Merge pull request #231 from nf-core/dev

Patch release v1.0.1

CHANGELOG.md

@@ -3,6 +3,21 @@
 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).
 
+## v1.0.1 - [2023-02-27]
+
+### `Added`
+
+- [#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`
+
+- [#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`
+
+### `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.

README.md

@@ -75,8 +75,7 @@ For further information or help, don't hesitate to get in touch on the [Slack `#
 
 ## Citations
 
-<!-- TODO nf-core: Add citation for pipeline after first release. Uncomment lines below and update Zenodo doi and badge at the top of this file. -->
-<!-- If you use  nf-core/funcscan for your analysis, please cite it using the following doi: [10.5281/zenodo.XXXXXX](https://doi.org/10.5281/zenodo.XXXXXX) -->
+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.
 

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
 

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
 

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" +

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         = '1.0.1'
     doi             = '10.5281/zenodo.7643099'
 }