From 0f86e9eb9c6993726e1a184bca6a508cf455f3d3 Mon Sep 17 00:00:00 2001 From: jasmezz Date: Fri, 31 Jan 2025 16:07:44 +0100 Subject: [PATCH 1/6] Add `--annotation_pyrodigal_stopcodon` parameter --- CHANGELOG.md | 1 + conf/modules.config | 1 + nextflow.config | 1 + nextflow_schema.json | 7 +++++++ 4 files changed, 10 insertions(+) diff --git a/CHANGELOG.md b/CHANGELOG.md index 293470cf..07ed99bc 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -23,6 +23,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 - [#435](https://github.com/nf-core/funcscan/pull/435) Fixed dependency errors within taxonomy merging scripts, updated the code and output for all three workflows. Bumped to version 0.1.1. (by @darcy220606) - [#437](https://github.com/nf-core/funcscan/pull/437) Fixed file name error when supplying already preprocessed CARD database for ARG workflow. (by @jasmezz) - [#446](https://github.com/nf-core/funcscan/pull/446) Updated antiSMASH modules to fix apptainer execution. (by @jasmezz and @jfy133) +- [#447](https://github.com/nf-core/funcscan/pull/447) Added `--annotation_pyrodigal_stopcodon` parameter to improve AMPlify screening. (by @jasmezz) ### `Dependencies` diff --git a/conf/modules.config b/conf/modules.config index 5684b042..a43a8c8d 100644 --- a/conf/modules.config +++ b/conf/modules.config @@ -201,6 +201,7 @@ process { params.annotation_pyrodigal_singlemode ? "-p single" : "-p meta", params.annotation_pyrodigal_closed ? "-c" : "", params.annotation_pyrodigal_forcenonsd ? "-n" : "", + params.annotation_pyrodigal_nostopcodon ? '--no-stop-codon' : '', "-g ${params.annotation_pyrodigal_transtable}", ].join(' ').trim() } diff --git a/nextflow.config b/nextflow.config index 12283ffd..ad1a868b 100644 --- a/nextflow.config +++ b/nextflow.config @@ -66,6 +66,7 @@ params { annotation_pyrodigal_closed = false annotation_pyrodigal_transtable = 11 annotation_pyrodigal_forcenonsd = false + annotation_pyrodigal_stopcodon = false annotation_bakta_db = null annotation_bakta_db_downloadtype = 'full' diff --git a/nextflow_schema.json b/nextflow_schema.json index 46323109..e5119921 100644 --- a/nextflow_schema.json +++ b/nextflow_schema.json @@ -518,6 +518,13 @@ "fa_icon": "fas fa-barcode", "description": "Forces Pyrodigal to scan for motifs.", "help_text": "Forces Pyrodigal to a full scan for motifs rather than activating the Shine-Dalgarno RBS finder, the default scanner for Pyrodigal to train for motifs.\n\nFor more information check the Pyrodigal [documentation](https://pyrodigal.readthedocs.io).\n\n> Modifies tool parameter(s):\n> - PYRODIGAL: `-n`" + }, + "annotation_pyrodigal_stopcodon": { + "type": "boolean", + "fa_icon": "fa fa-star-of-life", + "description": "This forces Pyrodigal to append asterisks (`*`) as stop codon indicators.", + "help_text": "Some downstream tools like AMPlify cannot process sequences containing non-sequence characters like the stop codon indicator `*`. Thus, this flag is deactivated by default. Activate this flag to revert the behaviour and have Pyrodigal append `*` as stop codon indicator to annotated sequences.\n\nFor more information check the Pyrodigal [documentation](https://pyrodigal.readthedocs.io).