diff --git a/CHANGELOG.md b/CHANGELOG.md index 21c5a73..3891aa3 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -5,12 +5,62 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 ## v1.0dev - [date] -Initial release of nf-core/reportho, created with the [nf-core](https://nf-co.re/) template. +Although its location and design may vary greatly, the mainsail is always a key source of propulsion for a ship. + +This is the initial release of nf-core/reportho, created with the [nf-core](https://nf-co.re/) template. + +### `Credits` + +The following people have made significant contributions to the release through design, development and review: + +- [Igor Trujnara](https://github.com/itrujnara) +- [Luisa Santus](https://github.com/luisas) +- [Jose Espinosa-Carrasco](https://github.com/JoseEspinosa) +- [Alessio Vignoli](https://github.com/alessiovignoli) + +We also thank everyone else from the nf-core community who has participated in planning and development. ### `Added` +The pipeline was created. In particular, it has the following features: + +- fetching of ortholog predictions from public databases, through APIs and from local snapshots +- systematic comparison of the predictions and calculation of comparison statistics +- creation of an ortholog list with user-defined criteria +- basic downstream analysis of the obtained ortholog list +- generation of a human-readable report + ### `Fixed` +Nothing yet. + ### `Dependencies` +The pipeline has the following notable dependencies: + +| Program | Version | +| --------------- | ------- | +| Python | 3.11.0 | +| Python Requests | 2.31.0 | +| Biopython | 1.83 | +| R | 4.3.3 | +| PyYAML | 5.4.1 | +| T-COFFEE | 13.46.0 | +| pigz | 2.8 | +| csvtk | 0.26.0 | +| Node | 21.6.2 | +| Yarn | 1.22.19 | +| React | 18.3.1 | + +At release date, the following database versions were current and used for testing the pipeline: + +| Database | Version | +| -------------- | ------------- | +| OMA | Jul2023 | +| PANTHER | 18 | +| OrthoInspector | Eukaryota2023 | +| EggNOG | 5.0 | + ### `Deprecated` + +Nothing. diff --git a/README.md b/README.md index 0186d5b..c959964 100644 --- a/README.md +++ b/README.md @@ -18,9 +18,6 @@ ## Introduction -> [!WARNING] -> This pipeline is still in active development. While the overall design will remain stable, all technical details, such as parameter names, are subject to change without notice. - **nf-core/reportho** is a bioinformatics pipeline that compares and assembles orthology predictions for a query protein. It fetches ortholog lists for a query (or its closest annotated homolog) from public sources, calculates pairwise and global agreement, and generates a consensus list with the desired level of confidence. Optionally, it offers common analysis on the consensus orthologs, such as MSA and phylogeny reconstruction. Additionally, it generates a clean, human-readable report of the results. diff --git a/bin/fetch_oma_by_sequence.py b/bin/fetch_oma_by_sequence.py index eeab2ba..70f719b 100755 --- a/bin/fetch_oma_by_sequence.py +++ b/bin/fetch_oma_by_sequence.py @@ -35,7 +35,7 @@ def main() -> None: break # Write exact match status - if entry["identified_by"] == "exact match": + if json["identified_by"] == "exact match": print("true", file=open(sys.argv[4], 'w')) else: print("false", file=open(sys.argv[4], 'w')) diff --git a/modules.json b/modules.json index 251ab94..1b6165a 100644 --- a/modules.json +++ b/modules.json @@ -51,7 +51,7 @@ "nf-core": { "utils_nextflow_pipeline": { "branch": "master", - "git_sha": "cd08c91373cd00a73255081340e4914485846ba1", + "git_sha": "5caf7640a9ef1d18d765d55339be751bb0969dfa", "installed_by": ["subworkflows"] }, "utils_nfcore_pipeline": { @@ -61,7 +61,7 @@ }, "utils_nfvalidation_plugin": { "branch": "master", - "git_sha": "cd08c91373cd00a73255081340e4914485846ba1", + "git_sha": "5caf7640a9ef1d18d765d55339be751bb0969dfa", "installed_by": ["subworkflows"] } } diff --git a/modules/local/dump_params.nf b/modules/local/dump_params.nf index 323189b..de9747b 100644 --- a/modules/local/dump_params.nf +++ b/modules/local/dump_params.nf @@ -13,8 +13,8 @@ process DUMP_PARAMS { val use_centroid val min_score val skip_downstream - val use_iqtree - val use_fastme + val skip_iqtree + val skip_fastme output: tuple val(meta), path("params.yml"), emit: params @@ -32,8 +32,8 @@ process DUMP_PARAMS { use_centroid: ${use_centroid} min_score: ${min_score} skip_downstream: ${skip_downstream} - use_iqtree: ${use_iqtree} - use_fastme: ${use_fastme} + skip_iqtree: ${skip_iqtree} + skip_fastme: ${skip_fastme} END_PARAMS """ diff --git a/modules/local/identify_seq_online.nf b/modules/local/identify_seq_online.nf index 2ada143..719b325 100644 --- a/modules/local/identify_seq_online.nf +++ b/modules/local/identify_seq_online.nf @@ -21,7 +21,7 @@ process IDENTIFY_SEQ_ONLINE { prefix = task.ext.prefix ?: meta.id """ fetch_oma_by_sequence.py $fasta id_raw.txt ${prefix}_taxid.txt ${prefix}_exact.txt - uniprotize_oma.py id_raw.txt > ${prefix}_id.txt + uniprotize_oma_online.py id_raw.txt > ${prefix}_id.txt cat <<- END_VERSIONS > versions.yml "${task.process}": diff --git a/modules/local/make_report.nf b/modules/local/make_report.nf index cfcdd97..3505ed3 100644 --- a/modules/local/make_report.nf +++ b/modules/local/make_report.nf @@ -54,7 +54,7 @@ process MAKE_REPORT { ${task.process}: Node: \$(node --version) Yarn: \$(yarn --version) - React: \$(yarn view react version) + React: \$(yarn info react version | cut -d \$'\n' -f 2) Python: \$(python --version | cut -d ' ' -f 2) END_VERSIONS """ diff --git a/subworkflows/nf-core/utils_nextflow_pipeline/tests/main.function.nf.test b/subworkflows/nf-core/utils_nextflow_pipeline/tests/main.function.nf.test index 8ed4310..68718e4 100644 --- a/subworkflows/nf-core/utils_nextflow_pipeline/tests/main.function.nf.test +++ b/subworkflows/nf-core/utils_nextflow_pipeline/tests/main.function.nf.test @@ -51,4 +51,4 @@ nextflow_function { ) } } -} \ No newline at end of file +} diff --git a/subworkflows/nf-core/utils_nextflow_pipeline/tests/main.function.nf.test.snap b/subworkflows/nf-core/utils_nextflow_pipeline/tests/main.function.nf.test.snap index db2030f..e3f0baf 100644 --- a/subworkflows/nf-core/utils_nextflow_pipeline/tests/main.function.nf.test.snap +++ b/subworkflows/nf-core/utils_nextflow_pipeline/tests/main.function.nf.test.snap @@ -3,10 +3,18 @@ "content": [ "v9.9.9" ], - "timestamp": "2024-01-19T11:32:36.031083" + "meta": { + "nf-test": "0.8.4", + "nextflow": "23.10.1" + }, + "timestamp": "2024-02-28T12:02:05.308243" }, "Test Function checkCondaChannels": { "content": null, - "timestamp": "2024-01-19T11:32:50.456" + "meta": { + "nf-test": "0.8.4", + "nextflow": "23.10.1" + }, + "timestamp": "2024-02-28T12:02:12.425833" } } \ No newline at end of file diff --git a/subworkflows/nf-core/utils_nextflow_pipeline/tests/main.workflow.nf.test b/subworkflows/nf-core/utils_nextflow_pipeline/tests/main.workflow.nf.test index f7c54bc..ca964ce 100644 --- a/subworkflows/nf-core/utils_nextflow_pipeline/tests/main.workflow.nf.test +++ b/subworkflows/nf-core/utils_nextflow_pipeline/tests/main.workflow.nf.test @@ -11,9 +11,6 @@ nextflow_workflow { test("Should run no inputs") { when { - params { - outdir = "tests/results" - } workflow { """ print_version = false @@ -39,9 +36,6 @@ nextflow_workflow { test("Should print version") { when { - params { - outdir = "tests/results" - } workflow { """ print_version = true @@ -68,19 +62,16 @@ nextflow_workflow { test("Should dump params") { when { - params { - outdir = "$outputDir" - } workflow { """ print_version = false dump_parameters = true - outdir = params.outdir + outdir = 'results' check_conda_channels = false input[0] = false input[1] = true - input[2] = params.outdir + input[2] = outdir input[3] = false """ } @@ -96,19 +87,16 @@ nextflow_workflow { test("Should not create params JSON if no output directory") { when { - params { - outdir = "$outputDir" - } workflow { """ print_version = false dump_parameters = true - outdir = params.outdir + outdir = null check_conda_channels = false input[0] = false input[1] = true - input[2] = null + input[2] = outdir input[3] = false """ } diff --git a/subworkflows/nf-core/utils_nextflow_pipeline/tests/nextflow.config b/subworkflows/nf-core/utils_nextflow_pipeline/tests/nextflow.config index 53574ff..d0a926b 100644 --- a/subworkflows/nf-core/utils_nextflow_pipeline/tests/nextflow.config +++ b/subworkflows/nf-core/utils_nextflow_pipeline/tests/nextflow.config @@ -6,4 +6,4 @@ manifest { nextflowVersion = '!>=23.04.0' version = '9.9.9' doi = 'https://doi.org/10.5281/zenodo.5070524' -} \ No newline at end of file +} diff --git a/subworkflows/nf-core/utils_nfvalidation_plugin/tests/main.nf.test b/subworkflows/nf-core/utils_nfvalidation_plugin/tests/main.nf.test index 517ee54..5784a33 100644 --- a/subworkflows/nf-core/utils_nfvalidation_plugin/tests/main.nf.test +++ b/subworkflows/nf-core/utils_nfvalidation_plugin/tests/main.nf.test @@ -197,4 +197,4 @@ nextflow_workflow { ) } } -} \ No newline at end of file +}