sniffer = csv.Sniffer() + if not sniffer.has_header(peek): + logger.critical(f"The given sample sheet does not appear to contain a header.") + sys.exit(1) + dialect = sniffer.sniff(peek) + handle.seek(0) + return dialect - sample,fastq_1,fastq_2 - SAMPLE_PE,SAMPLE_PE_RUN1_1.fastq.gz,SAMPLE_PE_RUN1_2.fastq.gz - SAMPLE_PE,SAMPLE_PE_RUN2_1.fastq.gz,SAMPLE_PE_RUN2_2.fastq.gz - SAMPLE_SE,SAMPLE_SE_RUN1_1.fastq.gz, - For an example see: - https://raw.githubusercontent.com/nf-core/test-datasets/viralrecon/samplesheet/samplesheet_test_illumina_amplicon.csv +def check_samplesheet(file_in, file_out): """ + Check that the tabular samplesheet has the structure expected by nf-core pipelines. - sample_mapping_dict = {} - with open(file_in, "r") as fin: + Validate the general shape of the table, expected columns, and each row. Also add + an additional column which records whether one or two FASTQ reads were found. - ## Check header - MIN_COLS = 2 - # TODO nf-core: Update the column names for the input samplesheet - HEADER = ["sample", "fastq_1", "fastq_2"] - header = [x.strip('"') for x in fin.readline().strip().split(",")] - if header[: len(HEADER)] != HEADER: - print("ERROR: Please check samplesheet header -> {} != {}".format(",".join(header), ",".join(HEADER))) - sys.exit(1) + Args: + file_in (pathlib.Path): The given tabular samplesheet. The format can be either + CSV, TSV, or any other format automatically recognized by ``csv.Sniffer``. + file_out (pathlib.Path): Where the validated and transformed samplesheet should + be created; always in CSV format. - ## Check sample entries - for line in fin: - lspl = [x.strip().strip('"') for x in line.strip().split(",")] - - # Check valid number of columns per row - if len(lspl) < len(HEADER): - print_error( - "Invalid number of columns (minimum = {})!".format(len(HEADER)), - "Line", - line, - ) - num_cols = len([x for x in lspl if x]) - if num_cols < MIN_COLS: - print_error( - "Invalid number of populated columns (minimum = {})!".format(MIN_COLS), - "Line", - line, - ) - - ## Check sample name entries - sample, fastq_1, fastq_2 = lspl[: len(HEADER)] - sample = sample.replace(" ", "_") - if not sample: - print_error("Sample entry has not been specified!", "Line", line) - - ## Check FastQ file extension - for fastq in [fastq_1, fastq_2]: - if fastq: - if fastq.find(" ") != -1: - print_error("FastQ file contains spaces!", "Line", line) - if not fastq.endswith(".fastq.gz") and not fastq.endswith(".fq.gz"): - print_error( - "FastQ file does not have extension '.fastq.gz' or '.fq.gz'!", - "Line", - line, - ) - - ## Auto-detect paired-end/single-end - sample_info = [] ## [single_end, fastq_1, fastq_2] - if sample and fastq_1 and fastq_2: ## Paired-end short reads - sample_info = ["0", fastq_1, fastq_2] - elif sample and fastq_1 and not fastq_2: ## Single-end short reads - sample_info = ["1", fastq_1, fastq_2] - else: - print_error("Invalid combination of columns provided!", "Line", line) - - ## Create sample mapping dictionary = { sample: [ single_end, fastq_1, fastq_2 ] } - if sample not in sample_mapping_dict: - sample_mapping_dict[sample] = [sample_info] - else: - if sample_info in sample_mapping_dict[sample]: - print_error("Samplesheet contains duplicate rows!", "Line", line) - else: - sample_mapping_dict[sample].append(sample_info) - - ## Write validated samplesheet with appropriate columns - if len(sample_mapping_dict) > 0: - out_dir = os.path.dirname(file_out) - make_dir(out_dir) - with open(file_out, "w") as fout: - fout.write(",".join(["sample", "single_end", "fastq_1", "fastq_2"]) + "\n") - for sample in sorted(sample_mapping_dict.keys()): - - ## Check that multiple runs of the same sample are of the same datatype - if not all(x[0] == sample_mapping_dict[sample][0][0] for x in sample_mapping_dict[sample]): - print_error("Multiple runs of a sample must be of the same datatype!", "Sample: {}".format(sample)) - - for idx, val in enumerate(sample_mapping_dict[sample]): - fout.write(",".join(["{}_T{}".format(sample, idx + 1)] + val) + "\n") - else: - print_error("No entries to process!", "Samplesheet: {}".format(file_in)) - - -def main(args=None): - args = parse_args(args) - check_samplesheet(args.FILE_IN, args.FILE_OUT) + Example: + This function checks that the samplesheet follows the following structure, + see also the `viral recon samplesheet`_:: + + sample,fastq_1,fastq_2 + SAMPLE_PE,SAMPLE_PE_RUN1_1.fastq.gz,SAMPLE_PE_RUN1_2.fastq.gz + SAMPLE_PE,SAMPLE_PE_RUN2_1.fastq.gz,SAMPLE_PE_RUN2_2.fastq.gz + SAMPLE_SE,SAMPLE_SE_RUN1_1.fastq.gz, + + .. _viral recon samplesheet: + https://raw.githubusercontent.com/nf-core/test-datasets/viralrecon/samplesheet/samplesheet_test_illumina_amplicon.csv + + """ + required_columns = {"sample", "fastq_1", "fastq_2"} + # See https://docs.python.org/3.9/library/csv.html#id3 to read up on `newline=""`. + with file_in.open(newline="") as in_handle: + reader = csv.DictReader(in_handle, dialect=sniff_format(in_handle)) + # Validate the existence of the expected header columns. + if not required_columns.issubset(reader.fieldnames): + logger.critical(f"The sample sheet **must** contain the column headers: {', '.join(required_columns)}.") + sys.exit(1) + # Validate each row. + checker = RowChecker() + for i, row in enumerate(reader): + try: + checker.validate_and_transform(row) + except AssertionError as error: + logger.critical(f"{str(error)} On line {i + 2}.") + sys.exit(1) + checker.validate_unique_samples() + header = list(reader.fieldnames) + header.insert(1, "single_end") + # See https://docs.python.org/3.9/library/csv.html#id3 to read up on `newline=""`. + with file_out.open(mode="w", newline="") as out_handle: + writer = csv.DictWriter(out_handle, header, delimiter=",") + writer.writeheader() + for row in checker.modified: + writer.writerow(row) + + +def parse_args(argv=None): + """Define and immediately parse command line arguments.""" + parser = argparse.ArgumentParser( + description="Validate and transform a tabular samplesheet.", + epilog="Example: python check_samplesheet.py samplesheet.csv samplesheet.valid.csv", + ) + parser.add_argument( + "file_in", + metavar="FILE_IN", + type=Path, + help="Tabular input samplesheet in CSV or TSV format.", + ) + parser.add_argument( + "file_out", + metavar="FILE_OUT", + type=Path, + help="Transformed output samplesheet in CSV format.", + ) + parser.add_argument( + "-l", + "--log-level", + help="The desired log level (default WARNING).", + choices=("CRITICAL", "ERROR", "WARNING", "INFO", "DEBUG"), + default="WARNING", + ) + return parser.parse_args(argv) + + +def main(argv=None): + """Coordinate argument parsing and program execution.""" + args = parse_args(argv) + logging.basicConfig(level=args.log_level, format="[%(levelname)s] %(message)s") + if not args.file_in.is_file(): + logger.error(f"The given input file {args.file_in} was not found!") + sys.exit(2) + args.file_out.parent.mkdir(parents=True, exist_ok=True) + check_samplesheet(args.file_in, args.file_out) if __name__ == "__main__": diff --git a/conf/base.config b/conf/base.config index 8ee679ad..a3173752 100644 --- a/conf/base.config +++ b/conf/base.config @@ -1,7 +1,7 @@ /* -======================================================================================== +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ nf-core/mag Nextflow base config file -======================================================================================== +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ A 'blank slate' config file, appropriate for general use on most high performance compute environments. Assumes that all software is installed and available on the PATH. Runs in `local` mode - all jobs will be run on the logged in environment. diff --git a/conf/igenomes.config b/conf/igenomes.config index 855948de..7a1b3ac6 100644 --- a/conf/igenomes.config +++ b/conf/igenomes.config @@ -1,7 +1,7 @@ /* -======================================================================================== +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Nextflow config file for iGenomes paths -======================================================================================== +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Defines reference genomes using iGenome paths. Can be used by any config that customises the base path using: $params.igenomes_base / --igenomes_base @@ -13,7 +13,7 @@ params { genomes { 'GRCh37' { fasta = "${params.igenomes_base}/Homo_sapiens/Ensembl/GRCh37/Sequence/WholeGenomeFasta/genome.fa" - bwa = "${params.igenomes_base}/Homo_sapiens/Ensembl/GRCh37/Sequence/BWAIndex/genome.fa" + bwa = "${params.igenomes_base}/Homo_sapiens/Ensembl/GRCh37/Sequence/BWAIndex/version0.6.0/" bowtie2 = "${params.igenomes_base}/Homo_sapiens/Ensembl/GRCh37/Sequence/Bowtie2Index/" star = "${params.igenomes_base}/Homo_sapiens/Ensembl/GRCh37/Sequence/STARIndex/" bismark = "${params.igenomes_base}/Homo_sapiens/Ensembl/GRCh37/Sequence/BismarkIndex/" @@ -26,7 +26,7 @@ params { } 'GRCh38' { fasta = "${params.igenomes_base}/Homo_sapiens/NCBI/GRCh38/Sequence/WholeGenomeFasta/genome.fa" - bwa = "${params.igenomes_base}/Homo_sapiens/NCBI/GRCh38/Sequence/BWAIndex/genome.fa" + bwa = "${params.igenomes_base}/Homo_sapiens/NCBI/GRCh38/Sequence/BWAIndex/version0.6.0/" bowtie2 = "${params.igenomes_base}/Homo_sapiens/NCBI/GRCh38/Sequence/Bowtie2Index/" star = "${params.igenomes_base}/Homo_sapiens/NCBI/GRCh38/Sequence/STARIndex/" bismark = "${params.igenomes_base}/Homo_sapiens/NCBI/GRCh38/Sequence/BismarkIndex/" @@ -38,7 +38,7 @@ params { } 'GRCm38' { fasta = "${params.igenomes_base}/Mus_musculus/Ensembl/GRCm38/Sequence/WholeGenomeFasta/genome.fa" - bwa = "${params.igenomes_base}/Mus_musculus/Ensembl/GRCm38/Sequence/BWAIndex/genome.fa" + bwa = "${params.igenomes_base}/Mus_musculus/Ensembl/GRCm38/Sequence/BWAIndex/version0.6.0/" bowtie2 = "${params.igenomes_base}/Mus_musculus/Ensembl/GRCm38/Sequence/Bowtie2Index/" star = "${params.igenomes_base}/Mus_musculus/Ensembl/GRCm38/Sequence/STARIndex/" bismark = "${params.igenomes_base}/Mus_musculus/Ensembl/GRCm38/Sequence/BismarkIndex/" @@ -51,7 +51,7 @@ params { } 'TAIR10' { fasta = "${params.igenomes_base}/Arabidopsis_thaliana/Ensembl/TAIR10/Sequence/WholeGenomeFasta/genome.fa" - bwa = "${params.igenomes_base}/Arabidopsis_thaliana/Ensembl/TAIR10/Sequence/BWAIndex/genome.fa" + bwa = "${params.igenomes_base}/Arabidopsis_thaliana/Ensembl/TAIR10/Sequence/BWAIndex/version0.6.0/" bowtie2 = "${params.igenomes_base}/Arabidopsis_thaliana/Ensembl/TAIR10/Sequence/Bowtie2Index/" star = "${params.igenomes_base}/Arabidopsis_thaliana/Ensembl/TAIR10/Sequence/STARIndex/" bismark = "${params.igenomes_base}/Arabidopsis_thaliana/Ensembl/TAIR10/Sequence/BismarkIndex/" @@ -62,7 +62,7 @@ params { } 'EB2' { fasta = "${params.igenomes_base}/Bacillus_subtilis_168/Ensembl/EB2/Sequence/WholeGenomeFasta/genome.fa" - bwa = "${params.igenomes_base}/Bacillus_subtilis_168/Ensembl/EB2/Sequence/BWAIndex/genome.fa" + bwa = "${params.igenomes_base}/Bacillus_subtilis_168/Ensembl/EB2/Sequence/BWAIndex/version0.6.0/" bowtie2 = "${params.igenomes_base}/Bacillus_subtilis_168/Ensembl/EB2/Sequence/Bowtie2Index/" star = "${params.igenomes_base}/Bacillus_subtilis_168/Ensembl/EB2/Sequence/STARIndex/" bismark = "${params.igenomes_base}/Bacillus_subtilis_168/Ensembl/EB2/Sequence/BismarkIndex/" @@ -72,7 +72,7 @@ params { } 'UMD3.1' { fasta = "${params.igenomes_base}/Bos_taurus/Ensembl/UMD3.1/Sequence/WholeGenomeFasta/genome.fa" - bwa = "${params.igenomes_base}/Bos_taurus/Ensembl/UMD3.1/Sequence/BWAIndex/genome.fa" + bwa = "${params.igenomes_base}/Bos_taurus/Ensembl/UMD3.1/Sequence/BWAIndex/version0.6.0/" bowtie2 = "${params.igenomes_base}/Bos_taurus/Ensembl/UMD3.1/Sequence/Bowtie2Index/" star = "${params.igenomes_base}/Bos_taurus/Ensembl/UMD3.1/Sequence/STARIndex/" bismark = "${params.igenomes_base}/Bos_taurus/Ensembl/UMD3.1/Sequence/BismarkIndex/" @@ -83,7 +83,7 @@ params { } 'WBcel235' { fasta = "${params.igenomes_base}/Caenorhabditis_elegans/Ensembl/WBcel235/Sequence/WholeGenomeFasta/genome.fa" - bwa = "${params.igenomes_base}/Caenorhabditis_elegans/Ensembl/WBcel235/Sequence/BWAIndex/genome.fa" + bwa = "${params.igenomes_base}/Caenorhabditis_elegans/Ensembl/WBcel235/Sequence/BWAIndex/version0.6.0/" bowtie2 = "${params.igenomes_base}/Caenorhabditis_elegans/Ensembl/WBcel235/Sequence/Bowtie2Index/" star = "${params.igenomes_base}/Caenorhabditis_elegans/Ensembl/WBcel235/Sequence/STARIndex/" bismark = "${params.igenomes_base}/Caenorhabditis_elegans/Ensembl/WBcel235/Sequence/BismarkIndex/" @@ -94,7 +94,7 @@ params { } 'CanFam3.1' { fasta = "${params.igenomes_base}/Canis_familiaris/Ensembl/CanFam3.1/Sequence/WholeGenomeFasta/genome.fa" - bwa = "${params.igenomes_base}/Canis_familiaris/Ensembl/CanFam3.1/Sequence/BWAIndex/genome.fa" + bwa = "${params.igenomes_base}/Canis_familiaris/Ensembl/CanFam3.1/Sequence/BWAIndex/version0.6.0/" bowtie2 = "${params.igenomes_base}/Canis_familiaris/Ensembl/CanFam3.1/Sequence/Bowtie2Index/" star = "${params.igenomes_base}/Canis_familiaris/Ensembl/CanFam3.1/Sequence/STARIndex/" bismark = "${params.igenomes_base}/Canis_familiaris/Ensembl/CanFam3.1/Sequence/BismarkIndex/" @@ -105,7 +105,7 @@ params { } 'GRCz10' { fasta = "${params.igenomes_base}/Danio_rerio/Ensembl/GRCz10/Sequence/WholeGenomeFasta/genome.fa" - bwa = "${params.igenomes_base}/Danio_rerio/Ensembl/GRCz10/Sequence/BWAIndex/genome.fa" + bwa = "${params.igenomes_base}/Danio_rerio/Ensembl/GRCz10/Sequence/BWAIndex/version0.6.0/" bowtie2 = "${params.igenomes_base}/Danio_rerio/Ensembl/GRCz10/Sequence/Bowtie2Index/" star = "${params.igenomes_base}/Danio_rerio/Ensembl/GRCz10/Sequence/STARIndex/" bismark = "${params.igenomes_base}/Danio_rerio/Ensembl/GRCz10/Sequence/BismarkIndex/" @@ -115,7 +115,7 @@ params { } 'BDGP6' { fasta = "${params.igenomes_base}/Drosophila_melanogaster/Ensembl/BDGP6/Sequence/WholeGenomeFasta/genome.fa" - bwa = "${params.igenomes_base}/Drosophila_melanogaster/Ensembl/BDGP6/Sequence/BWAIndex/genome.fa" + bwa = "${params.igenomes_base}/Drosophila_melanogaster/Ensembl/BDGP6/Sequence/BWAIndex/version0.6.0/" bowtie2 = "${params.igenomes_base}/Drosophila_melanogaster/Ensembl/BDGP6/Sequence/Bowtie2Index/" star = "${params.igenomes_base}/Drosophila_melanogaster/Ensembl/BDGP6/Sequence/STARIndex/" bismark = "${params.igenomes_base}/Drosophila_melanogaster/Ensembl/BDGP6/Sequence/BismarkIndex/" @@ -126,7 +126,7 @@ params { } 'EquCab2' { fasta = "${params.igenomes_base}/Equus_caballus/Ensembl/EquCab2/Sequence/WholeGenomeFasta/genome.fa" - bwa = "${params.igenomes_base}/Equus_caballus/Ensembl/EquCab2/Sequence/BWAIndex/genome.fa" + bwa = "${params.igenomes_base}/Equus_caballus/Ensembl/EquCab2/Sequence/BWAIndex/version0.6.0/" bowtie2 = "${params.igenomes_base}/Equus_caballus/Ensembl/EquCab2/Sequence/Bowtie2Index/" star = "${params.igenomes_base}/Equus_caballus/Ensembl/EquCab2/Sequence/STARIndex/" bismark = "${params.igenomes_base}/Equus_caballus/Ensembl/EquCab2/Sequence/BismarkIndex/" @@ -137,7 +137,7 @@ params { } 'EB1' { fasta = "${params.igenomes_base}/Escherichia_coli_K_12_DH10B/Ensembl/EB1/Sequence/WholeGenomeFasta/genome.fa" - bwa = "${params.igenomes_base}/Escherichia_coli_K_12_DH10B/Ensembl/EB1/Sequence/BWAIndex/genome.fa" + bwa = "${params.igenomes_base}/Escherichia_coli_K_12_DH10B/Ensembl/EB1/Sequence/BWAIndex/version0.6.0/" bowtie2 = "${params.igenomes_base}/Escherichia_coli_K_12_DH10B/Ensembl/EB1/Sequence/Bowtie2Index/" star = "${params.igenomes_base}/Escherichia_coli_K_12_DH10B/Ensembl/EB1/Sequence/STARIndex/" bismark = "${params.igenomes_base}/Escherichia_coli_K_12_DH10B/Ensembl/EB1/Sequence/BismarkIndex/" @@ -147,7 +147,7 @@ params { } 'Galgal4' { fasta = "${params.igenomes_base}/Gallus_gallus/Ensembl/Galgal4/Sequence/WholeGenomeFasta/genome.fa" - bwa = "${params.igenomes_base}/Gallus_gallus/Ensembl/Galgal4/Sequence/BWAIndex/genome.fa" + bwa = "${params.igenomes_base}/Gallus_gallus/Ensembl/Galgal4/Sequence/BWAIndex/version0.6.0/" bowtie2 = "${params.igenomes_base}/Gallus_gallus/Ensembl/Galgal4/Sequence/Bowtie2Index/" star = "${params.igenomes_base}/Gallus_gallus/Ensembl/Galgal4/Sequence/STARIndex/" bismark = "${params.igenomes_base}/Gallus_gallus/Ensembl/Galgal4/Sequence/BismarkIndex/" @@ -157,7 +157,7 @@ params { } 'Gm01' { fasta = "${params.igenomes_base}/Glycine_max/Ensembl/Gm01/Sequence/WholeGenomeFasta/genome.fa" - bwa = "${params.igenomes_base}/Glycine_max/Ensembl/Gm01/Sequence/BWAIndex/genome.fa" + bwa = "${params.igenomes_base}/Glycine_max/Ensembl/Gm01/Sequence/BWAIndex/version0.6.0/" bowtie2 = "${params.igenomes_base}/Glycine_max/Ensembl/Gm01/Sequence/Bowtie2Index/" star = "${params.igenomes_base}/Glycine_max/Ensembl/Gm01/Sequence/STARIndex/" bismark = "${params.igenomes_base}/Glycine_max/Ensembl/Gm01/Sequence/BismarkIndex/" @@ -167,7 +167,7 @@ params { } 'Mmul_1' { fasta = "${params.igenomes_base}/Macaca_mulatta/Ensembl/Mmul_1/Sequence/WholeGenomeFasta/genome.fa" - bwa = "${params.igenomes_base}/Macaca_mulatta/Ensembl/Mmul_1/Sequence/BWAIndex/genome.fa" + bwa = "${params.igenomes_base}/Macaca_mulatta/Ensembl/Mmul_1/Sequence/BWAIndex/version0.6.0/" bowtie2 = "${params.igenomes_base}/Macaca_mulatta/Ensembl/Mmul_1/Sequence/Bowtie2Index/" star = "${params.igenomes_base}/Macaca_mulatta/Ensembl/Mmul_1/Sequence/STARIndex/" bismark = "${params.igenomes_base}/Macaca_mulatta/Ensembl/Mmul_1/Sequence/BismarkIndex/" @@ -178,7 +178,7 @@ params { } 'IRGSP-1.0' { fasta = "${params.igenomes_base}/Oryza_sativa_japonica/Ensembl/IRGSP-1.0/Sequence/WholeGenomeFasta/genome.fa" - bwa = "${params.igenomes_base}/Oryza_sativa_japonica/Ensembl/IRGSP-1.0/Sequence/BWAIndex/genome.fa" + bwa = "${params.igenomes_base}/Oryza_sativa_japonica/Ensembl/IRGSP-1.0/Sequence/BWAIndex/version0.6.0/" bowtie2 = "${params.igenomes_base}/Oryza_sativa_japonica/Ensembl/IRGSP-1.0/Sequence/Bowtie2Index/" star = "${params.igenomes_base}/Oryza_sativa_japonica/Ensembl/IRGSP-1.0/Sequence/STARIndex/" bismark = "${params.igenomes_base}/Oryza_sativa_japonica/Ensembl/IRGSP-1.0/Sequence/BismarkIndex/" @@ -188,7 +188,7 @@ params { } 'CHIMP2.1.4' { fasta = "${params.igenomes_base}/Pan_troglodytes/Ensembl/CHIMP2.1.4/Sequence/WholeGenomeFasta/genome.fa" - bwa = "${params.igenomes_base}/Pan_troglodytes/Ensembl/CHIMP2.1.4/Sequence/BWAIndex/genome.fa" + bwa = "${params.igenomes_base}/Pan_troglodytes/Ensembl/CHIMP2.1.4/Sequence/BWAIndex/version0.6.0/" bowtie2 = "${params.igenomes_base}/Pan_troglodytes/Ensembl/CHIMP2.1.4/Sequence/Bowtie2Index/" star = "${params.igenomes_base}/Pan_troglodytes/Ensembl/CHIMP2.1.4/Sequence/STARIndex/" bismark = "${params.igenomes_base}/Pan_troglodytes/Ensembl/CHIMP2.1.4/Sequence/BismarkIndex/" @@ -199,7 +199,7 @@ params { } 'Rnor_5.0' { fasta = "${params.igenomes_base}/Rattus_norvegicus/Ensembl/Rnor_5.0/Sequence/WholeGenomeFasta/genome.fa" - bwa = "${params.igenomes_base}/Rattus_norvegicus/Ensembl/Rnor_5.0/Sequence/BWAIndex/genome.fa" + bwa = "${params.igenomes_base}/Rattus_norvegicus/Ensembl/Rnor_5.0/Sequence/BWAIndex/version0.6.0/" bowtie2 = "${params.igenomes_base}/Rattus_norvegicus/Ensembl/Rnor_5.0/Sequence/Bowtie2Index/" star = "${params.igenomes_base}/Rattus_norvegicus/Ensembl/Rnor_5.0/Sequence/STARIndex/" bismark = "${params.igenomes_base}/Rattus_norvegicus/Ensembl/Rnor_5.0/Sequence/BismarkIndex/" @@ -209,7 +209,7 @@ params { } 'Rnor_6.0' { fasta = "${params.igenomes_base}/Rattus_norvegicus/Ensembl/Rnor_6.0/Sequence/WholeGenomeFasta/genome.fa" - bwa = "${params.igenomes_base}/Rattus_norvegicus/Ensembl/Rnor_6.0/Sequence/BWAIndex/genome.fa" + bwa = "${params.igenomes_base}/Rattus_norvegicus/Ensembl/Rnor_6.0/Sequence/BWAIndex/version0.6.0/" bowtie2 = "${params.igenomes_base}/Rattus_norvegicus/Ensembl/Rnor_6.0/Sequence/Bowtie2Index/" star = "${params.igenomes_base}/Rattus_norvegicus/Ensembl/Rnor_6.0/Sequence/STARIndex/" bismark = "${params.igenomes_base}/Rattus_norvegicus/Ensembl/Rnor_6.0/Sequence/BismarkIndex/" @@ -219,7 +219,7 @@ params { } 'R64-1-1' { fasta = "${params.igenomes_base}/Saccharomyces_cerevisiae/Ensembl/R64-1-1/Sequence/WholeGenomeFasta/genome.fa" - bwa = "${params.igenomes_base}/Saccharomyces_cerevisiae/Ensembl/R64-1-1/Sequence/BWAIndex/genome.fa" + bwa = "${params.igenomes_base}/Saccharomyces_cerevisiae/Ensembl/R64-1-1/Sequence/BWAIndex/version0.6.0/" bowtie2 = "${params.igenomes_base}/Saccharomyces_cerevisiae/Ensembl/R64-1-1/Sequence/Bowtie2Index/" star = "${params.igenomes_base}/Saccharomyces_cerevisiae/Ensembl/R64-1-1/Sequence/STARIndex/" bismark = "${params.igenomes_base}/Saccharomyces_cerevisiae/Ensembl/R64-1-1/Sequence/BismarkIndex/" @@ -230,7 +230,7 @@ params { } 'EF2' { fasta = "${params.igenomes_base}/Schizosaccharomyces_pombe/Ensembl/EF2/Sequence/WholeGenomeFasta/genome.fa" - bwa = "${params.igenomes_base}/Schizosaccharomyces_pombe/Ensembl/EF2/Sequence/BWAIndex/genome.fa" + bwa = "${params.igenomes_base}/Schizosaccharomyces_pombe/Ensembl/EF2/Sequence/BWAIndex/version0.6.0/" bowtie2 = "${params.igenomes_base}/Schizosaccharomyces_pombe/Ensembl/EF2/Sequence/Bowtie2Index/" star = "${params.igenomes_base}/Schizosaccharomyces_pombe/Ensembl/EF2/Sequence/STARIndex/" bismark = "${params.igenomes_base}/Schizosaccharomyces_pombe/Ensembl/EF2/Sequence/BismarkIndex/" @@ -242,7 +242,7 @@ params { } 'Sbi1' { fasta = "${params.igenomes_base}/Sorghum_bicolor/Ensembl/Sbi1/Sequence/WholeGenomeFasta/genome.fa" - bwa = "${params.igenomes_base}/Sorghum_bicolor/Ensembl/Sbi1/Sequence/BWAIndex/genome.fa" + bwa = "${params.igenomes_base}/Sorghum_bicolor/Ensembl/Sbi1/Sequence/BWAIndex/version0.6.0/" bowtie2 = "${params.igenomes_base}/Sorghum_bicolor/Ensembl/Sbi1/Sequence/Bowtie2Index/" star = "${params.igenomes_base}/Sorghum_bicolor/Ensembl/Sbi1/Sequence/STARIndex/" bismark = "${params.igenomes_base}/Sorghum_bicolor/Ensembl/Sbi1/Sequence/BismarkIndex/" @@ -252,7 +252,7 @@ params { } 'Sscrofa10.2' { fasta = "${params.igenomes_base}/Sus_scrofa/Ensembl/Sscrofa10.2/Sequence/WholeGenomeFasta/genome.fa" - bwa = "${params.igenomes_base}/Sus_scrofa/Ensembl/Sscrofa10.2/Sequence/BWAIndex/genome.fa" + bwa = "${params.igenomes_base}/Sus_scrofa/Ensembl/Sscrofa10.2/Sequence/BWAIndex/version0.6.0/" bowtie2 = "${params.igenomes_base}/Sus_scrofa/Ensembl/Sscrofa10.2/Sequence/Bowtie2Index/" star = "${params.igenomes_base}/Sus_scrofa/Ensembl/Sscrofa10.2/Sequence/STARIndex/" bismark = "${params.igenomes_base}/Sus_scrofa/Ensembl/Sscrofa10.2/Sequence/BismarkIndex/" @@ -263,7 +263,7 @@ params { } 'AGPv3' { fasta = "${params.igenomes_base}/Zea_mays/Ensembl/AGPv3/Sequence/WholeGenomeFasta/genome.fa" - bwa = "${params.igenomes_base}/Zea_mays/Ensembl/AGPv3/Sequence/BWAIndex/genome.fa" + bwa = "${params.igenomes_base}/Zea_mays/Ensembl/AGPv3/Sequence/BWAIndex/version0.6.0/" bowtie2 = "${params.igenomes_base}/Zea_mays/Ensembl/AGPv3/Sequence/Bowtie2Index/" star = "${params.igenomes_base}/Zea_mays/Ensembl/AGPv3/Sequence/STARIndex/" bismark = "${params.igenomes_base}/Zea_mays/Ensembl/AGPv3/Sequence/BismarkIndex/" @@ -273,7 +273,7 @@ params { } 'hg38' { fasta = "${params.igenomes_base}/Homo_sapiens/UCSC/hg38/Sequence/WholeGenomeFasta/genome.fa" - bwa = "${params.igenomes_base}/Homo_sapiens/UCSC/hg38/Sequence/BWAIndex/genome.fa" + bwa = "${params.igenomes_base}/Homo_sapiens/UCSC/hg38/Sequence/BWAIndex/version0.6.0/" bowtie2 = "${params.igenomes_base}/Homo_sapiens/UCSC/hg38/Sequence/Bowtie2Index/" star = "${params.igenomes_base}/Homo_sapiens/UCSC/hg38/Sequence/STARIndex/" bismark = "${params.igenomes_base}/Homo_sapiens/UCSC/hg38/Sequence/BismarkIndex/" @@ -285,7 +285,7 @@ params { } 'hg19' { fasta = "${params.igenomes_base}/Homo_sapiens/UCSC/hg19/Sequence/WholeGenomeFasta/genome.fa" - bwa = "${params.igenomes_base}/Homo_sapiens/UCSC/hg19/Sequence/BWAIndex/genome.fa" + bwa = "${params.igenomes_base}/Homo_sapiens/UCSC/hg19/Sequence/BWAIndex/version0.6.0/" bowtie2 = "${params.igenomes_base}/Homo_sapiens/UCSC/hg19/Sequence/Bowtie2Index/" star = "${params.igenomes_base}/Homo_sapiens/UCSC/hg19/Sequence/STARIndex/" bismark = "${params.igenomes_base}/Homo_sapiens/UCSC/hg19/Sequence/BismarkIndex/" @@ -298,7 +298,7 @@ params { } 'mm10' { fasta = "${params.igenomes_base}/Mus_musculus/UCSC/mm10/Sequence/WholeGenomeFasta/genome.fa" - bwa = "${params.igenomes_base}/Mus_musculus/UCSC/mm10/Sequence/BWAIndex/genome.fa" + bwa = "${params.igenomes_base}/Mus_musculus/UCSC/mm10/Sequence/BWAIndex/version0.6.0/" bowtie2 = "${params.igenomes_base}/Mus_musculus/UCSC/mm10/Sequence/Bowtie2Index/" star = "${params.igenomes_base}/Mus_musculus/UCSC/mm10/Sequence/STARIndex/" bismark = "${params.igenomes_base}/Mus_musculus/UCSC/mm10/Sequence/BismarkIndex/" @@ -311,7 +311,7 @@ params { } 'bosTau8' { fasta = "${params.igenomes_base}/Bos_taurus/UCSC/bosTau8/Sequence/WholeGenomeFasta/genome.fa" - bwa = "${params.igenomes_base}/Bos_taurus/UCSC/bosTau8/Sequence/BWAIndex/genome.fa" + bwa = "${params.igenomes_base}/Bos_taurus/UCSC/bosTau8/Sequence/BWAIndex/version0.6.0/" bowtie2 = "${params.igenomes_base}/Bos_taurus/UCSC/bosTau8/Sequence/Bowtie2Index/" star = "${params.igenomes_base}/Bos_taurus/UCSC/bosTau8/Sequence/STARIndex/" bismark = "${params.igenomes_base}/Bos_taurus/UCSC/bosTau8/Sequence/BismarkIndex/" @@ -321,7 +321,7 @@ params { } 'ce10' { fasta = "${params.igenomes_base}/Caenorhabditis_elegans/UCSC/ce10/Sequence/WholeGenomeFasta/genome.fa" - bwa = "${params.igenomes_base}/Caenorhabditis_elegans/UCSC/ce10/Sequence/BWAIndex/genome.fa" + bwa = "${params.igenomes_base}/Caenorhabditis_elegans/UCSC/ce10/Sequence/BWAIndex/version0.6.0/" bowtie2 = "${params.igenomes_base}/Caenorhabditis_elegans/UCSC/ce10/Sequence/Bowtie2Index/" star = "${params.igenomes_base}/Caenorhabditis_elegans/UCSC/ce10/Sequence/STARIndex/" bismark = "${params.igenomes_base}/Caenorhabditis_elegans/UCSC/ce10/Sequence/BismarkIndex/" @@ -333,7 +333,7 @@ params { } 'canFam3' { fasta = "${params.igenomes_base}/Canis_familiaris/UCSC/canFam3/Sequence/WholeGenomeFasta/genome.fa" - bwa = "${params.igenomes_base}/Canis_familiaris/UCSC/canFam3/Sequence/BWAIndex/genome.fa" + bwa = "${params.igenomes_base}/Canis_familiaris/UCSC/canFam3/Sequence/BWAIndex/version0.6.0/" bowtie2 = "${params.igenomes_base}/Canis_familiaris/UCSC/canFam3/Sequence/Bowtie2Index/" star = "${params.igenomes_base}/Canis_familiaris/UCSC/canFam3/Sequence/STARIndex/" bismark = "${params.igenomes_base}/Canis_familiaris/UCSC/canFam3/Sequence/BismarkIndex/" @@ -344,7 +344,7 @@ params { } 'danRer10' { fasta = "${params.igenomes_base}/Danio_rerio/UCSC/danRer10/Sequence/WholeGenomeFasta/genome.fa" - bwa = "${params.igenomes_base}/Danio_rerio/UCSC/danRer10/Sequence/BWAIndex/genome.fa" + bwa = "${params.igenomes_base}/Danio_rerio/UCSC/danRer10/Sequence/BWAIndex/version0.6.0/" bowtie2 = "${params.igenomes_base}/Danio_rerio/UCSC/danRer10/Sequence/Bowtie2Index/" star = "${params.igenomes_base}/Danio_rerio/UCSC/danRer10/Sequence/STARIndex/" bismark = "${params.igenomes_base}/Danio_rerio/UCSC/danRer10/Sequence/BismarkIndex/" @@ -355,7 +355,7 @@ params { } 'dm6' { fasta = "${params.igenomes_base}/Drosophila_melanogaster/UCSC/dm6/Sequence/WholeGenomeFasta/genome.fa" - bwa = "${params.igenomes_base}/Drosophila_melanogaster/UCSC/dm6/Sequence/BWAIndex/genome.fa" + bwa = "${params.igenomes_base}/Drosophila_melanogaster/UCSC/dm6/Sequence/BWAIndex/version0.6.0/" bowtie2 = "${params.igenomes_base}/Drosophila_melanogaster/UCSC/dm6/Sequence/Bowtie2Index/" star = "${params.igenomes_base}/Drosophila_melanogaster/UCSC/dm6/Sequence/STARIndex/" bismark = "${params.igenomes_base}/Drosophila_melanogaster/UCSC/dm6/Sequence/BismarkIndex/" @@ -366,7 +366,7 @@ params { } 'equCab2' { fasta = "${params.igenomes_base}/Equus_caballus/UCSC/equCab2/Sequence/WholeGenomeFasta/genome.fa" - bwa = "${params.igenomes_base}/Equus_caballus/UCSC/equCab2/Sequence/BWAIndex/genome.fa" + bwa = "${params.igenomes_base}/Equus_caballus/UCSC/equCab2/Sequence/BWAIndex/version0.6.0/" bowtie2 = "${params.igenomes_base}/Equus_caballus/UCSC/equCab2/Sequence/Bowtie2Index/" star = "${params.igenomes_base}/Equus_caballus/UCSC/equCab2/Sequence/STARIndex/" bismark = "${params.igenomes_base}/Equus_caballus/UCSC/equCab2/Sequence/BismarkIndex/" @@ -377,7 +377,7 @@ params { } 'galGal4' { fasta = "${params.igenomes_base}/Gallus_gallus/UCSC/galGal4/Sequence/WholeGenomeFasta/genome.fa" - bwa = "${params.igenomes_base}/Gallus_gallus/UCSC/galGal4/Sequence/BWAIndex/genome.fa" + bwa = "${params.igenomes_base}/Gallus_gallus/UCSC/galGal4/Sequence/BWAIndex/version0.6.0/" bowtie2 = "${params.igenomes_base}/Gallus_gallus/UCSC/galGal4/Sequence/Bowtie2Index/" star = "${params.igenomes_base}/Gallus_gallus/UCSC/galGal4/Sequence/STARIndex/" bismark = "${params.igenomes_base}/Gallus_gallus/UCSC/galGal4/Sequence/BismarkIndex/" @@ -388,7 +388,7 @@ params { } 'panTro4' { fasta = "${params.igenomes_base}/Pan_troglodytes/UCSC/panTro4/Sequence/WholeGenomeFasta/genome.fa" - bwa = "${params.igenomes_base}/Pan_troglodytes/UCSC/panTro4/Sequence/BWAIndex/genome.fa" + bwa = "${params.igenomes_base}/Pan_troglodytes/UCSC/panTro4/Sequence/BWAIndex/version0.6.0/" bowtie2 = "${params.igenomes_base}/Pan_troglodytes/UCSC/panTro4/Sequence/Bowtie2Index/" star = "${params.igenomes_base}/Pan_troglodytes/UCSC/panTro4/Sequence/STARIndex/" bismark = "${params.igenomes_base}/Pan_troglodytes/UCSC/panTro4/Sequence/BismarkIndex/" @@ -399,7 +399,7 @@ params { } 'rn6' { fasta = "${params.igenomes_base}/Rattus_norvegicus/UCSC/rn6/Sequence/WholeGenomeFasta/genome.fa" - bwa = "${params.igenomes_base}/Rattus_norvegicus/UCSC/rn6/Sequence/BWAIndex/genome.fa" + bwa = "${params.igenomes_base}/Rattus_norvegicus/UCSC/rn6/Sequence/BWAIndex/version0.6.0/" bowtie2 = "${params.igenomes_base}/Rattus_norvegicus/UCSC/rn6/Sequence/Bowtie2Index/" star = "${params.igenomes_base}/Rattus_norvegicus/UCSC/rn6/Sequence/STARIndex/" bismark = "${params.igenomes_base}/Rattus_norvegicus/UCSC/rn6/Sequence/BismarkIndex/" @@ -409,7 +409,7 @@ params { } 'sacCer3' { fasta = "${params.igenomes_base}/Saccharomyces_cerevisiae/UCSC/sacCer3/Sequence/WholeGenomeFasta/genome.fa" - bwa = "${params.igenomes_base}/Saccharomyces_cerevisiae/UCSC/sacCer3/Sequence/BWAIndex/genome.fa" + bwa = "${params.igenomes_base}/Saccharomyces_cerevisiae/UCSC/sacCer3/Sequence/BWAIndex/version0.6.0/" bowtie2 = "${params.igenomes_base}/Saccharomyces_cerevisiae/UCSC/sacCer3/Sequence/Bowtie2Index/" star = "${params.igenomes_base}/Saccharomyces_cerevisiae/UCSC/sacCer3/Sequence/STARIndex/" bismark = "${params.igenomes_base}/Saccharomyces_cerevisiae/UCSC/sacCer3/Sequence/BismarkIndex/" @@ -419,7 +419,7 @@ params { } 'susScr3' { fasta = "${params.igenomes_base}/Sus_scrofa/UCSC/susScr3/Sequence/WholeGenomeFasta/genome.fa" - bwa = "${params.igenomes_base}/Sus_scrofa/UCSC/susScr3/Sequence/BWAIndex/genome.fa" + bwa = "${params.igenomes_base}/Sus_scrofa/UCSC/susScr3/Sequence/BWAIndex/version0.6.0/" bowtie2 = "${params.igenomes_base}/Sus_scrofa/UCSC/susScr3/Sequence/Bowtie2Index/" star = "${params.igenomes_base}/Sus_scrofa/UCSC/susScr3/Sequence/STARIndex/" bismark = "${params.igenomes_base}/Sus_scrofa/UCSC/susScr3/Sequence/BismarkIndex/" diff --git a/conf/modules.config b/conf/modules.config index a0506a4d..da58a5d8 100644 --- a/conf/modules.config +++ b/conf/modules.config @@ -1,12 +1,12 @@ /* -======================================================================================== +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Config file for defining DSL2 per module options and publishing paths -======================================================================================== +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Available keys to override module options: - ext.args = Additional arguments appended to command in module. - ext.args2 = Second set of arguments appended to command in module (multi-tool modules). - ext.args3 = Third set of arguments appended to command in module (multi-tool modules). - ext.prefix = File name prefix for output files. + ext.args = Additional arguments appended to command in module. + ext.args2 = Second set of arguments appended to command in module (multi-tool modules). + ext.args3 = Third set of arguments appended to command in module (multi-tool modules). + ext.prefix = File name prefix for output files. ---------------------------------------------------------------------------------------- */ @@ -14,14 +14,14 @@ process { publishDir = [ path: { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }, - mode: 'copy', + mode: params.publish_dir_mode, saveAs: { filename -> filename.equals('versions.yml') ? null : filename } ] withName: SAMPLESHEET_CHECK { publishDir = [ path: { "${params.outdir}/pipeline_info" }, - mode: 'copy', + mode: params.publish_dir_mode, saveAs: { filename -> filename.equals('versions.yml') ? null : filename } ] } @@ -33,7 +33,7 @@ process { withName: CUSTOM_DUMPSOFTWAREVERSIONS { publishDir = [ path: { "${params.outdir}/pipeline_info" }, - mode: 'copy', + mode: params.publish_dir_mode, pattern: '*_versions.yml' ] } diff --git a/conf/test.config b/conf/test.config index 6ce1192d..50d51ccc 100644 --- a/conf/test.config +++ b/conf/test.config @@ -1,11 +1,11 @@ /* -======================================================================================== +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Nextflow config file for running minimal tests -======================================================================================== +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Defines input files and everything required to run a fast and simple pipeline test. Use as follows: - nextflow run nf-core/mag -profile test, + nextflow run nf-core/mag -profile test, --outdir ---------------------------------------------------------------------------------------- */ diff --git a/conf/test_full.config b/conf/test_full.config index 5e0fbbda..a470da07 100644 --- a/conf/test_full.config +++ b/conf/test_full.config @@ -1,11 +1,11 @@ /* -======================================================================================== +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Nextflow config file for running full-size tests -======================================================================================== +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Defines input files and everything required to run a full size pipeline test. 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J-waT~81OO72jb}RoLJM9sUyE8jGGwP=P zT({r52Hx8DE$sF$+szslcT#Se_EpNdtuM&KawTQ+v8aUV!(c1b6Y4w!6D(Cvt4H`E zKADbS@9>1i;=z)V7g#7c)78Q2R21&3KiPRN)L6AW!IagA!AuZn7(F8!n;^O(3&GEL z`IdZS!SoYp3ZUbR4QN~-hc4sVpItBmfoJG&#Lk2yM)p}|n3k}!gi}7^1bED6U@;Ic zl^ka$&sv*cyhCf#Eg<}pQxJ33KjQ@CIv?|QCJpD_6tkR+I~LC|e?kXMA=kc(1G!N4 VJvv>8IrcTl)qtG)%H@^D#V=*Sk$eCE diff --git a/docs/usage.md b/docs/usage.md index db7f656b..0cb8bd3f 100644 --- a/docs/usage.md +++ b/docs/usage.md @@ -57,7 +57,7 @@ An [example samplesheet](../assets/samplesheet.csv) has been provided with the p The typical command for running the pipeline is as follows: ```console -nextflow run nf-core/mag --input samplesheet.csv --genome GRCh37 -profile docker +nextflow run nf-core/mag --input samplesheet.csv --outdir --genome GRCh37 -profile docker ``` This will launch the pipeline with the `docker` configuration profile. See below for more information about profiles. @@ -141,11 +141,11 @@ Whilst the default requirements set within the pipeline will hopefully work for For example, if the nf-core/rnaseq pipeline is failing after multiple re-submissions of the `STAR_ALIGN` process due to an exit code of `137` this would indicate that there is an out of memory issue: ```console -[62/149eb0] NOTE: Process `RNASEQ:ALIGN_STAR:STAR_ALIGN (WT_REP1)` terminated with an error exit status (137) -- Execution is retried (1) -Error executing process > 'RNASEQ:ALIGN_STAR:STAR_ALIGN (WT_REP1)' +[62/149eb0] NOTE: Process `NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:STAR_ALIGN (WT_REP1)` terminated with an error exit status (137) -- Execution is retried (1) +Error executing process > 'NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:STAR_ALIGN (WT_REP1)' Caused by: - Process `RNASEQ:ALIGN_STAR:STAR_ALIGN (WT_REP1)` terminated with an error exit status (137) + Process `NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:STAR_ALIGN (WT_REP1)` terminated with an error exit status (137) Command executed: STAR \ @@ -169,17 +169,24 @@ Work dir: Tip: you can replicate the issue by changing to the process work dir and entering the command `bash .command.run` ``` -To bypass this error you would need to find exactly which resources are set by the `STAR_ALIGN` process. The quickest way is to search for `process STAR_ALIGN` in the [nf-core/rnaseq Github repo](https://github.com/nf-core/rnaseq/search?q=process+STAR_ALIGN). We have standardised the structure of Nextflow DSL2 pipelines such that all module files will be present in the `modules/` directory and so based on the search results the file we want is `modules/nf-core/software/star/align/main.nf`. If you click on the link to that file you will notice that there is a `label` directive at the top of the module that is set to [`label process_high`](https://github.com/nf-core/rnaseq/blob/4c27ef5610c87db00c3c5a3eed10b1d161abf575/modules/nf-core/software/star/align/main.nf#L9). The [Nextflow `label`](https://www.nextflow.io/docs/latest/process.html#label) directive allows us to organise workflow processes in separate groups which can be referenced in a configuration file to select and configure subset of processes having similar computing requirements. The default values for the `process_high` label are set in the pipeline's [`base.config`](https://github.com/nf-core/rnaseq/blob/4c27ef5610c87db00c3c5a3eed10b1d161abf575/conf/base.config#L33-L37) which in this case is defined as 72GB. Providing you haven't set any other standard nf-core parameters to __cap__ the [maximum resources](https://nf-co.re/usage/configuration#max-resources) used by the pipeline then we can try and bypass the `STAR_ALIGN` process failure by creating a custom config file that sets at least 72GB of memory, in this case increased to 100GB. The custom config below can then be provided to the pipeline via the [`-c`](#-c) parameter as highlighted in previous sections. +To bypass this error you would need to find exactly which resources are set by the `STAR_ALIGN` process. The quickest way is to search for `process STAR_ALIGN` in the [nf-core/rnaseq Github repo](https://github.com/nf-core/rnaseq/search?q=process+STAR_ALIGN). +We have standardised the structure of Nextflow DSL2 pipelines such that all module files will be present in the `modules/` directory and so, based on the search results, the file we want is `modules/nf-core/software/star/align/main.nf`. +If you click on the link to that file you will notice that there is a `label` directive at the top of the module that is set to [`label process_high`](https://github.com/nf-core/rnaseq/blob/4c27ef5610c87db00c3c5a3eed10b1d161abf575/modules/nf-core/software/star/align/main.nf#L9). +The [Nextflow `label`](https://www.nextflow.io/docs/latest/process.html#label) directive allows us to organise workflow processes in separate groups which can be referenced in a configuration file to select and configure subset of processes having similar computing requirements. +The default values for the `process_high` label are set in the pipeline's [`base.config`](https://github.com/nf-core/rnaseq/blob/4c27ef5610c87db00c3c5a3eed10b1d161abf575/conf/base.config#L33-L37) which in this case is defined as 72GB. +Providing you haven't set any other standard nf-core parameters to **cap** the [maximum resources](https://nf-co.re/usage/configuration#max-resources) used by the pipeline then we can try and bypass the `STAR_ALIGN` process failure by creating a custom config file that sets at least 72GB of memory, in this case increased to 100GB. +The custom config below can then be provided to the pipeline via the [`-c`](#-c) parameter as highlighted in previous sections. ```nextflow process { - withName: STAR_ALIGN { + withName: 'NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:STAR_ALIGN' { memory = 100.GB } } ``` -> **NB:** We specify just the process name i.e. `STAR_ALIGN` in the config file and not the full task name string that is printed to screen in the error message or on the terminal whilst the pipeline is running i.e. `RNASEQ:ALIGN_STAR:STAR_ALIGN`. You may get a warning suggesting that the process selector isn't recognised but you can ignore that if the process name has been specified correctly. This is something that needs to be fixed upstream in core Nextflow. +> **NB:** We specify the full process name i.e. `NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:STAR_ALIGN` in the config file because this takes priority over the short name (`STAR_ALIGN`) and allows existing configuration using the full process name to be correctly overridden. +> If you get a warning suggesting that the process selector isn't recognised check that the process name has been specified correctly. ### Updating containers diff --git a/lib/NfcoreSchema.groovy b/lib/NfcoreSchema.groovy index 40ab65f2..b3d092f8 100755 --- a/lib/NfcoreSchema.groovy +++ b/lib/NfcoreSchema.groovy @@ -27,7 +27,7 @@ class NfcoreSchema { /* groovylint-disable-next-line UnusedPrivateMethodParameter */ public static void validateParameters(workflow, params, log, schema_filename='nextflow_schema.json') { def has_error = false - //=====================================================================// + //~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~// // Check for nextflow core params and unexpected params def json = new File(getSchemaPath(workflow, schema_filename=schema_filename)).text def Map schemaParams = (Map) new JsonSlurper().parseText(json).get('definitions') @@ -135,7 +135,7 @@ class NfcoreSchema { } } - //=====================================================================// + //~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~// // Validate parameters against the schema InputStream input_stream = new File(getSchemaPath(workflow, schema_filename=schema_filename)).newInputStream() JSONObject raw_schema = new JSONObject(new JSONTokener(input_stream)) diff --git a/lib/Utils.groovy b/lib/Utils.groovy index 1b88aec0..28567bd7 100755 --- a/lib/Utils.groovy +++ b/lib/Utils.groovy @@ -29,12 +29,12 @@ class Utils { conda_check_failed |= !