From 00ebb589cf474b8f3bb165a0886baeec8b44230d Mon Sep 17 00:00:00 2001 From: jasmezz Date: Wed, 15 Feb 2023 12:49:06 +0100 Subject: [PATCH 01/12] Update version --- nextflow.config | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/nextflow.config b/nextflow.config index e2651f0a..d927c549 100644 --- a/nextflow.config +++ b/nextflow.config @@ -344,7 +344,7 @@ manifest { description = """Pipeline for screening for functional components of assembled contigs""" mainScript = 'main.nf' nextflowVersion = '!>=22.10.1' - version = '1.0.0' + version = '1.1.0dev' doi = '10.5281/zenodo.7643099' } From a7279315f47300b6a1181a30bc5a773eaef97c39 Mon Sep 17 00:00:00 2001 From: jasmezz Date: Wed, 15 Feb 2023 12:52:40 +0100 Subject: [PATCH 02/12] Update changelog + DOI --- CHANGELOG.md | 10 ++++++++++ README.md | 3 +-- 2 files changed, 11 insertions(+), 2 deletions(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index 197d2091..50e2abad 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -3,6 +3,16 @@ 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). +## v1.1.0dev [unreleased] + +### `Added` + +### `Fixed` + +### `Dependencies` + +### `Deprecated` + ## v1.0.0 - German Rollmops - [2023-02-15] Initial release of nf-core/funcscan, created with the [nf-core](https://nf-co.re/) template. diff --git a/README.md b/README.md index 8ea5ee53..5920856a 100644 --- a/README.md +++ b/README.md @@ -75,8 +75,7 @@ For further information or help, don't hesitate to get in touch on the [Slack `# ## Citations - - +If 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) An extensive list of references for the tools used by the pipeline can be found in the [`CITATIONS.md`](CITATIONS.md) file. From ee8c91eb36b77cd45fc39c1555afdad585d7629a Mon Sep 17 00:00:00 2001 From: nf-core-bot Date: Wed, 15 Feb 2023 11:54:45 +0000 Subject: [PATCH 03/12] [automated] Fix linting with Prettier --- README.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/README.md b/README.md index 5920856a..16bee297 100644 --- a/README.md +++ b/README.md @@ -75,7 +75,7 @@ For further information or help, don't hesitate to get in touch on the [Slack `# ## Citations -If 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) +If 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) An extensive list of references for the tools used by the pipeline can be found in the [`CITATIONS.md`](CITATIONS.md) file. From 26dc2e44dd1545dc9683b2bb2f0158aa659ef044 Mon Sep 17 00:00:00 2001 From: "Moritz E. Beber" Date: Thu, 23 Feb 2023 16:39:45 +0100 Subject: [PATCH 04/12] fix: remove check for header by sniffer The `csv.Sniffer`'s `has_header` method produces false negatives. Since we anyway check for the presence of columns, we can simply remove this check. --- bin/check_samplesheet.py | 3 --- 1 file changed, 3 deletions(-) diff --git a/bin/check_samplesheet.py b/bin/check_samplesheet.py index aa84488d..16c8279a 100755 --- a/bin/check_samplesheet.py +++ b/bin/check_samplesheet.py @@ -121,9 +121,6 @@ def sniff_format(handle): peek = read_head(handle) handle.seek(0) sniffer = csv.Sniffer() - if not sniffer.has_header(peek): - logger.critical("The given sample sheet does not appear to contain a header.") - sys.exit(1) dialect = sniffer.sniff(peek) return dialect From 1be550c67e97a0261cc4397a5a2b8da8ccd48474 Mon Sep 17 00:00:00 2001 From: "Moritz E. Beber" Date: Thu, 23 Feb 2023 16:57:06 +0100 Subject: [PATCH 05/12] docs: create changelog entry --- CHANGELOG.md | 2 ++ 1 file changed, 2 insertions(+) diff --git a/CHANGELOG.md b/CHANGELOG.md index 50e2abad..006c2624 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -9,6 +9,8 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 ### `Fixed` +- Removed a header check in the `check_samplesheet.py` script that was producing false negatives. Presence of required columns is still validated. + ### `Dependencies` ### `Deprecated` From 670af8dc90abe4623166adb8661cfef9473eb184 Mon Sep 17 00:00:00 2001 From: "James A. Fellows Yates" Date: Fri, 24 Feb 2023 08:58:23 +0000 Subject: [PATCH 06/12] Improve docs re database downloading --- CHANGELOG.md | 3 ++- docs/usage.md | 10 ++++++++-- 2 files changed, 10 insertions(+), 3 deletions(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index 006c2624..94f5f804 