From 2590a2e8903e5f58d7355b8e667217e063e84d7e Mon Sep 17 00:00:00 2001 From: Florian De Temmerman Date: Tue, 19 Sep 2023 14:54:44 +0200 Subject: [PATCH 1/7] fix: relative path resolving with remote paths without trailing slash --- subworkflows/local/input_check.nf | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/subworkflows/local/input_check.nf b/subworkflows/local/input_check.nf index 86304238..573c692c 100644 --- a/subworkflows/local/input_check.nf +++ b/subworkflows/local/input_check.nf @@ -139,8 +139,8 @@ def get_data_basedir(URI samplesheet, String input_basedir) { if (uri.getScheme() != null) { if (!uri.path.endsWith('/')) { def newUrl = new URI( - uri.getProtocol(), uri.getUserInfo(), uri.getHost(), - uri.getPort(), uri.getPath() + '/', url.getQuery(), url.getRef() + uri.getScheme(), uri.getUserInfo(), uri.getHost(), + uri.getPort(), uri.getPath() + '/', uri.getQuery(), uri.getFragment() ) return newUrl } From dcce5e41b69a2d560df4a3ec867d7f876ccf7566 Mon Sep 17 00:00:00 2001 From: Florian De Temmerman Date: Tue, 19 Sep 2023 14:55:21 +0200 Subject: [PATCH 2/7] fix: use nf-core/test-datasets for test.config --- conf/test.config | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/conf/test.config b/conf/test.config index 36c7feb5..e30c9238 100644 --- a/conf/test.config +++ b/conf/test.config @@ -23,8 +23,8 @@ params { max_memory = '6.GB' max_time = '6.h' - input = "https://raw.githubusercontent.com/pixelgentechnologies/test-datasets/pixelator/samplesheet/samplesheet.csv" - input_basedir = "s3://pixelgen-technologies-datasets/nf-core-pixelator/testdata/micro/" + input = "https://raw.githubusercontent.com/nf-core/test-datasets/pixelator/samplesheet/samplesheet.csv" + input_basedir = "https://raw.githubusercontent.com/nf-core/test-datasets/pixelator/testdata" multiplet_recovery = true min_size = 2 From 3f6097ceb269964c33eb6d60be64c77ebb2ec6f6 Mon Sep 17 00:00:00 2001 From: Florian De Temmerman Date: Tue, 19 Sep 2023 14:58:29 +0200 Subject: [PATCH 3/7] fix: use proper biocontainer tags --- modules/local/pixelator/collect_metadata.nf | 2 +- modules/local/pixelator/list_options.nf | 2 +- modules/local/pixelator/single-cell/amplicon/main.nf | 2 +- modules/local/pixelator/single-cell/analysis/main.nf | 2 +- modules/local/pixelator/single-cell/annotate/main.nf | 2 +- modules/local/pixelator/single-cell/collapse/main.nf | 2 +- modules/local/pixelator/single-cell/demux/main.nf | 2 +- modules/local/pixelator/single-cell/graph/main.nf | 2 +- modules/local/pixelator/single-cell/qc/main.nf | 2 +- modules/local/pixelator/single-cell/report/main.nf | 2 +- 10 files changed, 10 insertions(+), 10 deletions(-) diff --git a/modules/local/pixelator/collect_metadata.nf b/modules/local/pixelator/collect_metadata.nf index 0fe8eb7d..09e48e60 100644 --- a/modules/local/pixelator/collect_metadata.nf +++ b/modules/local/pixelator/collect_metadata.nf @@ -9,7 +9,7 @@ process PIXELATOR_COLLECT_METADATA { cache false conda "bioconda::pixelator=0.13.1" - container "biocontainers/pixelator:0.13.1" + container "biocontainers/pixelator:0.13.1--pyh7cba7a3_0" input: diff --git a/modules/local/pixelator/list_options.nf b/modules/local/pixelator/list_options.nf index 35582796..b7f59850 100644 --- a/modules/local/pixelator/list_options.nf +++ b/modules/local/pixelator/list_options.nf @@ -3,7 +3,7 @@ process PIXELATOR_LIST_OPTIONS { conda "bioconda::pixelator=0.13.1" - container "biocontainers/pixelator:0.13.1" + container "biocontainers/pixelator:0.13.1--pyh7cba7a3_0" output: path "design_options.txt" , emit: designs diff --git a/modules/local/pixelator/single-cell/amplicon/main.nf b/modules/local/pixelator/single-cell/amplicon/main.nf index 712dd6d0..f22d3fb6 100644 --- a/modules/local/pixelator/single-cell/amplicon/main.nf +++ b/modules/local/pixelator/single-cell/amplicon/main.nf @@ -4,7 +4,7 @@ process PIXELATOR_AMPLICON { conda "bioconda::pixelator=0.13.1" - container "biocontainers/pixelator:0.13.1" + container "biocontainers/pixelator:0.13.1--pyh7cba7a3_0" input: tuple val(meta), path(reads) diff --git a/modules/local/pixelator/single-cell/analysis/main.nf b/modules/local/pixelator/single-cell/analysis/main.nf index aa907662..6d80647e 100644 --- a/modules/local/pixelator/single-cell/analysis/main.nf +++ b/modules/local/pixelator/single-cell/analysis/main.nf @@ -4,7 +4,7 @@ process PIXELATOR_ANALYSIS { conda "bioconda::pixelator=0.13.1" - container "biocontainers/pixelator:0.13.1" + container "biocontainers/pixelator:0.13.1--pyh7cba7a3_0" input: tuple val(meta), path(data) diff --git a/modules/local/pixelator/single-cell/annotate/main.nf b/modules/local/pixelator/single-cell/annotate/main.nf index a211503f..d8d508e6 100644 --- a/modules/local/pixelator/single-cell/annotate/main.nf +++ b/modules/local/pixelator/single-cell/annotate/main.nf @@ -4,7 +4,7 @@ process PIXELATOR_ANNOTATE { conda "bioconda::pixelator=0.13.1" - container "biocontainers/pixelator:0.13.1" + container "biocontainers/pixelator:0.13.1--pyh7cba7a3_0" input: tuple val(meta), path(dataset), path(panel_file), val(panel) diff --git a/modules/local/pixelator/single-cell/collapse/main.nf b/modules/local/pixelator/single-cell/collapse/main.nf index 41aa7702..a29f2c5f 100644 --- a/modules/local/pixelator/single-cell/collapse/main.nf +++ b/modules/local/pixelator/single-cell/collapse/main.nf @@ -3,7 +3,7 @@ process PIXELATOR_COLLAPSE { label 'process_medium' conda "bioconda::pixelator=0.13.1" - container "biocontainers/pixelator:0.13.1" + container "biocontainers/pixelator:0.13.1--pyh7cba7a3_0" input: tuple val(meta), path(reads), path(panel_file), val(panel) diff --git a/modules/local/pixelator/single-cell/demux/main.nf b/modules/local/pixelator/single-cell/demux/main.nf index 2da35be7..68529e90 100644 --- a/modules/local/pixelator/single-cell/demux/main.nf +++ b/modules/local/pixelator/single-cell/demux/main.nf @@ -4,7 +4,7 @@ process PIXELATOR_DEMUX { conda "bioconda::pixelator=0.13.1" - container "biocontainers/pixelator:0.13.1" + container "biocontainers/pixelator:0.13.1--pyh7cba7a3_0" input: tuple val(meta), path(reads), path(panel_file), val(panel) diff --git a/modules/local/pixelator/single-cell/graph/main.nf b/modules/local/pixelator/single-cell/graph/main.nf index 04d85e6e..e1bef04d 100644 --- a/modules/local/pixelator/single-cell/graph/main.nf +++ b/modules/local/pixelator/single-cell/graph/main.nf @@ -4,7 +4,7 @@ process PIXELATOR_GRAPH { conda "bioconda::pixelator=0.13.1" - container "biocontainers/pixelator:0.13.1" + container "biocontainers/pixelator:0.13.1--pyh7cba7a3_0" input: tuple val(meta), path(edge_list) diff --git a/modules/local/pixelator/single-cell/qc/main.nf b/modules/local/pixelator/single-cell/qc/main.nf index b3888ef4..642ad660 100644 --- a/modules/local/pixelator/single-cell/qc/main.nf +++ b/modules/local/pixelator/single-cell/qc/main.nf @@ -4,7 +4,7 @@ process PIXELATOR_QC { conda "bioconda::pixelator=0.13.1" - container "biocontainers/pixelator:0.13.1" + container "biocontainers/pixelator:0.13.1--pyh7cba7a3_0" input: tuple val(meta), path(reads) diff --git a/modules/local/pixelator/single-cell/report/main.nf b/modules/local/pixelator/single-cell/report/main.nf index eea3d8b8..aa89d9d7 100644 --- a/modules/local/pixelator/single-cell/report/main.nf +++ b/modules/local/pixelator/single-cell/report/main.nf @@ -4,7 +4,7 @@ process PIXELATOR_REPORT { conda "bioconda::pixelator=0.13.1" - container "biocontainers/pixelator:0.13.1" + container "biocontainers/pixelator:0.13.1--pyh7cba7a3_0" input: tuple val(meta), path(panel_file), val(panel) From 417587552a0981164dd551f3004ee781491466ab Mon Sep 17 00:00:00 2001 From: Florian De Temmerman Date: Tue, 19 Sep 2023 16:10:18 +0200 Subject: [PATCH 4/7] chore: remove some TODO's, add CI status badges, update pixelgen.com link --- README.md | 33 +++------------------------------ 1 file changed, 3 insertions(+), 30 deletions(-) diff --git a/README.md b/README.md index 0ae1e855..ef9e6f57 100644 --- a/README.md +++ b/README.md @@ -1,5 +1,7 @@ # ![nf-core/pixelator](docs/images/nf-core-pixelator_logo_light.png#gh-light-mode-only) ![nf-core/pixelator](docs/images/nf-core-pixelator_logo_dark.png#gh-dark-mode-only) +[![nf-core CI](https://github.com/nf-core/pixelator/actions/workflows/ci.yml/badge.svg)](https://github.com/nf-core/pixelator/actions/workflows/ci.yml) +[![nf-core linting](https://github.com/nf-core/pixelator/actions/workflows/linting.yml/badge.svg)](https://github.com/nf-core/pixelator/actions/workflows/linting.yml) [![AWS CI](https://img.shields.io/badge/CI%20tests-full%20size-FF9900?labelColor=000000&logo=Amazon%20AWS)](https://nf-co.re/pixelator/results)[![Cite with Zenodo](http://img.shields.io/badge/DOI-10.5281/zenodo.XXXXXXX-1073c8?labelColor=000000)](https://doi.org/10.5281/zenodo.XXXXXXX) [![Nextflow](https://img.shields.io/badge/nextflow%20DSL2-%E2%89%A523.04.0-23aa62.svg)](https://www.nextflow.io/) @@ -12,22 +14,11 @@ ## Introduction - - **nf-core/pixelator** is a bioinformatics best-practice analysis pipeline for analysis of Molecular Pixelation assays. It takes a samplesheet as input and will process your data using `pixelator` to produce final antibody counts. - - ![](./docs/images/nf_core_pixelator_metromap.svg) - - 1. Build amplicon from input reads ([`pixelator amplicon`](https://github.com/PixelgenTechnologies/pixelator)) 2. Read QC and filtering, correctness of the pixel binding sequence sequences ([`pixelator preqc | pixelator adapterqc`](https://github.com/PixelgenTechnologies/pixelator)) 3. Assign a marker (barcode) to each read ([`pixelator demux`](https://github.com/PixelgenTechnologies/pixelator)) @@ -44,22 +35,6 @@ It takes a samplesheet as input and will process your data using `pixelator` to > to set-up Nextflow. Make sure to [test your setup](https://nf-co.re/docs/usage/introduction#how-to-run-a-pipeline) > with `-profile test` before running the workflow on actual data. - - First, prepare a samplesheet with your input data that looks as follows: `samplesheet.csv`: @@ -95,7 +70,7 @@ For more details about the output files and reports, please refer to the ## Credits -nf-core/pixelator was originally written for [Pixelgen Technologies AB](https://www.pixelgen.tech/) by: +nf-core/pixelator was originally written for [Pixelgen Technologies AB](https://www.pixelgen.com/) by: - Florian De Temmerman - Johan Dahlberg @@ -114,8 +89,6 @@ 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: From c3f5c31544cdfb789b43c338f69304cdce6f3279 Mon Sep 17 00:00:00 2001 From: Florian De Temmerman Date: Tue, 19 Sep 2023 16:18:38 +0200 Subject: [PATCH 5/7] chore: remove TODOs --- .github/workflows/awsfulltest.yml | 3 --- .github/workflows/ci.yml | 3 --- 2 files changed, 6 deletions(-) diff --git a/.github/workflows/awsfulltest.yml b/.github/workflows/awsfulltest.yml index 33799cac..d8a09749 100644 --- a/.github/workflows/awsfulltest.yml +++ b/.github/workflows/awsfulltest.yml @@ -15,9 +15,6 @@ jobs: steps: - name: Launch workflow via tower uses: seqeralabs/action-tower-launch@v2 - # 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/ci.yml b/.github/workflows/ci.yml index 33092acf..001aab7c 100644 --- a/.github/workflows/ci.yml +++ b/.github/workflows/ci.yml @@ -43,8 +43,5 @@ jobs: password: ${{ secrets.GITHUB_TOKEN }} - name: Run pipeline with test data - # TODO nf-core: You can customise CI pipeline run tests as required - # For example: adding multiple test runs with different parameters - # Remember that you can parallelise this by using strategy.matrix run: | nextflow run ${GITHUB_WORKSPACE} -profile test,docker --outdir ./results From 36b1c9e523e0b4830dda3842decda3d6fc2a75a9 Mon Sep 17 00:00:00 2001 From: Florian De Temmerman Date: Tue, 19 Sep 2023 16:23:26 +0200 Subject: [PATCH 6/7] chore: add mimetype to input --- nextflow_schema.json | 1 + 1 file changed, 1 insertion(+) diff --git a/nextflow_schema.json b/nextflow_schema.json index 71f0d8c0..c7b76423 100644 --- a/nextflow_schema.json +++ b/nextflow_schema.json @@ -16,6 +16,7 @@ "type": "string", "format": "file-path", "schema": "assets/schema_input.json", + "mimetype": "text/csv", "exists": true, "pattern": "^\\S+\\.(csv|tsv)$", "description": "Path to comma-separated file containing information about the samples in the experiment.", From 772489d218fba4fb35b8e8bbb071f5e5b4bc6832 Mon Sep 17 00:00:00 2001 From: Florian De Temmerman Date: Tue, 19 Sep 2023 16:27:24 +0200 Subject: [PATCH 7/7] chore: remove unused multiqc config file --- assets/methods_description_template.yml | 29 ------------------------- 1 file changed, 29 deletions(-) delete mode 100644 assets/methods_description_template.yml diff --git a/assets/methods_description_template.yml b/assets/methods_description_template.yml deleted file mode 100644 index 2b6ed3cd..00000000 --- a/assets/methods_description_template.yml +++ /dev/null @@ -1,29 +0,0 @@ -id: "nf-core-pixelator-methods-description" -description: "Suggested text and references to use when describing pipeline usage within the methods section of a publication." -section_name: "nf-core/pixelator Methods Description" -section_href: "https://github.com/nf-core/pixelator" -plot_type: "html" -## TODO nf-core: Update the HTML below to your preferred methods description, e.g. add publication citation for this pipeline -## You inject any metadata in the Nextflow '${workflow}' object -data: | -