(channels.indexOf('bioconda') < channels.indexOf('defaults')) if (conda_check_failed) { - log.warn "=============================================================================\n" + + log.warn "~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~\n" + " There is a problem with your Conda configuration!\n\n" + " You will need to set-up the conda-forge and bioconda channels correctly.\n" + " Please refer to https://bioconda.github.io/user/install.html#set-up-channels\n" + " NB: The order of the channels matters!\n" + - "===================================================================================" + "~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~" } } } diff --git a/lib/WorkflowMag.groovy b/lib/WorkflowMag.groovy index b3a06427..9e3adf54 100755 --- a/lib/WorkflowMag.groovy +++ b/lib/WorkflowMag.groovy @@ -48,11 +48,11 @@ class WorkflowMag { // private static void genomeExistsError(params, log) { if (params.genomes && params.genome && !params.genomes.containsKey(params.genome)) { - log.error "=============================================================================\n" + + log.error "~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~\n" + " Genome '${params.genome}' not found in any config files provided to the pipeline.\n" + " Currently, the available genome keys are:\n" + " ${params.genomes.keySet().join(", ")}\n" + - "===================================================================================" + "~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~" System.exit(1) } } diff --git a/main.nf b/main.nf index 97a6f29d..1bcbb091 100644 --- a/main.nf +++ b/main.nf @@ -1,8 +1,8 @@ #!/usr/bin/env nextflow /* -======================================================================================== +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ nf-core/mag -======================================================================================== +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Github : https://github.com/nf-core/mag Website: https://nf-co.re/mag Slack : https://nfcore.slack.com/channels/mag @@ -12,25 +12,25 @@ nextflow.enable.dsl = 2 /* -======================================================================================== +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ GENOME PARAMETER VALUES -======================================================================================== +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ */ params.fasta = WorkflowMain.getGenomeAttribute(params, 'fasta') /* -======================================================================================== +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ VALIDATE & PRINT PARAMETER SUMMARY -======================================================================================== +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ */ WorkflowMain.initialise(workflow, params, log) /* -======================================================================================== +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ NAMED WORKFLOW FOR PIPELINE -======================================================================================== +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ */ include { MAG } from './workflows/mag' @@ -43,9 +43,9 @@ workflow NFCORE_MAG { } /* -======================================================================================== +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ RUN ALL WORKFLOWS -======================================================================================== +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ */ // @@ -57,7 +57,7 @@ workflow { } /* -======================================================================================== +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ THE END -======================================================================================== +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ */ diff --git a/nextflow.config b/nextflow.config index 6a929ee8..50dbaf7e 100644 --- a/nextflow.config +++ b/nextflow.config @@ -1,7 +1,7 @@ /* -======================================================================================== +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ nf-core/mag Nextflow config file -======================================================================================== +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Default config options for all compute environments ---------------------------------------------------------------------------------------- */ @@ -24,8 +24,9 @@ params { max_multiqc_email_size = '25.MB' // Boilerplate options - outdir = './results' + outdir = null tracedir = "${params.outdir}/pipeline_info" + publish_dir_mode = 'copy' email = null email_on_fail = null plaintext_email = false @@ -62,6 +63,15 @@ try { System.err.println("WARNING: Could not load nf-core/config profiles: ${params.custom_config_base}/nfcore_custom.config") } +// Load nf-core/mag custom profiles from different institutions. +// Warning: Uncomment only if a pipeline-specific instititutional config already exists on nf-core/configs! +// try { +// includeConfig "${params.custom_config_base}/pipeline/mag.config" +// } catch (Exception e) { +// System.err.println("WARNING: Could not load nf-core/config/mag profiles: ${params.custom_config_base}/pipeline/mag.config") +// } + + profiles { debug { process.beforeScript = 'echo $HOSTNAME' } conda { @@ -121,7 +131,7 @@ if (!params.igenomes_ignore) { } // Export these variables to prevent local Python/R libraries from conflicting with those in the container -// The JULIA depot path has been adjusted to a fixed path `/usr/local/share/julia` that needs to be used for packages in the container. +// The JULIA depot path has been adjusted to a fixed path `/usr/local/share/julia` that needs to be used for packages in the container. // See https://apeltzer.github.io/post/03-julia-lang-nextflow/ for details on that. Once we have a common agreement on where to keep Julia packages, this is adjustable. env { @@ -159,7 +169,7 @@ manifest { description = 'Assembly, binning and annotation of metagenomes' mainScript = 'main.nf' nextflowVersion = '!>=21.10.3' - version = '2.1.1' + version = '2.2.0dev' } // Load modules.config for DSL2 module specific options diff --git a/nextflow_schema.json b/nextflow_schema.json index 22133aa1..bc78304a 100644 --- a/nextflow_schema.json +++ b/nextflow_schema.json @@ -11,7 +11,8 @@ "fa_icon": "fas fa-terminal", "description": "Define where the pipeline should find input data and save output data.", "required": [ - "input" + "input", + "outdir" ], "properties": { "input": { @@ -26,8 +27,8 @@ }, "outdir": { "type": "string", - "description": "Path to the output directory where the results will be saved.", - "default": "./results", + "format": "directory-path", + "description": "The output directory where the results will be saved. You have to use absolute paths to storage on Cloud infrastructure.", "fa_icon": "fas fa-folder-open" }, "email": { @@ -178,6 +179,22 @@ "fa_icon": "fas fa-question-circle", "hidden": true }, + "publish_dir_mode": { + "type": "string", + "default": "copy", + "description": "Method used to save pipeline results to output directory.", + "help_text": "The Nextflow `publishDir` option specifies which intermediate files should be saved to the output directory. This option tells the pipeline what method should be used to move these files. See [Nextflow docs](https://www.nextflow.io/docs/latest/process.html#publishdir) for details.", + "fa_icon": "fas fa-copy", + "enum": [ + "symlink", + "rellink", + "link", + "copy", + "copyNoFollow", + "move" + ], + "hidden": true + }, "email_on_fail": { "type": "string", "description": "Email address for completion summary, only when pipeline fails.", diff --git a/subworkflows/local/input_check.nf b/subworkflows/local/input_check.nf index cddcbb3c..0aecf87f 100644 --- a/subworkflows/local/input_check.nf +++ b/subworkflows/local/input_check.nf @@ -12,7 +12,7 @@ workflow INPUT_CHECK { SAMPLESHEET_CHECK ( samplesheet ) .csv .splitCsv ( header:true, sep:',' ) - .map { create_fastq_channels(it) } + .map { create_fastq_channel(it) } .set { reads } emit: @@ -21,22 +21,24 @@ workflow INPUT_CHECK { } // Function to get list of [ meta, [ fastq_1, fastq_2 ] ] -def create_fastq_channels(LinkedHashMap row) { +def create_fastq_channel(LinkedHashMap row) { + // create meta map def meta = [:] - meta.id = row.sample - meta.single_end = row.single_end.toBoolean() + meta.id = row.sample + meta.single_end = row.single_end.toBoolean() - def array = [] + // add path(s) of the fastq file(s) to the meta map + def fastq_meta = [] if (!file(row.fastq_1).exists()) { exit 1, "ERROR: Please check input samplesheet -> Read 1 FastQ file does not exist!\n${row.fastq_1}" } if (meta.single_end) { - array = [ meta, [ file(row.fastq_1) ] ] + fastq_meta = [ meta, [ file(row.fastq_1) ] ] } else { if (!file(row.fastq_2).exists()) { exit 1, "ERROR: Please check input samplesheet -> Read 2 FastQ file does not exist!\n${row.fastq_2}" } - array = [ meta, [ file(row.fastq_1), file(row.fastq_2) ] ] + fastq_meta = [ meta, [ file(row.fastq_1), file(row.fastq_2) ] ] } - return array + return fastq_meta } diff --git a/workflows/mag.nf b/workflows/mag.nf index a454563b..9dc9e53a 100644 --- a/workflows/mag.nf +++ b/workflows/mag.nf @@ -1,7 +1,7 @@ /* -======================================================================================== +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ VALIDATE INPUTS -======================================================================================== +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ */ def summary_params = NfcoreSchema.paramsSummaryMap(workflow, params) @@ -18,18 +18,18 @@ for (param in checkPathParamList) { if (param) { file(param, checkIfExists: true if (params.input) { ch_input = file(params.input) } else { exit 1, 'Input samplesheet not specified!' } /* -======================================================================================== +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ CONFIG FILES -======================================================================================== +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ */ ch_multiqc_config = file("$projectDir/assets/multiqc_config.yaml", checkIfExists: true) ch_multiqc_custom_config = params.multiqc_config ? Channel.fromPath(params.multiqc_config) : Channel.empty() /* -======================================================================================== +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ IMPORT LOCAL MODULES/SUBWORKFLOWS -======================================================================================== +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ */ // @@ -38,9 +38,9 @@ ch_multiqc_custom_config = params.multiqc_config ? Channel.fromPath(params.multi include { INPUT_CHECK } from '../subworkflows/local/input_check' /* -======================================================================================== +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ IMPORT NF-CORE MODULES/SUBWORKFLOWS -======================================================================================== +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ */ // @@ -51,9 +51,9 @@ include { MULTIQC } from '../modules/nf-core/modules/multiqc include { CUSTOM_DUMPSOFTWAREVERSIONS } from '../modules/nf-core/modules/custom/dumpsoftwareversions/main' /* -======================================================================================== +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ RUN MAIN WORKFLOW -======================================================================================== +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ */ // Info required for completion email and summary @@ -104,9 +104,9 @@ workflow MAG { } /* -======================================================================================== +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ COMPLETION EMAIL AND SUMMARY -======================================================================================== +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ */ workflow.onComplete { @@ -117,7 +117,7 @@ workflow.onComplete { } /* -======================================================================================== +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ THE END -======================================================================================== +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ */ From 7c866e905da3280480c33a84ebff12f7458ccfc3 Mon Sep 17 00:00:00 2001 From: nf-core-bot Date: Wed, 23 Mar 2022 13:52:17 +0000 Subject: [PATCH 2/3] Template update for nf-core/tools version 2.3.1 --- .editorconfig | 5 +- .github/CONTRIBUTING.md | 15 +- .github/ISSUE_TEMPLATE/bug_report.yml | 1 - .github/PULL_REQUEST_TEMPLATE.md | 6 +- .github/workflows/awsfulltest.yml | 1 - .github/workflows/awstest.yml | 2 +- .github/workflows/branch.yml | 5 +- .github/workflows/ci.yml | 12 +- .github/workflows/linting.yml | 85 ++--------- .github/workflows/linting_comment.yml | 3 +- .gitpod.yml | 16 +- .markdownlint.yml | 14 -- .prettierrc.yml | 1 + .yamllint.yml | 6 - CHANGELOG.md | 2 + CITATIONS.md | 27 ++-- README.md | 31 ++-- assets/email_template.html | 142 ++++++++++++------ assets/multiqc_config.yaml | 11 -- assets/multiqc_config.yml | 11 ++ assets/schema_input.json | 5 +- docs/README.md | 8 +- docs/output.md | 28 ++-- docs/usage.md | 109 +++++++------- modules.json | 8 +- .../custom/dumpsoftwareversions/main.nf | 3 + .../custom/dumpsoftwareversions/meta.yml | 2 +- modules/nf-core/modules/fastqc/main.nf | 3 + modules/nf-core/modules/fastqc/meta.yml | 90 +++++------ modules/nf-core/modules/multiqc/main.nf | 9 +- modules/nf-core/modules/multiqc/meta.yml | 66 ++++---- nextflow_schema.json | 14 +- workflows/mag.nf | 2 +- 33 files changed, 361 insertions(+), 382 deletions(-) delete mode 100644 .markdownlint.yml create mode 100644 .prettierrc.yml delete mode 100644 .yamllint.yml delete mode 100644 assets/multiqc_config.yaml create mode 100644 assets/multiqc_config.yml diff --git a/.editorconfig b/.editorconfig index 95549501..b6b31907 100644 --- a/.editorconfig +++ b/.editorconfig @@ -8,12 +8,9 @@ trim_trailing_whitespace = true indent_size = 4 indent_style = space -[*.