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -9,7 +9,8 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 ### `Fixed` -- Removed a header check in the `check_samplesheet.py` script that was producing false negatives. Presence of required columns is still validated. +- Removed a header check in the `check_samplesheet.py` script that was producing false negatives. Presence of required columns is still validated. (by @Midnighter) +- Improved database downloading guidance to emphasise it is recommended to let nf-core/funcscan do the downloading on a first run, rather than manually downloading yourself (reported by @alexhbnr, fixed by @jfy133) ### `Dependencies` diff --git a/docs/usage.md b/docs/usage.md index 104a9805..002014f2 100644 --- a/docs/usage.md +++ b/docs/usage.md @@ -86,9 +86,15 @@ When the annotation is run with Prokka, the resulting `.gbk` file passed to anti ## Databases and reference files -Various tools of nf-core/funcscan use databases and reference files to operate. While nf-core/funcscan offers the functionality to autodownload databases for you, these databases can be very large, and it is more efficient to store these files in a central place from where you can reuse them across pipeline runs. +Various tools of nf-core/funcscan use databases and reference files to operate. -Here we will describe where you can obtain databases and reference files for tools included in the pipeline. +nf-core/funcscan offers the functionality to auto-download databases for you, and as these databases can be very large, and we suggest to store these files in a central place from where you can reuse them across pipeline runs. + +We **highly recommend** allowing the pipeline to download these databases for you on a first run, saving these to your results directory with `--save_databases`, then moving these to a different location (in case you wish to delete the results directory of this first run). An exception to this is HMM files where no auto-downloading functionality is possible. + +> ⚠️ We generally do not recommend downloading the databases yourself, as this can often be non-trivial to do! + +As a reference, we will describe below where and how you can obtain databases and reference files used for tools included in the pipeline. ### Bakta From 180ecd9d82cac399d5c6b6d8c37cc400a504269b Mon Sep 17 00:00:00 2001 From: jasmezz Date: Mon, 27 Feb 2023 11:08:17 +0100 Subject: [PATCH 07/12] Add pipeline citation DOI --- lib/WorkflowMain.groovy | 5 ++--- 1 file changed, 2 insertions(+), 3 deletions(-) diff --git a/lib/WorkflowMain.groovy b/lib/WorkflowMain.groovy index adc3ca98..35ec9684 100755 --- a/lib/WorkflowMain.groovy +++ b/lib/WorkflowMain.groovy @@ -9,9 +9,8 @@ class WorkflowMain { // public static String citation(workflow) { return "If you use ${workflow.manifest.name} for your analysis please cite:\n\n" + - // TODO nf-core: Add Zenodo DOI for pipeline after first release - //"* The pipeline\n" + - //" https://doi.org/10.5281/zenodo.XXXXXXX\n\n" + + "* The pipeline\n" + + " https://doi.org/10.5281/zenodo.7643099\n\n" + "* The nf-core framework\n" + " https://doi.org/10.1038/s41587-020-0439-x\n\n" + "* Software dependencies\n" + From e4b57a7c8227684e18145d2cd06e62abb2e879d0 Mon Sep 17 00:00:00 2001 From: jasmezz Date: Mon, 27 Feb 2023 11:16:42 +0100 Subject: [PATCH 08/12] Added citation DOI [skip ci] --- CHANGELOG.md | 2 ++ 1 file changed, 2 insertions(+) diff --git a/CHANGELOG.md b/CHANGELOG.md index 94f5f804..fded656c 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -7,6 +7,8 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 ### `Added` +- Added pipeline citation DOI to `WorkflowMain.groovy` to display it when executing the pipeline + ### `Fixed` - Removed a header check in the `check_samplesheet.py` script that was producing false negatives. Presence of required columns is still validated. (by @Midnighter) From 3ae65040d553fc96e0778a0877434bcc91497280 Mon Sep 17 00:00:00 2001 From: jasmezz Date: Mon, 27 Feb 2023 11:31:38 +0100 Subject: [PATCH 09/12] version bump [skip ci] --- CHANGELOG.md | 6 +++--- nextflow.config | 2 +- 2 files changed, 4 insertions(+), 4 deletions(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index fded656c..bdbe0864 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -3,16 +3,16 @@ 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). -## v1.1.0dev [unreleased] +## v1.0.1 - [2023-02-27] ### `Added` -- Added pipeline citation DOI to `WorkflowMain.groovy` to display it when executing the pipeline +- Added pipeline citation DOI to `WorkflowMain.groovy` to display it when executing the pipeline. (by @jasmezz) ### `Fixed` - Removed a header check in the `check_samplesheet.py` script that was producing false negatives. Presence of required columns is still validated. (by @Midnighter) -- Improved database downloading guidance to emphasise it is recommended to let nf-core/funcscan do the downloading on a first run, rather than manually downloading yourself (reported by @alexhbnr, fixed by @jfy133) +- Improved database downloading guidance to emphasise it is recommended to let nf-core/funcscan do the downloading on a first run, rather than manually downloading yourself. (reported by @alexhbnr, fixed by @jfy133) ### `Dependencies` diff --git a/nextflow.config b/nextflow.config index d927c549..ce6f312f 100644 --- a/nextflow.config +++ b/nextflow.config @@ -344,7 +344,7 @@ manifest { description = """Pipeline for screening for functional components of assembled contigs""" mainScript = 'main.nf' nextflowVersion = '!>=22.10.1' - version = '1.1.0dev' + version = '1.0.1' doi = '10.5281/zenodo.7643099' } From 2e7fb49f45a479e72f8a4c48b6da0e58efb2aae2 Mon Sep 17 00:00:00 2001 From: jasmezz Date: Mon, 27 Feb 2023 11:37:24 +0100 Subject: [PATCH 10/12] Update changelog with links to PRs --- CHANGELOG.md | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index bdbe0864..741a1d04 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -7,12 +7,12 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 ### `Added` -- Added pipeline citation DOI to `WorkflowMain.groovy` to display it when executing the pipeline. (by @jasmezz) +- [#229](https://github.com/nf-core/funcscan/pull/229) Added pipeline citation DOI to `WorkflowMain.groovy` to display it when executing the pipeline. (by @jasmezz) ### `Fixed` -- Removed a header check in the `check_samplesheet.py` script that was producing false negatives. Presence of required columns is still validated. (by @Midnighter) -- Improved database downloading guidance to emphasise it is recommended to let nf-core/funcscan do the downloading on a first run, rather than manually downloading yourself. (reported by @alexhbnr, fixed by @jfy133) +- [#227](https://github.com/nf-core/funcscan/pull/227) Removed a header check in the `check_samplesheet.py` script that was producing false negatives. Presence of required columns is still validated. (by @Midnighter) +- [#228](https://github.com/nf-core/funcscan/pull/228) Improved database downloading guidance to emphasise it is recommended to let nf-core/funcscan do the downloading on a first run, rather than manually downloading yourself. (reported by @alexhbnr, fixed by @jfy133) ### `Dependencies` From c4f3fdded6454cd7b1838ce098b053ed47ab884a Mon Sep 17 00:00:00 2001 From: jasmezz Date: Mon, 27 Feb 2023 11:41:11 +0100 Subject: [PATCH 11/12] Update wording in changelog [skip ci] --- CHANGELOG.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index 741a1d04..05be2e94 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -7,7 +7,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 ### `Added` -- [#229](https://github.com/nf-core/funcscan/pull/229) Added pipeline citation DOI to `WorkflowMain.groovy` to display it when executing the pipeline. (by @jasmezz) +- [#229](https://github.com/nf-core/funcscan/pull/229) Added pipeline DOI to `WorkflowMain.groovy` to display citation info when executing the pipeline. (by @jasmezz) ### `Fixed` From 54042b8a5f653dabefbd0e2f76186e2ec78ea1fd Mon Sep 17 00:00:00 2001 From: jasmezz Date: Mon, 27 Feb 2023 11:43:10 +0100 Subject: [PATCH 12/12] Fix indentation [skip ci] --- nextflow.config | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/nextflow.config b/nextflow.config index ce6f312f..3fbf9558 100644 --- a/nextflow.config +++ b/nextflow.config @@ -344,7 +344,7 @@ manifest { description = """Pipeline for screening for functional components of assembled contigs""" mainScript = 'main.nf' nextflowVersion = '!>=22.10.1' - version = '1.0.1' + version = '1.0.1' doi = '10.5281/zenodo.7643099' }