Methods

-

Data was processed using nf-core/pixelator v${workflow.manifest.version} ${doi_text} of the nf-core collection of workflows (Ewels et al., 2020), utilising reproducible software environments from the Bioconda (Grüning et al., 2018) and Biocontainers (da Veiga Leprevost et al., 2017) projects.

-

The pipeline was executed with Nextflow v${workflow.nextflow.version} (Di Tommaso et al., 2017) with the following command:

- 
${workflow.commandLine}
-

${tool_citations}

-

References

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    -
  • Di Tommaso, P., Chatzou, M., Floden, E. W., Barja, P. P., Palumbo, E., & Notredame, C. (2017). Nextflow enables reproducible computational workflows. Nature Biotechnology, 35(4), 316-319. doi: 10.1038/nbt.3820
    • -
  • Ewels, P. A., Peltzer, A., Fillinger, S., Patel, H., Alneberg, J., Wilm, A., Garcia, M. U., Di Tommaso, P., & Nahnsen, S. (2020). The nf-core framework for community-curated bioinformatics pipelines. Nature Biotechnology, 38(3), 276-278. doi: 10.1038/s41587-020-0439-x
    • -
  • Grüning, B., Dale, R., Sjödin, A., Chapman, B. A., Rowe, J., Tomkins-Tinch, C. H., Valieris, R., Köster, J., & Bioconda Team. (2018). Bioconda: sustainable and comprehensive software distribution for the life sciences. Nature Methods, 15(7), 475–476. doi: 10.1038/s41592-018-0046-7
    • -
  • da Veiga Leprevost, F., Grüning, B. A., Alves Aflitos, S., Röst, H. L., Uszkoreit, J., Barsnes, H., Vaudel, M., Moreno, P., Gatto, L., Weber, J., Bai, M., Jimenez, R. C., Sachsenberg, T., Pfeuffer, J., Vera Alvarez, R., Griss, J., Nesvizhskii, A. I., & Perez-Riverol, Y. (2017). BioContainers: an open-source and community-driven framework for software standardization. Bioinformatics (Oxford, England), 33(16), 2580–2582. doi: 10.1093/bioinformatics/btx192
    • - ${tool_bibliography} -
-
-
Notes:
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    - ${nodoi_text} -
  • The command above does not include parameters contained in any configs or profiles that may have been used. Ensure the config file is also uploaded with your publication!
    • -
  • You should also cite all software used within this run. Check the "Software Versions" of this report to get version information.
    • -
-