\n\n> Modifies tool parameter(s):\n> - PYRODIGAL: `--no-stop-codon`", + "default": false } }, "fa_icon": "fas fa-file-signature" From e76b0b43a74231264761611ee7a0238c822d2d0c Mon Sep 17 00:00:00 2001 From: Jasmin Frangenberg <73216762+jasmezz@users.noreply.github.com> Date: Fri, 31 Jan 2025 17:49:13 +0100 Subject: [PATCH 2/6] Fix modules.config --- conf/modules.config | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/conf/modules.config b/conf/modules.config index a43a8c8d..e5f81e3c 100644 --- a/conf/modules.config +++ b/conf/modules.config @@ -201,7 +201,7 @@ process { params.annotation_pyrodigal_singlemode ? "-p single" : "-p meta", params.annotation_pyrodigal_closed ? "-c" : "", params.annotation_pyrodigal_forcenonsd ? "-n" : "", - params.annotation_pyrodigal_nostopcodon ? '--no-stop-codon' : '', + params.annotation_pyrodigal_stopcodon ? '--no-stop-codon' : '', "-g ${params.annotation_pyrodigal_transtable}", ].join(' ').trim() } From 894ddebfd866bacbd2d559f46b670f7926918757 Mon Sep 17 00:00:00 2001 From: jasmezz Date: Mon, 3 Feb 2025 12:37:54 +0100 Subject: [PATCH 3/6] Fix logic of "stopcodon" param --- conf/modules.config | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/conf/modules.config b/conf/modules.config index e5f81e3c..3f4d2932 100644 --- a/conf/modules.config +++ b/conf/modules.config @@ -201,7 +201,7 @@ process { params.annotation_pyrodigal_singlemode ? "-p single" : "-p meta", params.annotation_pyrodigal_closed ? "-c" : "", params.annotation_pyrodigal_forcenonsd ? "-n" : "", - params.annotation_pyrodigal_stopcodon ? '--no-stop-codon' : '', + params.annotation_pyrodigal_stopcodon ? '' : '--no-stop-codon', "-g ${params.annotation_pyrodigal_transtable}", ].join(' ').trim() } From dbe492f5056c9326cbcf09019d4a475a7475f3ec Mon Sep 17 00:00:00 2001 From: jasmezz Date: Tue, 4 Feb 2025 17:15:45 +0100 Subject: [PATCH 4/6] Fix failing snapshots --- tests/test.nf.test.snap | 2 +- tests/test_preannotated.nf.test.snap | 6 +++--- 2 files changed, 4 insertions(+), 4 deletions(-) diff --git a/tests/test.nf.test.snap b/tests/test.nf.test.snap index c09747ac..d312a612 100644 --- a/tests/test.nf.test.snap +++ b/tests/test.nf.test.snap @@ -47,7 +47,7 @@ "deeparg_tsv_ARG": { "content": [ "sample_1.align.daa.tsv:md5,21822364379fe8f991d27cdb52a33d1d", - "sample_2.align.daa.tsv:md5,f448465df58785a87cdee53691a77bfe", + "sample_2.align.daa.tsv:md5,d59287f357de198639bdca5dbaede173", "sample_1.mapping.ARG:md5,0e049e99eab4c55666062df21707d5b9", "sample_2.mapping.ARG:md5,0e049e99eab4c55666062df21707d5b9" ], diff --git a/tests/test_preannotated.nf.test.snap b/tests/test_preannotated.nf.test.snap index 107b6e1c..de54e2ba 100644 --- a/tests/test_preannotated.nf.test.snap +++ b/tests/test_preannotated.nf.test.snap @@ -3,7 +3,7 @@ "content": [ "sample_1.align.daa.tsv:md5,0e71c37318bdc6cba792196d0455293d", "sample_2.align.daa.tsv:md5,1092ecd3cd6931653168b46c7afeb9e3", - "sample_3.align.daa.tsv:md5,b79070fe26acd1a10ae3aaf06b0d5901", + "sample_3.align.daa.tsv:md5,a9ed2f0651d75b318fde07a76b06d7b8", true, true, true @@ -71,8 +71,8 @@ "sample_1.potential.ARG.normalized.tsv:md5,d6732b4b9765bfa47e27ba673e24b6a4", "sample_2.ARG.normalized.tsv:md5,1a19b894a7315aaae5f799e4539e6619", "sample_2.potential.ARG.normalized.tsv:md5,b241e22f9116d8f518ba8526d52ac4dc", - "sample_3.ARG.normalized.tsv:md5,d40d387176649ce80827420fef6a0169", - "sample_3.potential.ARG.normalized.tsv:md5,f331efd21ea143c180a15ae56a5210d3" + "sample_3.ARG.normalized.tsv:md5,d7577c0066a31e173f9cb545820650bf", + "sample_3.potential.ARG.normalized.tsv:md5,6d0889215f0ad7f601502ca67c0ca89e" ], "meta": { "nf-test": "0.9.0", From 