{yml,yaml}] +[*.{md,yml,yaml,html,css,scss,js}] indent_size = 2 -[*.json] -insert_final_newline = unset - # These files are edited and tested upstream in nf-core/modules [/modules/nf-core/**] charset = unset diff --git a/.github/CONTRIBUTING.md b/.github/CONTRIBUTING.md index be1d64be..3bd0f323 100644 --- a/.github/CONTRIBUTING.md +++ b/.github/CONTRIBUTING.md @@ -15,8 +15,7 @@ Contributions to the code are even more welcome ;) If you'd like to write some code for nf-core/mag, the standard workflow is as follows: -1. Check that there isn't already an issue about your idea in the [nf-core/mag issues](https://github.com/nf-core/mag/issues) to avoid duplicating work - * If there isn't one already, please create one so that others know you're working on this +1. Check that there isn't already an issue about your idea in the [nf-core/mag issues](https://github.com/nf-core/mag/issues) to avoid duplicating work. If there isn't one already, please create one so that others know you're working on this 2. [Fork](https://help.github.com/en/github/getting-started-with-github/fork-a-repo) the [nf-core/mag repository](https://github.com/nf-core/mag) to your GitHub account 3. Make the necessary changes / additions within your forked repository following [Pipeline conventions](#pipeline-contribution-conventions) 4. Use `nf-core schema build` and add any new parameters to the pipeline JSON schema (requires [nf-core tools](https://github.com/nf-core/tools) >= 1.10). @@ -49,9 +48,9 @@ These tests are run both with the latest available version of `Nextflow` and als :warning: Only in the unlikely and regretful event of a release happening with a bug. -* On your own fork, make a new branch `patch` based on `upstream/master`. -* Fix the bug, and bump version (X.Y.Z+1). -* A PR should be made on `master` from patch to directly this particular bug. +- On your own fork, make a new branch `patch` based on `upstream/master`. +- Fix the bug, and bump version (X.Y.Z+1). +- A PR should be made on `master` from patch to directly this particular bug. ## Getting help @@ -73,7 +72,7 @@ If you wish to contribute a new step, please use the following coding standards: 6. Add sanity checks and validation for all relevant parameters. 7. Perform local tests to validate that the new code works as expected. 8. If applicable, add a new test command in `.github/workflow/ci.yml`. -9. Update MultiQC config `assets/multiqc_config.yaml` so relevant suffixes, file name clean up and module plots are in the appropriate order. If applicable, add a [MultiQC](https://https://multiqc.info/) module. +9. Update MultiQC config `assets/multiqc_config.yml` so relevant suffixes, file name clean up and module plots are in the appropriate order. If applicable, add a [MultiQC](https://https://multiqc.info/) module. 10. Add a description of the output files and if relevant any appropriate images from the MultiQC report to `docs/output.md`. ### Default values @@ -92,8 +91,8 @@ The process resources can be passed on to the tool dynamically within the proces Please use the following naming schemes, to make it easy to understand what is going where. -* initial process channel: `ch_output_from_` -* intermediate and terminal channels: `ch__for_` +- initial process channel: `ch_output_from_` +- intermediate and terminal channels: `ch__for_` ### Nextflow version bumping diff --git a/.github/ISSUE_TEMPLATE/bug_report.yml b/.github/ISSUE_TEMPLATE/bug_report.yml index a9dff0f9..d32afe01 100644 --- a/.github/ISSUE_TEMPLATE/bug_report.yml +++ b/.github/ISSUE_TEMPLATE/bug_report.yml @@ -2,7 +2,6 @@ name: Bug report description: Report something that is broken or incorrect labels: bug body: - - type: markdown attributes: value: | diff --git a/.github/PULL_REQUEST_TEMPLATE.md b/.github/PULL_REQUEST_TEMPLATE.md index 39b8c44a..1e68020b 100644 --- a/.github/PULL_REQUEST_TEMPLATE.md +++ b/.github/PULL_REQUEST_TEMPLATE.md @@ -16,10 +16,10 @@ Learn more about contributing: [CONTRIBUTING.md](https://github.com/nf-core/mag/ - [ ] This comment contains a description of changes (with reason). - [ ] If you've fixed a bug or added code that should be tested, add tests! - - [ ] If you've added a new tool - have you followed the pipeline conventions in the [contribution docs](https://github.com/nf-core/mag/tree/master/.github/CONTRIBUTING.md) - - [ ] If necessary, also make a PR on the nf-core/mag _branch_ on the [nf-core/test-datasets](https://github.com/nf-core/test-datasets) repository. + - [ ] If you've added a new tool - have you followed the pipeline conventions in the [contribution docs](https://github.com/nf-core/mag/tree/master/.github/CONTRIBUTING.md) + - [ ] If necessary, also make a PR on the nf-core/mag _branch_ on the [nf-core/test-datasets](https://github.com/nf-core/test-datasets) repository. - [ ] Make sure your code lints (`nf-core lint`). -- [ ] Ensure the test suite passes (`nextflow run . -profile test,docker` --outdir `). +- [ ] Ensure the test suite passes (`nextflow run . -profile test,docker --outdir `). - [ ] Usage Documentation in `docs/usage.md` is updated. - [ ] Output Documentation in `docs/output.md` is updated. - [ ] `CHANGELOG.md` is updated. diff --git a/.github/workflows/awsfulltest.yml b/.github/workflows/awsfulltest.yml index 0a02db8f..b74d2047 100644 --- a/.github/workflows/awsfulltest.yml +++ b/.github/workflows/awsfulltest.yml @@ -18,7 +18,6 @@ jobs: # TODO nf-core: You can customise AWS full pipeline tests as required # Add full size test data (but still relatively small datasets for few samples) # on the `test_full.config` test runs with only one set of parameters - with: workspace_id: ${{ secrets.TOWER_WORKSPACE_ID }} access_token: ${{ secrets.TOWER_ACCESS_TOKEN }} diff --git a/.github/workflows/awstest.yml b/.github/workflows/awstest.yml index 6e009f41..f4aff861 100644 --- a/.github/workflows/awstest.yml +++ b/.github/workflows/awstest.yml @@ -10,9 +10,9 @@ jobs: if: github.repository == 'nf-core/mag' runs-on: ubuntu-latest steps: + # Launch workflow using Tower CLI tool action - name: Launch workflow via tower uses: nf-core/tower-action@v3 - with: workspace_id: ${{ secrets.TOWER_WORKSPACE_ID }} access_token: ${{ secrets.TOWER_ACCESS_TOKEN }} diff --git a/.github/workflows/branch.yml b/.github/workflows/branch.yml index d5ee9bae..55f14919 100644 --- a/.github/workflows/branch.yml +++ b/.github/workflows/branch.yml @@ -13,8 +13,7 @@ jobs: - name: Check PRs if: github.repository == 'nf-core/mag' run: | - { [[ ${{github.event.pull_request.head.repo.full_name }} == nf-core/mag ]] && [[ $GITHUB_HEAD_REF = "dev" ]]; } || [[ $GITHUB_HEAD_REF == "patch" ]] - + "{ [[ ${{github.event.pull_request.head.repo.full_name }} == nf-core/mag ]] && [[ $GITHUB_HEAD_REF = "dev" ]]; } || [[ $GITHUB_HEAD_REF == "patch" ]]" # If the above check failed, post a comment on the PR explaining the failure # NOTE - this doesn't currently work if the PR is coming from a fork, due to limitations in GitHub actions secrets @@ -43,4 +42,4 @@ jobs: Thanks again for your contribution! repo-token: ${{ secrets.GITHUB_TOKEN }} allow-repeats: false - +# diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml index b1c578c1..f5885cbc 100644 --- a/.github/workflows/ci.yml +++ b/.github/workflows/ci.yml @@ -16,18 +16,18 @@ jobs: test: name: Run pipeline with test data # Only run on push if this is the nf-core dev branch (merged PRs) - if: ${{ github.event_name != 'push' || (github.event_name == 'push' && github.repository == 'nf-core/mag') }} + if: "${{ github.event_name != 'push' || (github.event_name == 'push' && github.repository == 'nf-core/mag') }}" runs-on: ubuntu-latest strategy: matrix: # Nextflow versions include: # Test pipeline minimum Nextflow version - - NXF_VER: '21.10.3' - NXF_EDGE: '' + - NXF_VER: "21.10.3" + NXF_EDGE: "" # Test latest edge release of Nextflow - - NXF_VER: '' - NXF_EDGE: '1' + - NXF_VER: "" + NXF_EDGE: "1" steps: - name: Check out pipeline code uses: actions/checkout@v2 @@ -48,3 +48,5 @@ jobs: # Remember that you can parallelise this by using strategy.matrix run: | nextflow run ${GITHUB_WORKSPACE} -profile test,docker --outdir ./results + +# diff --git a/.github/workflows/linting.yml b/.github/workflows/linting.yml index fda934c0..e9cf5de3 100644 --- a/.github/workflows/linting.yml +++ b/.github/workflows/linting.yml @@ -1,6 +1,7 @@ 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 that the code meets the nf-core guidelines +# It runs the `nf-core lint` and markdown lint tests to ensure +# that the code meets the nf-core guidelines. on: push: pull_request: @@ -8,42 +9,6 @@ on: types: [published] jobs: - Markdown: - runs-on: ubuntu-latest - steps: - - uses: actions/checkout@v2 - - uses: actions/setup-node@v2 - - name: Install markdownlint - run: npm install -g markdownlint-cli - - name: Run Markdownlint - run: markdownlint . - - # If the above check failed, post a comment on the PR explaining the failure - - name: Post PR comment - if: failure() - uses: mshick/add-pr-comment@v1 - with: - message: | - ## Markdown linting is failing - - To keep the code consistent with lots of contributors, we run automated code consistency checks. - To fix this CI test, please run: - - * Install `markdownlint-cli` - * On Mac: `brew install markdownlint-cli` - * Everything else: [Install `npm`](https://www.npmjs.com/get-npm) then [install `markdownlint-cli`](https://www.npmjs.com/package/markdownlint-cli) (`npm install -g markdownlint-cli`) - * Fix the markdown errors - * Automatically: `markdownlint . --fix` - * Manually resolve anything left from `markdownlint .` - - Once you push these changes the test should pass, and you can hide this comment :+1: - - We highly recommend setting up markdownlint in your code editor so that this formatting is done automatically on save. Ask about it on Slack for help! - - Thanks again for your contribution! - repo-token: ${{ secrets.GITHUB_TOKEN }} - allow-repeats: false - EditorConfig: runs-on: ubuntu-latest steps: @@ -55,49 +20,24 @@ jobs: run: npm install -g editorconfig-checker - name: Run ECLint check - run: editorconfig-checker -exclude README.md $(git ls-files | grep -v test) + run: editorconfig-checker -exclude README.md $(find .* -type f | grep -v '.git\|.py\|.md\|json\|yml\|yaml\|html\|css\|work\|.nextflow\|build\|nf_core.egg-info\|log.txt\|Makefile') - YAML: + Prettier: runs-on: ubuntu-latest steps: - - name: Checkout - uses: actions/checkout@master - - name: 'Yamllint' - uses: karancode/yamllint-github-action@master - with: - yamllint_file_or_dir: '.' - yamllint_config_filepath: '.yamllint.yml' - - # If the above check failed, post a comment on the PR explaining the failure - - name: Post PR comment - if: failure() - uses: mshick/add-pr-comment@v1 - with: - message: | - ## YAML linting is failing - - To keep the code consistent with lots of contributors, we run automated code consistency checks. - To fix this CI test, please run: - - * Install `yamllint` - * Install `yamllint` following [this](https://yamllint.readthedocs.io/en/stable/quickstart.html#installing-yamllint) - instructions or alternative install it in your [conda environment](https://anaconda.org/conda-forge/yamllint) - * Fix the markdown errors - * Run the test locally: `yamllint $(find . -type f -name "*.yml" -o -name "*.yaml") -c ./.yamllint.yml` - * Fix any reported errors in your YAML files + - uses: actions/checkout@v2 - Once you push these changes the test should pass, and you can hide this comment :+1: + - uses: actions/setup-node@v2 - We highly recommend setting up yaml-lint in your code editor so that this formatting is done automatically on save. Ask about it on Slack for help! + - name: Install Prettier + run: npm install -g prettier - Thanks again for your contribution! - repo-token: ${{ secrets.GITHUB_TOKEN }} - allow-repeats: false + - name: Run Prettier --check + run: prettier --check ${GITHUB_WORKSPACE} nf-core: runs-on: ubuntu-latest steps: - - name: Check out pipeline code uses: actions/checkout@v2 @@ -110,8 +50,8 @@ jobs: - uses: actions/setup-python@v1 with: - python-version: '3.6' - architecture: 'x64' + python-version: "3.6" + architecture: "x64" - name: Install dependencies run: | @@ -139,3 +79,4 @@ jobs: lint_results.md PR_number.txt +# diff --git a/.github/workflows/linting_comment.yml b/.github/workflows/linting_comment.yml index 44d72994..91c487a1 100644 --- a/.github/workflows/linting_comment.yml +++ b/.github/workflows/linting_comment.yml @@ -1,4 +1,3 @@ - name: nf-core linting comment # This workflow is triggered after the linting action is complete # It posts an automated comment to the PR, even if the PR is coming from a fork @@ -27,4 +26,4 @@ jobs: GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} number: ${{ steps.pr_number.outputs.pr_number }} path: linting-logs/lint_results.md - +# diff --git a/.gitpod.yml b/.gitpod.yml index b7d4cee1..c452ee93 100644 --- a/.gitpod.yml +++ b/.gitpod.yml @@ -2,13 +2,13 @@ image: nfcore/gitpod:latest vscode: extensions: # based on nf-core.nf-core-extensionpack - - codezombiech.gitignore # Language support for .gitignore files + - codezombiech.gitignore # Language support for .gitignore files # - cssho.vscode-svgviewer # SVG viewer - - davidanson.vscode-markdownlint # Markdown/CommonMark linting and style checking for Visual Studio Code - - eamodio.gitlens # Quickly glimpse into whom, why, and when a line or code block was changed - - EditorConfig.EditorConfig # override user/workspace settings with settings found in .editorconfig files - - Gruntfuggly.todo-tree # Display TODO and FIXME in a tree view in the activity bar - - mechatroner.rainbow-csv # Highlight columns in csv files in different colors + - davidanson.vscode-markdownlint # Markdown/CommonMark linting and style checking for Visual Studio Code + - eamodio.gitlens # Quickly glimpse into whom, why, and when a line or code block was changed + - EditorConfig.EditorConfig # override user/workspace settings with settings found in .editorconfig files + - Gruntfuggly.todo-tree # Display TODO and FIXME in a tree view in the activity bar + - mechatroner.rainbow-csv # Highlight columns in csv files in different colors # - nextflow.nextflow # Nextflow syntax highlighting - - oderwat.indent-rainbow # Highlight indentation level - - streetsidesoftware.code-spell-checker # Spelling checker for source code + - oderwat.indent-rainbow # Highlight indentation level + - streetsidesoftware.code-spell-checker # Spelling checker for source code diff --git a/.markdownlint.yml b/.markdownlint.yml deleted file mode 100644 index 9e605fcf..00000000 --- a/.markdownlint.yml +++ /dev/null @@ -1,14 +0,0 @@ -# Markdownlint configuration file -default: true -line-length: false -ul-indent: - indent: 4 -no-duplicate-header: - siblings_only: true -no-inline-html: - allowed_elements: - - img - - p - - kbd - - details - - summary diff --git a/.prettierrc.yml b/.prettierrc.yml new file mode 100644 index 00000000..c81f9a76 --- /dev/null +++ b/.prettierrc.yml @@ -0,0 +1 @@ +printWidth: 120 diff --git a/.yamllint.yml b/.yamllint.yml deleted file mode 100644 index d466deec..00000000 --- a/.yamllint.yml +++ /dev/null @@ -1,6 +0,0 @@ -extends: default - -rules: - document-start: disable - line-length: disable - truthy: disable diff --git a/CHANGELOG.md b/CHANGELOG.md index 0803027f..0f46b560 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -11,6 +11,8 @@ Initial release of nf-core/mag, created with the [nf-core](https://nf-co.re/) te ### `Fixed` +- Clarified conda usage and added an installation tutorial for Singularity since the one on Syllabs' website uses an outdate version of GO Compiler + ### `Dependencies` ### `Deprecated` diff --git a/CITATIONS.md b/CITATIONS.md index 256b0739..f6921e00 100644 --- a/CITATIONS.md +++ b/CITATIONS.md @@ -10,23 +10,26 @@ ## Pipeline tools -* [FastQC](https://www.bioinformatics.babraham.ac.uk/projects/fastqc/) +- [FastQC](https://www.bioinformatics.babraham.ac.uk/projects/fastqc/) -* [MultiQC](https://pubmed.ncbi.nlm.nih.gov/27312411/) - > Ewels P, Magnusson M, Lundin S, Käller M. MultiQC: summarize analysis results for multiple tools and samples in a single report. Bioinformatics. 2016 Oct 1;32(19):3047-8. doi: 10.1093/bioinformatics/btw354. Epub 2016 Jun 16. PubMed PMID: 27312411; PubMed Central PMCID: PMC5039924. +- [MultiQC](https://pubmed.ncbi.nlm.nih.gov/27312411/) + > Ewels P, Magnusson M, Lundin S, Käller M. MultiQC: summarize analysis results for multiple tools and samples in a single report. Bioinformatics. 2016 Oct 1;32(19):3047-8. doi: 10.1093/bioinformatics/btw354. Epub 2016 Jun 16. PubMed PMID: 27312411; PubMed Central PMCID: PMC5039924. ## Software packaging/containerisation tools -* [Anaconda](https://anaconda.com) - > Anaconda Software Distribution. Computer software. Vers. 2-2.4.0. Anaconda, Nov. 2016. Web. +- [Anaconda](https://anaconda.com) -* [Bioconda](https://pubmed.ncbi.nlm.nih.gov/29967506/) - > Grüning B, Dale R, Sjödin A, Chapman BA, Rowe J, Tomkins-Tinch CH, Valieris R, Köster J; Bioconda Team. Bioconda: sustainable and comprehensive software distribution for the life sciences. Nat Methods. 2018 Jul;15(7):475-476. doi: 10.1038/s41592-018-0046-7. PubMed PMID: 29967506. + > Anaconda Software Distribution. Computer software. Vers. 2-2.4.0. Anaconda, Nov. 2016. Web. -* [BioContainers](https://pubmed.ncbi.nlm.nih.gov/28379341/) - > da Veiga Leprevost F, Grüning B, Aflitos SA, Röst HL, Uszkoreit J, Barsnes H, Vaudel M, Moreno P, Gatto L, Weber J, Bai M, Jimenez RC, Sachsenberg T, Pfeuffer J, Alvarez RV, Griss J, Nesvizhskii AI, Perez-Riverol Y. BioContainers: an open-source and community-driven framework for software standardization. Bioinformatics. 2017 Aug 15;33(16):2580-2582. doi: 10.1093/bioinformatics/btx192. PubMed PMID: 28379341; PubMed Central PMCID: PMC5870671. +- [Bioconda](https://pubmed.ncbi.nlm.nih.gov/29967506/) -* [Docker](https://dl.acm.org/doi/10.5555/2600239.2600241) + > Grüning B, Dale R, Sjödin A, Chapman BA, Rowe J, Tomkins-Tinch CH, Valieris R, Köster J; Bioconda Team. Bioconda: sustainable and comprehensive software distribution for the life sciences. Nat Methods. 2018 Jul;15(7):475-476. doi: 10.1038/s41592-018-0046-7. PubMed PMID: 29967506. -* [Singularity](https://pubmed.ncbi.nlm.nih.gov/28494014/) - > Kurtzer GM, Sochat V, Bauer MW. Singularity: Scientific containers for mobility of compute. PLoS One. 2017 May 11;12(5):e0177459. doi: 10.1371/journal.pone.0177459. eCollection 2017. PubMed PMID: 28494014; PubMed Central PMCID: PMC5426675. +- [BioContainers](https://pubmed.ncbi.nlm.nih.gov/28379341/) + + > da Veiga Leprevost F, Grüning B, Aflitos SA, Röst HL, Uszkoreit J, Barsnes H, Vaudel M, Moreno P, Gatto L, Weber J, Bai M, Jimenez RC, Sachsenberg T, Pfeuffer J, Alvarez RV, Griss J, Nesvizhskii AI, Perez-Riverol Y. BioContainers: an open-source and community-driven framework for software standardization. Bioinformatics. 2017 Aug 15;33(16):2580-2582. doi: 10.1093/bioinformatics/btx192. PubMed PMID: 28379341; PubMed Central PMCID: PMC5870671. + +- [Docker](https://dl.acm.org/doi/10.5555/2600239.2600241) + +- [Singularity](https://pubmed.ncbi.nlm.nih.gov/28494014/) + > Kurtzer GM, Sochat V, Bauer MW. Singularity: Scientific containers for mobility of compute. PLoS One. 2017 May 11;12(5):e0177459. doi: 10.1371/journal.pone.0177459. eCollection 2017. PubMed PMID: 28494014; PubMed Central PMCID: PMC5426675. diff --git a/README.md b/README.md index 39f3d98e..8819a575 100644 --- a/README.md +++ b/README.md @@ -1,4 +1,4 @@ -# ![nf-core/mag](docs/images/nf-core-mag_logo_light.png#gh-light-mode-only) ![nf-core/mag](docs/images/nf-core-mag_logo_dark.png#gh-dark-mode-only) +# ![nf-core/mag](docs/images/nf-core/mag_logo_light.png#gh-light-mode-only) ![nf-core/mag](docs/images/nf-core/mag_logo_dark.png#gh-dark-mode-only) [![GitHub Actions CI Status](https://github.com/nf-core/mag/workflows/nf-core%20CI/badge.svg)](https://github.com/nf-core/mag/actions?query=workflow%3A%22nf-core+CI%22) [![GitHub Actions Linting Status](https://github.com/nf-core/mag/workflows/nf-core%20linting/badge.svg)](https://github.com/nf-core/mag/actions?query=workflow%3A%22nf-core+linting%22) @@ -17,11 +17,13 @@ ## Introduction + **nf-core/mag** is a bioinformatics best-practice analysis pipeline for Assembly, binning and annotation of metagenomes. The pipeline is built using [Nextflow](https://www.nextflow.io), a workflow tool to run tasks across multiple compute infrastructures in a very portable manner. It uses Docker/Singularity containers making installation trivial and results highly reproducible. The [Nextflow DSL2](https://www.nextflow.io/docs/latest/dsl2.html) implementation of this pipeline uses one container per process which makes it much easier to maintain and update software dependencies. Where possible, these processes have been submitted to and installed from [nf-core/modules](https://github.com/nf-core/modules) in order to make them available to all nf-core pipelines, and to everyone within the Nextflow community! + On release, automated continuous integration tests run the pipeline on a full-sized dataset on the AWS cloud infrastructure. This ensures that the pipeline runs on AWS, has sensible resource allocation defaults set to run on real-world datasets, and permits the persistent storage of results to benchmark between pipeline releases and other analysis sources. The results obtained from the full-sized test can be viewed on the [nf-core website](https://nf-co.re/mag/results). ## Pipeline summary @@ -35,28 +37,28 @@ On release, automated continuous integration tests run the pipeline on a full-si 1. Install [`Nextflow`](https://www.nextflow.io/docs/latest/getstarted.html#installation) (`>=21.10.3`) -2. Install any of [`Docker`](https://docs.docker.com/engine/installation/), [`Singularity`](https://www.sylabs.io/guides/3.0/user-guide/), [`Podman`](https://podman.io/), [`Shifter`](https://nersc.gitlab.io/development/shifter/how-to-use/) or [`Charliecloud`](https://hpc.github.io/charliecloud/) for full pipeline reproducibility _(please only use [`Conda`](https://conda.io/miniconda.html) as a last resort; see [docs](https://nf-co.re/usage/configuration#basic-configuration-profiles))_ +2. Install any of [`Docker`](https://docs.docker.com/engine/installation/), [`Singularity`](https://www.sylabs.io/guides/3.0/user-guide/) (you can follow [this tutorial](https://singularity-tutorial.github.io/01-installation/)), [`Podman`](https://podman.io/), [`Shifter`](https://nersc.gitlab.io/development/shifter/how-to-use/) or [`Charliecloud`](https://hpc.github.io/charliecloud/) for full pipeline reproducibility _(you can use [`Conda`](https://conda.io/miniconda.html) both to install Nextflow itself and also to manage software within pipelines. Please only use it within pipelines as a last resort; see [docs](https://nf-co.re/usage/configuration#basic-configuration-profiles))_. 3. Download the pipeline and test it on a minimal dataset with a single command: - ```console - nextflow run nf-core/mag -profile test,YOURPROFILE --outdir - ``` + ```console + nextflow run nf-core/mag -profile test,YOURPROFILE --outdir + ``` - Note that some form of configuration will be needed so that Nextflow knows how to fetch the required software. This is usually done in the form of a config profile (`YOURPROFILE` in the example command above). You can chain multiple config profiles in a comma-separated string. + Note that some form of configuration will be needed so that Nextflow knows how to fetch the required software. This is usually done in the form of a config profile (`YOURPROFILE` in the example command above). You can chain multiple config profiles in a comma-separated string. - > * The pipeline comes with config profiles called `docker`, `singularity`, `podman`, `shifter`, `charliecloud` and `conda` which instruct the pipeline to use the named tool for software management. For example, `-profile test,docker`. - > * Please check [nf-core/configs](https://github.com/nf-core/configs#documentation) to see if a custom config file to run nf-core pipelines already exists for your Institute. If so, you can simply use `-profile ` in your command. This will enable either `docker` or `singularity` and set the appropriate execution settings for your local compute environment. - > * If you are using `singularity`, please use the [`nf-core download`](https://nf-co.re/tools/#downloading-pipelines-for-offline-use) command to download images first, before running the pipeline. Setting the [`NXF_SINGULARITY_CACHEDIR` or `singularity.cacheDir`](https://www.nextflow.io/docs/latest/singularity.html?#singularity-docker-hub) Nextflow options enables you to store and re-use the images from a central location for future pipeline runs. - > * If you are using `conda`, it is highly recommended to use the [`NXF_CONDA_CACHEDIR` or `conda.cacheDir`](https://www.nextflow.io/docs/latest/conda.html) settings to store the environments in a central location for future pipeline runs. + > - The pipeline comes with config profiles called `docker`, `singularity`, `podman`, `shifter`, `charliecloud` and `conda` which instruct the pipeline to use the named tool for software management. For example, `-profile test,docker`. + > - Please check [nf-core/configs](https://github.com/nf-core/configs#documentation) to see if a custom config file to run nf-core pipelines already exists for your Institute. If so, you can simply use `-profile ` in your command. This will enable either `docker` or `singularity` and set the appropriate execution settings for your local compute environment. + > - If you are using `singularity`, please use the [`nf-core download`](https://nf-co.re/tools/#downloading-pipelines-for-offline-use) command to download images first, before running the pipeline. Setting the [`NXF_SINGULARITY_CACHEDIR` or `singularity.cacheDir`](https://www.nextflow.io/docs/latest/singularity.html?#singularity-docker-hub) Nextflow options enables you to store and re-use the images from a central location for future pipeline runs. + > - If you are using `conda`, it is highly recommended to use the [`NXF_CONDA_CACHEDIR` or `conda.cacheDir`](https://www.nextflow.io/docs/latest/conda.html) settings to store the environments in a central location for future pipeline runs. 4. Start running your own analysis! - + - ```console - nextflow run nf-core/mag --input samplesheet.csv --outdir --genome GRCh37 -profile - ``` + ```console + nextflow run nf-core/mag --input samplesheet.csv --outdir --genome GRCh37 -profile + ``` ## Documentation @@ -82,6 +84,7 @@ For further information or help, don't hesitate to get in touch on the [Slack `# + An extensive list of references for the tools used by the pipeline can be found in the [`CITATIONS.md`](CITATIONS.md) file. You can cite the `nf-core` publication as follows: diff --git a/assets/email_template.html b/assets/email_template.html index 13cdbf26..1563166a 100644 --- a/assets/email_template.html +++ b/assets/email_template.html @@ -1,53 +1,111 @@ - - - - + + + + - - nf-core/mag Pipeline Report - - -