19aff23ff7099496bca0a134e6868bc6d1235402 Mon Sep 17 00:00:00 2001 From: jasmezz Date: Wed, 5 Feb 2025 12:10:19 +0100 Subject: [PATCH 5/6] Apply suggestions from code review; fix linting warning (rocrate) --- CHANGELOG.md | 2 +- conf/modules.config | 2 +- nextflow.config | 2 +- nextflow_schema.json | 2 +- ro-crate-metadata.json | 76 ++++++++++++++++++++++++++++++++++-------- 5 files changed, 66 insertions(+), 18 deletions(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index e9e401c7..abafaa47 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -24,7 +24,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 - [#437](https://github.com/nf-core/funcscan/pull/437) Fixed file name error when supplying already preprocessed CARD database for ARG workflow. (by @jasmezz) - [#446](https://github.com/nf-core/funcscan/pull/446) Updated antiSMASH modules to fix apptainer execution. (by @jasmezz and @jfy133) - [#448](https://github.com/nf-core/funcscan/pull/448) Fixed taxonomy merge to work with output from GTDB/SILVA/KALAMARI. (by @darcy220606) -- [#447](https://github.com/nf-core/funcscan/pull/447) Added `--annotation_pyrodigal_stopcodon` parameter to improve AMPlify screening. (by @jasmezz) +- [#447](https://github.com/nf-core/funcscan/pull/447) Added `--annotation_pyrodigal_usespecialstopcharacter` parameter to improve AMPlify screening. (by @jasmezz) ### `Dependencies` diff --git a/conf/modules.config b/conf/modules.config index 3f4d2932..a348da3c 100644 --- a/conf/modules.config +++ b/conf/modules.config @@ -201,7 +201,7 @@ process { params.annotation_pyrodigal_singlemode ? "-p single" : "-p meta", params.annotation_pyrodigal_closed ? "-c" : "", params.annotation_pyrodigal_forcenonsd ? "-n" : "", - params.annotation_pyrodigal_stopcodon ? '' : '--no-stop-codon', + params.annotation_pyrodigal_usespecialstopcharacter ? '' : '--no-stop-codon', "-g ${params.annotation_pyrodigal_transtable}", ].join(' ').trim() } diff --git a/nextflow.config b/nextflow.config index ad1a868b..ae6b0038 100644 --- a/nextflow.config +++ b/nextflow.config @@ -66,7 +66,7 @@ params { annotation_pyrodigal_closed = false annotation_pyrodigal_transtable = 11 annotation_pyrodigal_forcenonsd = false - annotation_pyrodigal_stopcodon = false + annotation_pyrodigal_usespecialstopcharacter = false annotation_bakta_db = null annotation_bakta_db_downloadtype = 'full' diff --git a/nextflow_schema.json b/nextflow_schema.json index e5119921..fa55606a 100644 --- a/nextflow_schema.json +++ b/nextflow_schema.json @@ -519,7 +519,7 @@ "description": "Forces Pyrodigal to scan for motifs.", "help_text": "Forces Pyrodigal to a full scan for motifs rather than activating the Shine-Dalgarno RBS finder, the default scanner for Pyrodigal to train for motifs.\n\nFor more information check the Pyrodigal [documentation](https://pyrodigal.readthedocs.io).\n\n> Modifies tool parameter(s):\n> - PYRODIGAL: `-n`" }, - "annotation_pyrodigal_stopcodon": { + "annotation_pyrodigal_usespecialstopcharacter": { "type": "boolean", "fa_icon": "fa fa-star-of-life", "description": "This forces Pyrodigal to append asterisks (`*`) as stop codon indicators.", diff --git a/ro-crate-metadata.json b/ro-crate-metadata.json index 7f40a7cd..63577086 100644 --- a/ro-crate-metadata.json +++ b/ro-crate-metadata.json @@ -22,8 +22,8 @@ "@id": "./", "@type": "Dataset", "creativeWorkStatus": "InProgress", - "datePublished": "2025-01-27T14:45:55+00:00", - "description": "

\n \n \n \"nf-core/funcscan\"\n \n

\n\n[![GitHub Actions CI Status](https://github.com/nf-core/funcscan/actions/workflows/ci.yml/badge.svg)](https://github.com/nf-core/funcscan/actions/workflows/ci.yml)\n[![GitHub Actions Linting Status](https://github.com/nf-core/funcscan/actions/workflows/linting.yml/badge.svg)](https://github.com/nf-core/funcscan/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/funcscan/results)[![Cite with Zenodo](http://img.shields.io/badge/DOI-10.5281/zenodo.XXXXXXX-1073c8?labelColor=000000)](https://doi.org/10.5281/zenodo.XXXXXXX)\n[![nf-test](https://img.shields.io/badge/unit_tests-nf--test-337ab7.svg)](https://www.nf-test.com)\n\n[![Nextflow](https://img.shields.io/badge/nextflow%20DSL2-%E2%89%A524.04.2-23aa62.svg)](https://www.nextflow.io/)\n[![run with conda](http://img.shields.io/badge/run%20with-conda-3EB049?labelColor=000000&logo=anaconda)](https://docs.conda.io/en/latest/)\n[![run with docker](https://img.shields.io/badge/run%20with-docker-0db7ed?labelColor=000000&logo=docker)](https://www.docker.com/)\n[![run with singularity](https://img.shields.io/badge/run%20with-singularity-1d355c.svg?labelColor=000000)](https://sylabs.io/docs/)\n[![Launch on Seqera Platform](https://img.shields.io/badge/Launch%20%F0%9F%9A%80-Seqera%20Platform-%234256e7)](https://cloud.seqera.io/launch?pipeline=https://github.com/nf-core/funcscan)\n\n[![Get help on Slack](http://img.shields.io/badge/slack-nf--core%20%23funcscan-4A154B?labelColor=000000&logo=slack)](https://nfcore.slack.com/channels/funcscan)[![Follow on Twitter](http://img.shields.io/badge/twitter-%40nf__core-1DA1F2?labelColor=000000&logo=twitter)](https://twitter.com/nf_core)[![Follow on Mastodon](https://img.shields.io/badge/mastodon-nf__core-6364ff?labelColor=FFFFFF&logo=mastodon)](https://mstdn.science/@nf_core)[![Watch on YouTube](http://img.shields.io/badge/youtube-nf--core-FF0000?labelColor=000000&logo=youtube)](https://www.youtube.com/c/nf-core)\n\n## Introduction\n\n**nf-core/funcscan** is a bioinformatics pipeline that ...\n\n\n\n\n2. Present QC for raw reads ([`MultiQC`](http://multiqc.info/))\n\n## Usage\n\n> [!NOTE]\n> If you are new to Nextflow and nf-core, please refer to [this page](https://nf-co.re/docs/usage/installation) on how 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.\n\n\n\nNow, you can run the pipeline using:\n\n\n\n```bash\nnextflow run nf-core/funcscan \\\n -profile \\\n --input samplesheet.csv \\\n --outdir \n```\n\n> [!WARNING]\n> Please provide pipeline parameters via the CLI or Nextflow `-params-file` option. Custom config files including those provided by the `-c` Nextflow option can be used to provide any configuration _**except for parameters**_; see [docs](https://nf-co.re/docs/usage/getting_started/configuration#custom-configuration-files).\n\nFor more details and further functionality, please refer to the [usage documentation](https://nf-co.re/funcscan/usage) and the [parameter documentation](https://nf-co.re/funcscan/parameters).\n\n## Pipeline output\n\nTo see the results of an example test run with a full size dataset refer to the [results](https://nf-co.re/funcscan/results) tab on the nf-core website pipeline page.