+ + + nf-core/mag Pipeline Report + + +
+ - +

nf-core/mag v${version}

+

Run Name: $runName

-

nf-core/mag v${version}

-

Run Name: $runName

- -<% if (!success){ - out << """ -
-

nf-core/mag execution completed unsuccessfully!

+ <% if (!success){ out << """ +
+

nf-core/mag execution completed unsuccessfully!

The exit status of the task that caused the workflow execution to fail was: $exitStatus.

The full error message was:

- 
${errorReport}
-
- """ -} else { - out << """ -
+ 
${errorReport}
+
+ """ } else { out << """ +
nf-core/mag execution completed successfully! -
- """ -} -%> +
+ """ } %> -

The workflow was completed at $dateComplete (duration: $duration)

-

The command used to launch the workflow was as follows:

-
$commandLine
+

The workflow was completed at $dateComplete (duration: $duration)

+

The command used to launch the workflow was as follows:

+ 
+$commandLine
-

Pipeline Configuration:

- - - <% out << summary.collect{ k,v -> "" }.join("\n") %> - -
$k
$v
+

Pipeline Configuration:

+ + + <% out << summary.collect{ k,v -> " + + + + + " }.join("\n") %> + +
+ $k + + 
$v
+
-

nf-core/mag

-

https://github.com/nf-core/mag

- -
- - +

nf-core/mag

+

https://github.com/nf-core/mag

+
+ diff --git a/assets/multiqc_config.yaml b/assets/multiqc_config.yaml deleted file mode 100644 index 7b6b9073..00000000 --- a/assets/multiqc_config.yaml +++ /dev/null @@ -1,11 +0,0 @@ -report_comment: > - This report has been generated by the nf-core/mag - analysis pipeline. For information about how to interpret these results, please see the - documentation. -report_section_order: - software_versions: - order: -1000 - nf-core-mag-summary: - order: -1001 - -export_plots: true diff --git a/assets/multiqc_config.yml b/assets/multiqc_config.yml new file mode 100644 index 00000000..db2c548c --- /dev/null +++ b/assets/multiqc_config.yml @@ -0,0 +1,11 @@ +report_comment: > + This report has been generated by the nf-core/mag + analysis pipeline. For information about how to interpret these results, please see the + documentation. +report_section_order: + software_versions: + order: -1000 + "nf-core-mag-summary": + order: -1001 + +export_plots: true diff --git a/assets/schema_input.json b/assets/schema_input.json index 0091ae04..44d6d151 100644 --- a/assets/schema_input.json +++ b/assets/schema_input.json @@ -31,9 +31,6 @@ ] } }, - "required": [ - "sample", - "fastq_1" - ] + "required": ["sample", "fastq_1"] } } diff --git a/docs/README.md b/docs/README.md index 7b0a1c80..b1cbb97f 100644 --- a/docs/README.md +++ b/docs/README.md @@ -2,9 +2,9 @@ The nf-core/mag documentation is split into the following pages: -* [Usage](usage.md) - * An overview of how the pipeline works, how to run it and a description of all of the different command-line flags. -* [Output](output.md) - * An overview of the different results produced by the pipeline and how to interpret them. +- [Usage](usage.md) + - An overview of how the pipeline works, how to run it and a description of all of the different command-line flags. +- [Output](output.md) + - An overview of the different results produced by the pipeline and how to interpret them. You can find a lot more documentation about installing, configuring and running nf-core pipelines on the website: [https://nf-co.re](https://nf-co.re) diff --git a/docs/output.md b/docs/output.md index a2782c16..9efc681c 100644 --- a/docs/output.md +++ b/docs/output.md @@ -12,18 +12,18 @@ The directories listed below will be created in the results directory after the The pipeline is built using [Nextflow](https://www.nextflow.io/) and processes data using the following steps: -* [FastQC](#fastqc) - Raw read QC -* [MultiQC](#multiqc) - Aggregate report describing results and QC from the whole pipeline -* [Pipeline information](#pipeline-information) - Report metrics generated during the workflow execution +- [FastQC](#fastqc) - Raw read QC +- [MultiQC](#multiqc) - Aggregate report describing results and QC from the whole pipeline +- [Pipeline information](#pipeline-information) - Report metrics generated during the workflow execution ### FastQC
Output files -* `fastqc/` - * `*_fastqc.html`: FastQC report containing quality metrics. - * `*_fastqc.zip`: Zip archive containing the FastQC report, tab-delimited data file and plot images. +- `fastqc/` + - `*_fastqc.html`: FastQC report containing quality metrics. + - `*_fastqc.zip`: Zip archive containing the FastQC report, tab-delimited data file and plot images.
@@ -42,10 +42,10 @@ The pipeline is built using [Nextflow](https://www.nextflow.io/) and processes d
Output files -* `multiqc/` - * `multiqc_report.html`: a standalone HTML file that can be viewed in your web browser. - * `multiqc_data/`: directory containing parsed statistics from the different tools used in the pipeline. - * `multiqc_plots/`: directory containing static images from the report in various formats. +- `multiqc/` + - `multiqc_report.html`: a standalone HTML file that can be viewed in your web browser. + - `multiqc_data/`: directory containing parsed statistics from the different tools used in the pipeline. + - `multiqc_plots/`: directory containing static images from the report in various formats.
@@ -58,10 +58,10 @@ Results generated by MultiQC collate pipeline QC from supported tools e.g. FastQ
Output files -* `pipeline_info/` - * Reports generated by Nextflow: `execution_report.html`, `execution_timeline.html`, `execution_trace.txt` and `pipeline_dag.dot`/`pipeline_dag.svg`. - * Reports generated by the pipeline: `pipeline_report.html`, `pipeline_report.txt` and `software_versions.yml`. The `pipeline_report*` files will only be present if the `--email` / `--email_on_fail` parameter's are used when running the pipeline. - * Reformatted samplesheet files used as input to the pipeline: `samplesheet.valid.csv`. +- `pipeline_info/` + - Reports generated by Nextflow: `execution_report.html`, `execution_timeline.html`, `execution_trace.txt` and `pipeline_dag.dot`/`pipeline_dag.svg`. + - Reports generated by the pipeline: `pipeline_report.html`, `pipeline_report.txt` and `software_versions.yml`. The `pipeline_report*` files will only be present if the `--email` / `--email_on_fail` parameter's are used when running the pipeline. + - Reformatted samplesheet files used as input to the pipeline: `samplesheet.valid.csv`.
diff --git a/docs/usage.md b/docs/usage.md index 0cb8bd3f..81b33493 100644 --- a/docs/usage.md +++ b/docs/usage.md @@ -44,11 +44,11 @@ TREATMENT_REP3,AEG588A6_S6_L003_R1_001.fastq.gz, TREATMENT_REP3,AEG588A6_S6_L004_R1_001.fastq.gz, ``` -| Column | Description | -|----------------|----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------| -| `sample` | Custom sample name. This entry will be identical for multiple sequencing libraries/runs from the same sample. Spaces in sample names are automatically converted to underscores (`_`). | -| `fastq_1` | Full path to FastQ file for Illumina short reads 1. File has to be gzipped and have the extension ".fastq.gz" or ".fq.gz". | -| `fastq_2` | Full path to FastQ file for Illumina short reads 2. File has to be gzipped and have the extension ".fastq.gz" or ".fq.gz". | +| Column | Description | +| --------- | -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- | +| `sample` | Custom sample name. This entry will be identical for multiple sequencing libraries/runs from the same sample. Spaces in sample names are automatically converted to underscores (`_`). | +| `fastq_1` | Full path to FastQ file for Illumina short reads 1. File has to be gzipped and have the extension ".fastq.gz" or ".fq.gz". | +| `fastq_2` | Full path to FastQ file for Illumina short reads 2. File has to be gzipped and have the extension ".fastq.gz" or ".fq.gz". | An [example samplesheet](../assets/samplesheet.csv) has been provided with the pipeline. @@ -57,7 +57,7 @@ An [example samplesheet](../assets/samplesheet.csv) has been provided with the p The typical command for running the pipeline is as follows: ```console -nextflow run nf-core/mag --input samplesheet.csv --outdir --genome GRCh37 -profile docker +nextflow run nf-core/mag --input samplesheet.csv --outdir --genome GRCh37 -profile docker ``` This will launch the pipeline with the `docker` configuration profile. See below for more information about profiles. @@ -65,9 +65,9 @@ This will launch the pipeline with the `docker` configuration profile. See below Note that the pipeline will create the following files in your working directory: ```console -work # Directory containing the nextflow working files -results # Finished results (configurable, see below) -.nextflow_log # Log file from Nextflow +work # Directory containing the nextflow working files + # Finished results in specified location (defined with --outdir) +.nextflow_log # Log file from Nextflow # Other nextflow hidden files, eg. history of pipeline runs and old logs. ``` @@ -106,25 +106,25 @@ They are loaded in sequence, so later profiles can overwrite earlier profiles. If `-profile` is not specified, the pipeline will run locally and expect all software to be installed and available on the `PATH`. This is _not_ recommended. -* `docker` - * A generic configuration profile to be used with [Docker](https://docker.com/) -* `singularity` - * A generic configuration profile to be used with [Singularity](https://sylabs.io/docs/) -* `podman` - * A generic configuration profile to be used with [Podman](https://podman.io/) -* `shifter` - * A generic configuration profile to be used with [Shifter](https://nersc.gitlab.io/development/shifter/how-to-use/) -* `charliecloud` - * A generic configuration profile to be used with [Charliecloud](https://hpc.github.io/charliecloud/) -* `conda` - * A generic configuration profile to be used with [Conda](https://conda.io/docs/). Please only use Conda as a last resort i.e. when it's not possible to run the pipeline with Docker, Singularity, Podman, Shifter or Charliecloud. -* `test` - * A profile with a complete configuration for automated testing - * Includes links to test data so needs no other parameters +- `docker` + - A generic configuration profile to be used with [Docker](https://docker.com/) +- `singularity` + - A generic configuration profile to be used with [Singularity](https://sylabs.io/docs/) +- `podman` + - A generic configuration profile to be used with [Podman](https://podman.io/) +- `shifter` + - A generic configuration profile to be used with [Shifter](https://nersc.gitlab.io/development/shifter/how-to-use/) +- `charliecloud` + - A generic configuration profile to be used with [Charliecloud](https://hpc.github.io/charliecloud/) +- `conda` + - A generic configuration profile to be used with [Conda](https://conda.io/docs/). Please only use Conda as a last resort i.e. when it's not possible to run the pipeline with Docker, Singularity, Podman, Shifter or Charliecloud. +- `test` + - A profile with a complete configuration for automated testing + - Includes links to test data so needs no other parameters ### `-resume` -Specify this when restarting a pipeline. Nextflow will used cached results from any pipeline steps where the inputs are the same, continuing from where it got to previously. +Specify this when restarting a pipeline. Nextflow will use cached results from any pipeline steps where the inputs are the same, continuing from where it got to previously. For input to be considered the same, not only the names must be identical but the files' contents as well. For more info about this parameter, see [this blog post](https://www.nextflow.io/blog/2019/demystifying-nextflow-resume.html). You can also supply a run name to resume a specific run: `-resume [run-name]`. Use the `nextflow log` command to show previous run names. @@ -186,6 +186,7 @@ process { ``` > **NB:** We specify the full process name i.e. `NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:STAR_ALIGN` in the config file because this takes priority over the short name (`STAR_ALIGN`) and allows existing configuration using the full process name to be correctly overridden. +> > If you get a warning suggesting that the process selector isn't recognised check that the process name has been specified correctly. ### Updating containers @@ -196,35 +197,35 @@ The [Nextflow DSL2](https://www.nextflow.io/docs/latest/dsl2.html) implementatio 2. Find the latest version of the Biocontainer available on [Quay.io](https://quay.io/repository/biocontainers/pangolin?tag=latest&tab=tags) 3. Create the custom config accordingly: - * For Docker: - - ```nextflow - process { - withName: PANGOLIN { - container = 'quay.io/biocontainers/pangolin:3.0.5--pyhdfd78af_0' - } - } - ``` - - * For Singularity: - - ```nextflow - process { - withName: PANGOLIN { - container = 'https://depot.galaxyproject.org/singularity/pangolin:3.0.5--pyhdfd78af_0' - } - } - ``` - - * For Conda: - - ```nextflow - process { - withName: PANGOLIN { - conda = 'bioconda::pangolin=3.0.5' - } - } - ``` + - For Docker: + + ```nextflow + process { + withName: PANGOLIN { + container = 'quay.io/biocontainers/pangolin:3.0.5--pyhdfd78af_0' + } + } + ``` + + - For Singularity: + + ```nextflow + process { + withName: PANGOLIN { + container = 'https://depot.galaxyproject.org/singularity/pangolin:3.0.5--pyhdfd78af_0' + } + } + ``` + + - For Conda: + + ```nextflow + process { + withName: PANGOLIN { + conda = 'bioconda::pangolin=3.0.5' + } + } + ``` > **NB:** If you wish to periodically update individual tool-specific results (e.g. Pangolin) generated by the pipeline then you must ensure to keep the `work/` directory otherwise the `-resume` ability of the pipeline will be compromised and it will restart from scratch. diff --git a/modules.json b/modules.json index 6394e068..1768fed6 100644 --- a/modules.json +++ b/modules.json @@ -4,14 +4,14 @@ "repos": { "nf-core/modules": { "custom/dumpsoftwareversions": { - "git_sha": "20d8250d9f39ddb05dfb437603aaf99b5c0b2b41" + "git_sha": "e745e167c1020928ef20ea1397b6b4d230681b4d" }, "fastqc": { - "git_sha": "9d0cad583b9a71a6509b754fdf589cbfbed08961" + "git_sha": "e745e167c1020928ef20ea1397b6b4d230681b4d" }, "multiqc": { - "git_sha": "20d8250d9f39ddb05dfb437603aaf99b5c0b2b41" + "git_sha": "e745e167c1020928ef20ea1397b6b4d230681b4d" } } } -} \ No newline at end of file +} diff --git a/modules/nf-core/modules/custom/dumpsoftwareversions/main.nf b/modules/nf-core/modules/custom/dumpsoftwareversions/main.nf index 934bb467..327d5100 100644 --- a/modules/nf-core/modules/custom/dumpsoftwareversions/main.nf +++ b/modules/nf-core/modules/custom/dumpsoftwareversions/main.nf @@ -15,6 +15,9 @@ process CUSTOM_DUMPSOFTWAREVERSIONS { path "software_versions_mqc.yml", emit: mqc_yml path "versions.yml" , emit: versions + when: + task.ext.when == null || task.ext.when + script: def args = task.ext.args ?: '' template 'dumpsoftwareversions.py' diff --git a/modules/nf-core/modules/custom/dumpsoftwareversions/meta.yml b/modules/nf-core/modules/custom/dumpsoftwareversions/meta.yml index 5b5b8a60..60b546a0 100644 --- a/modules/nf-core/modules/custom/dumpsoftwareversions/meta.yml +++ b/modules/nf-core/modules/custom/dumpsoftwareversions/meta.yml @@ -8,7 +8,7 @@ tools: description: Custom module used to dump software versions within the nf-core pipeline template homepage: https://github.com/nf-core/tools documentation: https://github.com/nf-core/tools - licence: ['MIT'] + licence: ["MIT"] input: - versions: type: file diff --git a/modules/nf-core/modules/fastqc/main.nf b/modules/nf-core/modules/fastqc/main.nf index d250eca0..ed6b8c50 100644 --- a/modules/nf-core/modules/fastqc/main.nf +++ b/modules/nf-core/modules/fastqc/main.nf @@ -15,6 +15,9 @@ process FASTQC { tuple val(meta), path("*.zip") , emit: zip path "versions.yml" , emit: versions + when: + task.ext.when == null || task.ext.when + script: def args = task.ext.args ?: '' // Add soft-links to original FastQs for consistent naming in pipeline diff --git a/modules/nf-core/modules/fastqc/meta.yml b/modules/nf-core/modules/fastqc/meta.yml index b09553a3..4da5bb5a 100644 --- a/modules/nf-core/modules/fastqc/meta.yml +++ b/modules/nf-core/modules/fastqc/meta.yml @@ -1,52 +1,52 @@ name: fastqc description: Run FastQC on sequenced reads keywords: - - quality control - - qc - - adapters - - fastq + - quality control + - qc + - adapters + - fastq tools: - - fastqc: - description: | - FastQC gives general quality metrics about your reads. - It provides information about the quality score distribution - across your reads, the per base sequence content (%A/C/G/T). - You get information about adapter contamination and other - overrepresented sequences. - homepage: https://www.bioinformatics.babraham.ac.uk/projects/fastqc/ - documentation: https://www.bioinformatics.babraham.ac.uk/projects/fastqc/Help/ - licence: ['GPL-2.0-only'] + - fastqc: + description: | + FastQC gives general quality metrics about your reads. + It provides information about the quality score distribution + across your reads, the per base sequence content (%A/C/G/T). + You get information about adapter contamination and other + overrepresented sequences. + homepage: https://www.bioinformatics.babraham.ac.uk/projects/fastqc/ + documentation: https://www.bioinformatics.babraham.ac.uk/projects/fastqc/Help/ + licence: ["GPL-2.0-only"] input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - reads: - type: file - description: | - List of input FastQ files of size 1 and 2 for single-end and paired-end data, - respectively. + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - reads: + type: file + description: | + List of input FastQ files of size 1 and 2 for single-end and paired-end data, + respectively. output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - html: - type: file - description: FastQC report - pattern: "*_{fastqc.html}" - - zip: - type: file - description: FastQC report archive - pattern: "*_{fastqc.zip}" - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - html: + type: file + description: FastQC report + pattern: "*_{fastqc.html}" + - zip: + type: file + description: FastQC report archive + pattern: "*_{fastqc.zip}" + - versions: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - - "@drpatelh" - - "@grst" - - "@ewels" - - "@FelixKrueger" + - "@drpatelh" + - "@grst" + - "@ewels" + - "@FelixKrueger" diff --git a/modules/nf-core/modules/multiqc/main.nf b/modules/nf-core/modules/multiqc/main.nf index 3dceb162..1264aac1 100644 --- a/modules/nf-core/modules/multiqc/main.nf +++ b/modules/nf-core/modules/multiqc/main.nf @@ -1,10 +1,10 @@ process MULTIQC { label 'process_medium' - conda (params.enable_conda ? 'bioconda::multiqc=1.11' : null) + conda (params.enable_conda ? 'bioconda::multiqc=1.12' : null) container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/multiqc:1.11--pyhdfd78af_0' : - 'quay.io/biocontainers/multiqc:1.11--pyhdfd78af_0' }" + 'https://depot.galaxyproject.org/singularity/multiqc:1.12--pyhdfd78af_0' : + 'quay.io/biocontainers/multiqc:1.12--pyhdfd78af_0' }" input: path multiqc_files @@ -15,6 +15,9 @@ process MULTIQC { path "*_plots" , optional:true, emit: plots path "versions.yml" , emit: versions + when: + task.ext.when == null || task.ext.when + script: def args = task.ext.args ?: '' """ diff --git a/modules/nf-core/modules/multiqc/meta.yml b/modules/nf-core/modules/multiqc/meta.yml index 63c75a45..6fa891ef 100644 --- a/modules/nf-core/modules/multiqc/meta.yml +++ b/modules/nf-core/modules/multiqc/meta.yml @@ -1,40 +1,40 @@ name: MultiQC description: Aggregate results from bioinformatics analyses across many samples into a single report keywords: - - QC - - bioinformatics tools - - Beautiful stand-alone HTML report + - QC + - bioinformatics tools + - Beautiful stand-alone HTML report tools: - - multiqc: - description: | - MultiQC searches a given directory for analysis logs and compiles a HTML report. - It's a general use tool, perfect for summarising the output from numerous bioinformatics tools. - homepage: https://multiqc.info/ - documentation: https://multiqc.info/docs/ - licence: ['GPL-3.0-or-later'] + - multiqc: + description: | + MultiQC searches a given directory for analysis logs and compiles a HTML report. + It's a general use tool, perfect for summarising the output from numerous bioinformatics tools. + homepage: https://multiqc.info/ + documentation: https://multiqc.info/docs/ + licence: ["GPL-3.0-or-later"] input: - - multiqc_files: - type: file - description: | - List of reports / files recognised by MultiQC, for example the html and zip output of FastQC + - multiqc_files: + type: file + description: | + List of reports / files recognised by MultiQC, for example the html and zip output of FastQC output: - - report: - type: file - description: MultiQC report file - pattern: "multiqc_report.html" - - data: - type: dir - description: MultiQC data dir - pattern: "multiqc_data" - - plots: - type: file - description: Plots created by MultiQC - pattern: "*_data" - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - report: + type: file + description: MultiQC report file + pattern: "multiqc_report.html" + - data: + type: dir + description: MultiQC data dir + pattern: "multiqc_data" + - plots: + type: file + description: Plots created by MultiQC + pattern: "*_data" + - versions: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - - "@abhi18av" - - "@bunop" - - "@drpatelh" + - "@abhi18av" + - "@bunop" + - "@drpatelh" diff --git a/nextflow_schema.json b/nextflow_schema.json index bc78304a..2721a11e 100644 --- a/nextflow_schema.json +++ b/nextflow_schema.json @@ -10,10 +10,7 @@ "type": "object", "fa_icon": "fas fa-terminal", "description": "Define where the pipeline should find input data and save output data.", - "required": [ - "input", - "outdir" - ], + "required": ["input", "outdir"], "properties": { "input": { "type": "string", @@ -185,14 +182,7 @@ "description": "Method used to save pipeline results to output directory.", "help_text": "The Nextflow `publishDir` option specifies which intermediate files should be saved to the output directory. This option tells the pipeline what method should be used to move these files. See [Nextflow docs](https://www.nextflow.io/docs/latest/process.html#publishdir) for details.", "fa_icon": "fas fa-copy", - "enum": [ - "symlink", - "rellink", - "link", - "copy", - "copyNoFollow", - "move" - ], + "enum": ["symlink", "rellink", "link", "copy", "copyNoFollow", "move"], "hidden": true }, "email_on_fail": { diff --git a/workflows/mag.nf b/workflows/mag.nf index 9dc9e53a..9a755509 100644 --- a/workflows/mag.nf +++ b/workflows/mag.nf @@ -23,7 +23,7 @@ if (params.input) { ch_input = file(params.input) } else { exit 1, 'Input sample ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ */ -ch_multiqc_config = file("$projectDir/assets/multiqc_config.yaml", checkIfExists: true) +ch_multiqc_config = file("$projectDir/assets/multiqc_config.yml", checkIfExists: true) ch_multiqc_custom_config = params.multiqc_config ? Channel.fromPath(params.multiqc_config) : Channel.empty() /* From 2e5470068dce48562d76fba2d162ca7025c4665e Mon Sep 17 00:00:00 2001 From: nf-core-bot Date: Thu, 24 Mar 2022 11:40:39 +0000 Subject: [PATCH 3/3] Template update for nf-core/tools version 2.3.2 --- .github/PULL_REQUEST_TEMPLATE.md | 1 - .github/workflows/awsfulltest.yml | 2 -- .github/workflows/awstest.yml | 2 -- .gitpod.yml | 2 +- CHANGELOG.md | 2 -- 5 files changed, 1 insertion(+), 8 deletions(-) diff --git a/.github/PULL_REQUEST_TEMPLATE.md b/.github/PULL_REQUEST_TEMPLATE.md index 1e68020b..89c37cb4 100644 --- a/.github/PULL_REQUEST_TEMPLATE.md +++ b/.github/PULL_REQUEST_TEMPLATE.md @@ -10,7 +10,6 @@ Remember that PRs should be made against the dev branch, unless you're preparing Learn more about contributing: [CONTRIBUTING.md](https://github.com/nf-core/mag/tree/master/.github/CONTRIBUTING.md) --> - ## PR checklist diff --git a/.github/workflows/awsfulltest.yml b/.github/workflows/awsfulltest.yml index b74d2047..414181d9 100644 --- a/.github/workflows/awsfulltest.yml +++ b/.github/workflows/awsfulltest.yml @@ -22,8 +22,6 @@ jobs: workspace_id: ${{ secrets.TOWER_WORKSPACE_ID }} access_token: ${{ secrets.TOWER_ACCESS_TOKEN }} compute_env: ${{ secrets.TOWER_COMPUTE_ENV }} - pipeline: ${{ github.repository }} - revision: ${{ github.sha }} workdir: s3://${{ secrets.AWS_S3_BUCKET }}/work/mag/work-${{ github.sha }} parameters: | { diff --git a/.github/workflows/awstest.yml b/.github/workflows/awstest.yml index f4aff861..c277a5cb 100644 --- a/.github/workflows/awstest.yml +++ b/.github/workflows/awstest.yml @@ -17,8 +17,6 @@ jobs: workspace_id: ${{ secrets.TOWER_WORKSPACE_ID }} access_token: ${{ secrets.TOWER_ACCESS_TOKEN }} compute_env: ${{ secrets.TOWER_COMPUTE_ENV }} - pipeline: ${{ github.repository }} - revision: ${{ github.sha }} workdir: s3://${{ secrets.AWS_S3_BUCKET }}/work/mag/work-${{ github.sha }} parameters: | { diff --git a/.gitpod.yml b/.gitpod.yml index c452ee93..85d95ecc 100644 --- a/.gitpod.yml +++ b/.gitpod.yml @@ -4,7 +4,7 @@ vscode: extensions: # based on nf-core.nf-core-extensionpack - codezombiech.gitignore # Language support for .gitignore files # - cssho.vscode-svgviewer # SVG viewer - - davidanson.vscode-markdownlint # Markdown/CommonMark linting and style checking for Visual Studio Code + - esbenp.prettier-vscode # Markdown/CommonMark linting and style checking for Visual Studio Code - eamodio.gitlens # Quickly glimpse into whom, why, and when a line or code block was changed - EditorConfig.EditorConfig # override user/workspace settings with settings found in .editorconfig files - Gruntfuggly.todo-tree # Display TODO and FIXME in a tree view in the activity bar diff --git a/CHANGELOG.md b/CHANGELOG.md index 0f46b560..0803027f 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -11,8 +11,6 @@ Initial release of nf-core/mag, created with the [nf-core](https://nf-co.re/) te ### `Fixed` -- Clarified conda usage and added an installation tutorial for Singularity since the one on Syllabs' website uses an outdate version of GO Compiler - ### `Dependencies` ### `Deprecated`