\nFor more details about the output files and reports, please refer to the\n[output documentation](https://nf-co.re/funcscan/output).\n\n## Credits\n\nnf-core/funcscan was originally written by Jasmin Frangenberg, Anan Ibrahim, Louisa Perelo, Moritz E. Beber, James A. Fellows Yates.\n\nWe thank the following people for their extensive assistance in the development of this pipeline:\n\n\n\n## Contributions and Support\n\nIf you would like to contribute to this pipeline, please see the [contributing guidelines](.github/CONTRIBUTING.md).\n\nFor further information or help, don't hesitate to get in touch on the [Slack `#funcscan` channel](https://nfcore.slack.com/channels/funcscan) (you can join with [this invite](https://nf-co.re/join/slack)).\n\n## Citations\n\n\n\n\n\n\nAn extensive list of references for the tools used by the pipeline can be found in the [`CITATIONS.md`](CITATIONS.md) file.\n\nYou can cite the `nf-core` publication as follows:\n\n> **The nf-core framework for community-curated bioinformatics pipelines.**\n>\n> Philip Ewels, Alexander Peltzer, Sven Fillinger, Harshil Patel, Johannes Alneberg, Andreas Wilm, Maxime Ulysse Garcia, Paolo Di Tommaso & Sven Nahnsen.\n>\n> _Nat Biotechnol._ 2020 Feb 13. doi: [10.1038/s41587-020-0439-x](https://dx.doi.org/10.1038/s41587-020-0439-x).\n", + "datePublished": "2025-02-05T10:21:25+00:00", + "description": "

\n \n \n \"nf-core/funcscan\"\n \n

\n\n[![GitHub Actions CI Status](https://github.com/nf-core/funcscan/actions/workflows/ci.yml/badge.svg)](https://github.com/nf-core/funcscan/actions/workflows/ci.yml)\n[![GitHub Actions Linting Status](https://github.com/nf-core/funcscan/actions/workflows/linting.yml/badge.svg)](https://github.com/nf-core/funcscan/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/funcscan/results)[![Cite with Zenodo](http://img.shields.io/badge/DOI-10.5281/zenodo.7643099-1073c8?labelColor=000000)](https://doi.org/10.5281/zenodo.7643099)\n[![nf-test](https://img.shields.io/badge/unit_tests-nf--test-337ab7.svg)](https://www.nf-test.com)\n\n[![Nextflow](https://img.shields.io/badge/nextflow%20DSL2-%E2%89%A524.04.2-23aa62.svg)](https://www.nextflow.io/)\n[![run with conda](http://img.shields.io/badge/run%20with-conda-3EB049?labelColor=000000&logo=anaconda)](https://docs.conda.io/en/latest/)\n[![run with docker](https://img.shields.io/badge/run%20with-docker-0db7ed?labelColor=000000&logo=docker)](https://www.docker.com/)\n[![run with singularity](https://img.shields.io/badge/run%20with-singularity-1d355c.svg?labelColor=000000)](https://sylabs.io/docs/)\n[![Launch on Seqera Platform](https://img.shields.io/badge/Launch%20%F0%9F%9A%80-Seqera%20Platform-%234256e7)](https://cloud.seqera.io/launch?pipeline=https://github.com/nf-core/funcscan)\n\n[![Get help on Slack](http://img.shields.io/badge/slack-nf--core%20%23funcscan-4A154B?labelColor=000000&logo=slack)](https://nfcore.slack.com/channels/funcscan)[![Follow on Twitter](http://img.shields.io/badge/twitter-%40nf__core-1DA1F2?labelColor=000000&logo=twitter)](https://twitter.com/nf_core)[![Follow on Mastodon](https://img.shields.io/badge/mastodon-nf__core-6364ff?labelColor=FFFFFF&logo=mastodon)](https://mstdn.science/@nf_core)[![Watch on YouTube](http://img.shields.io/badge/youtube-nf--core-FF0000?labelColor=000000&logo=youtube)](https://www.youtube.com/c/nf-core)\n\n## Introduction\n\n**nf-core/funcscan** is a bioinformatics best-practice analysis pipeline for the screening of nucleotide sequences such as assembled contigs for functional genes. It currently features mining for antimicrobial peptides, antibiotic resistance genes and biosynthetic gene clusters.\n\nThe 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!\n\nOn 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/funcscan/results).\n\nThe nf-core/funcscan AWS full test dataset are contigs generated by the MGnify service from the ENA. We used contigs generated from assemblies of chicken cecum shotgun metagenomes (study accession: MGYS00005631).\n\n## Pipeline summary\n\n1. Quality control of input sequences with [`SeqKit`](https://bioinf.shenwei.me/seqkit/)\n2. Taxonomic classification of contigs of **prokaryotic origin** with [`MMseqs2`](https://github.com/soedinglab/MMseqs2)\n3. Annotation of assembled prokaryotic contigs with [`Prodigal`](https://github.com/hyattpd/Prodigal), [`Pyrodigal`](https://github.com/althonos/pyrodigal), [`Prokka`](https://github.com/tseemann/prokka), or [`Bakta`](https://github.com/oschwengers/bakta)\n4. Screening contigs for antimicrobial peptide-like sequences with [`ampir`](https://cran.r-project.org/web/packages/ampir/index.html), [`Macrel`](https://github.com/BigDataBiology/macrel), [`HMMER`](http://hmmer.org/), [`AMPlify`](https://github.com/bcgsc/AMPlify)\n5. Screening contigs for antibiotic resistant gene-like sequences with [`ABRicate`](https://github.com/tseemann/abricate), [`AMRFinderPlus`](https://github.com/ncbi/amr), [`fARGene`](https://github.com/fannyhb/fargene), [`RGI`](https://card.mcmaster.ca/analyze/rgi), [`DeepARG`](https://bench.cs.vt.edu/deeparg). [`argNorm`](https://github.com/BigDataBiology/argNorm) is used to map the outputs of `DeepARG`, `AMRFinderPlus`, and `ABRicate` to the [`Antibiotic Resistance Ontology`](https://www.ebi.ac.uk/ols4/ontologies/aro) for consistent ARG classification terms.\n6. Screening contigs for biosynthetic gene cluster-like sequences with [`antiSMASH`](https://antismash.secondarymetabolites.org), [`DeepBGC`](https://github.com/Merck/deepbgc), [`GECCO`](https://gecco.embl.de/), [`HMMER`](http://hmmer.org/)\n7. Creating aggregated reports for all samples across the workflows with [`AMPcombi`](https://github.com/Darcy220606/AMPcombi) for AMPs, [`hAMRonization`](https://github.com/pha4ge/hAMRonization) for ARGs, and [`comBGC`](https://raw.githubusercontent.com/nf-core/funcscan/master/bin/comBGC.py) for BGCs\n8. Software version and methods text reporting with [`MultiQC`](http://multiqc.info/)\n\n![funcscan metro workflow](docs/images/funcscan_metro_workflow.png)\n\n## Usage\n\n> [!NOTE]\n> If you are new to Nextflow and nf-core, please refer to [this page](https://nf-co.re/docs/usage/installation) on how 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.\n\nFirst, prepare a samplesheet with your input data that looks as follows:\n\n`samplesheet.csv`:\n\n```csv\nsample,fasta\nCONTROL_REP1,AEG588A1_001.fasta\nCONTROL_REP2,AEG588A1_002.fasta\nCONTROL_REP3,AEG588A1_003.fasta\n```\n\nEach row represents a (multi-)fasta file of assembled contig sequences.\n\nNow, you can run the pipeline using:\n\n```bash\nnextflow run nf-core/funcscan \\\n -profile \\\n --input samplesheet.csv \\\n --outdir \\\n --run_amp_screening \\\n --run_arg_screening \\\n --run_bgc_screening\n```\n\n> [!WARNING]\n> Please provide pipeline parameters via the CLI or Nextflow `-params-file` option. Custom config files including those provided by the `-c` Nextflow option can be used to provide any configuration _**except for parameters**_; see [docs](https://nf-co.re/docs/usage/getting_started/configuration#custom-configuration-files).\n\nFor more details and further functionality, please refer to the [usage documentation](https://nf-co.re/funcscan/usage) and the [parameter documentation](https://nf-co.re/funcscan/parameters).\n\n## Pipeline output\n\nTo see the results of an example test run with a full size dataset refer to the [results](https://nf-co.re/funcscan/results) tab on the nf-core website pipeline page.\nFor more details about the output files and reports, please refer to the\n[output documentation](https://nf-co.re/funcscan/output).\n\n## Credits\n\nnf-core/funcscan was originally written by Jasmin Frangenberg, Anan Ibrahim, Louisa Perelo, Moritz E. Beber, James A. Fellows Yates.\n\nWe thank the following people for their extensive assistance in the development of this pipeline:\n\nAdam Talbot, Alexandru Mizeranschi, Hugo Tavares, J\u00falia Mir Pedrol, Martin Klapper, Mehrdad Jaberi, Robert Syme, Rosa Herbst, Vedanth Ramji, @Microbion.\n\n## Contributions and Support\n\nIf you would like to contribute to this pipeline, please see the [contributing guidelines](.github/CONTRIBUTING.md).\n\nFor further information or help, don't hesitate to get in touch on the [Slack `#funcscan` channel](https://nfcore.slack.com/channels/funcscan) (you can join with [this invite](https://nf-co.re/join/slack)).\n\n## Citations\n\nIf you use nf-core/funcscan for your analysis, please cite it using the following doi: [10.5281/zenodo.7643099](https://doi.org/10.5281/zenodo.7643099)\n\nAn extensive list of references for the tools used by the pipeline can be found in the [`CITATIONS.md`](CITATIONS.md) file.\n\nYou can cite the `nf-core` publication as follows:\n\n> **The nf-core framework for community-curated bioinformatics pipelines.**\n>\n> Philip Ewels, Alexander Peltzer, Sven Fillinger, Harshil Patel, Johannes Alneberg, Andreas Wilm, Maxime Ulysse Garcia, Paolo Di Tommaso & Sven Nahnsen.\n>\n> _Nat Biotechnol._ 2020 Feb 13. doi: [10.1038/s41587-020-0439-x](https://dx.doi.org/10.1038/s41587-020-0439-x).\n", "hasPart": [ { "@id": "main.nf" @@ -31,6 +31,9 @@ { "@id": "assets/" }, + { + "@id": "bin/" + }, { "@id": "conf/" }, @@ -43,6 +46,9 @@ { "@id": "modules/" }, + { + "@id": "modules/local/" + }, { "@id": "modules/nf-core/" }, @@ -99,7 +105,7 @@ }, "mentions": [ { - "@id": "#a63ff768-a32a-4ee1-8ba3-fafeb18a6793" + "@id": "#1f9be113-27d3-4dcb-b12a-d0c1a16703bf" } ], "name": "nf-core/funcscan" @@ -121,14 +127,24 @@ }, { "@id": "main.nf", - "@type": ["File", "SoftwareSourceCode", "ComputationalWorkflow"], + "@type": [ + "File", + "SoftwareSourceCode", + "ComputationalWorkflow" + ], "creator": [ { "@id": "#jfy133@gmail.com" + }, + { + "@id": "#jfy133@gmail.com" + }, + { + "@id": "https://orcid.org/0009-0004-5961-4709" } ], "dateCreated": "", - "dateModified": "2025-01-27T14:45:55Z", + "dateModified": "2025-02-05T11:21:25Z", "dct:conformsTo": "https://bioschemas.org/profiles/ComputationalWorkflow/1.0-RELEASE/", "keywords": [ "nf-core", @@ -149,17 +165,33 @@ "screening", "secondary-metabolites" ], - "license": ["MIT"], - "name": ["nf-core/funcscan"], + "license": [ + "MIT" + ], + "maintainer": [ + { + "@id": "#jfy133@gmail.com" + }, + { + "@id": "https://orcid.org/0009-0004-5961-4709" + } + ], + "name": [ + "nf-core/funcscan" + ], "programmingLanguage": { "@id": "https://w3id.org/workflowhub/workflow-ro-crate#nextflow" }, "sdPublisher": { "@id": "https://nf-co.re/" }, - "url": ["https://github.com/nf-core/funcscan", "https://nf-co.re/funcscan/dev/"], - "version": ["2.1.0dev"] - + "url": [ + "https://github.com/nf-core/funcscan", + "https://nf-co.re/funcscan/dev/" + ], + "version": [ + "2.1.0dev" + ] }, { "@id": "https://w3id.org/workflowhub/workflow-ro-crate#nextflow", @@ -174,11 +206,11 @@ "version": "!>=24.04.2" }, { - "@id": "#a63ff768-a32a-4ee1-8ba3-fafeb18a6793", + "@id": "#1f9be113-27d3-4dcb-b12a-d0c1a16703bf", "@type": "TestSuite", "instance": [ { - "@id": "#f399a53f-20fc-47ed-b389-7e76797884bb" + "@id": "#e917d36b-75a7-45b5-86d1-e9157f00ac3b" } ], "mainEntity": { @@ -187,7 +219,7 @@ "name": "Test suite for nf-core/funcscan" }, { - "@id": "#f399a53f-20fc-47ed-b389-7e76797884bb", + "@id": "#e917d36b-75a7-45b5-86d1-e9157f00ac3b", "@type": "TestInstance", "name": "GitHub Actions workflow for testing nf-core/funcscan", "resource": "repos/nf-core/funcscan/actions/workflows/ci.yml", @@ -209,6 +241,11 @@ "@type": "Dataset", "description": "Additional files" }, + { + "@id": "bin/", + "@type": "Dataset", + "description": "Scripts that must be callable from a pipeline process" + }, { "@id": "conf/", "@type": "Dataset", @@ -229,6 +266,11 @@ "@type": "Dataset", "description": "Modules used by the pipeline" }, + { + "@id": "modules/local/", + "@type": "Dataset", + "description": "Pipeline-specific modules" + }, { "@id": "modules/nf-core/", "@type": "Dataset", @@ -320,6 +362,12 @@ "@type": "Person", "email": "jfy133@gmail.com", "name": "James Fellows Yates" + }, + { + "@id": "https://orcid.org/0009-0004-5961-4709", + "@type": "Person", + "email": "73216762+jasmezz@users.noreply.github.com", + "name": "Jasmin Frangenberg" } ] -} +} \ No newline at end of file From 5b2a679046bf788027b4d4356f4c47d49009a0f2 Mon Sep 17 00:00:00 2001 From: jasmezz Date: Thu, 6 Feb 2025 16:26:33 +0100 Subject: [PATCH 6/6] Update description of new param --- nextflow_schema.json | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/nextflow_schema.json b/nextflow_schema.json index fa55606a..8fc059f9 100644 --- a/nextflow_schema.json +++ b/nextflow_schema.json @@ -522,7 +522,7 @@ "annotation_pyrodigal_usespecialstopcharacter": { "type": "boolean", "fa_icon": "fa fa-star-of-life", - "description": "This forces Pyrodigal to append asterisks (`*`) as stop codon indicators.", + "description": "This forces Pyrodigal to append asterisks (`*`) as stop codon indicators. Do not use when running AMP workflow.", "help_text": "Some downstream tools like AMPlify cannot process sequences containing non-sequence characters like the stop codon indicator `*`. Thus, this flag is deactivated by default. Activate this flag to revert the behaviour and have Pyrodigal append `*` as stop codon indicator to annotated sequences.\n\nFor more information check the Pyrodigal [documentation](https://pyrodigal.readthedocs.io).\n\n> Modifies tool parameter(s):\n> - PYRODIGAL: `--no-stop-codon`", "default": false }