Merge pull request #314 from nf-core/release-version-bump

Release version bump to 1.1.4
nf-core · Nov 7, 2023 · 86ba79b · 86ba79b
2 parents ffba284 + c84e720
commit 86ba79b
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Showing 8 changed files with 13 additions and 10 deletions.
diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
@@ -70,7 +70,7 @@ jobs:
 
       - name: Run pipeline with test data (BGC workflow)
         run: |
-          nextflow run ${GITHUB_WORKSPACE} -profile test_bgc,docker --outdir ./results ${{ matrix.parameters }}
+          nextflow run ${GITHUB_WORKSPACE} -profile test_bgc,docker --outdir ./results ${{ matrix.parameters }} --bgc_skip_deepbgc
 
   test_deeparg:
     name: Run pipeline with test data (DeepARG only workflow)

diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -3,7 +3,7 @@
 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).
 
-## v1.1.4dev - [unreleased]
+## v1.1.4 - [2023-11-07]
 
 ### `Added`
 
@@ -12,6 +12,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 - [#306](https://github.com/nf-core/funcscan/pull/306) Added new parameter `annotation_prokka_retaincontigheaders` to allow prokka to retain the original contig headers/locus tag. (by @darcy220606)
 - [#307](https://github.com/nf-core/funcscan/pull/307) Fixed stability of deepARG tests by using Zenodo copy of database (❤️ to Gustavo Arango and Liqing Zhang for uploading, fix by @jfy133)
 - [#310](https://github.com/nf-core/funcscan/pull/310) Fixed error when supplying uncompressed input; added "fas" file extension for FASTA files. (by @tavareshugo)
+- [#311](https://github.com/nf-core/funcscan/pull/311) Merged pipeline template of nf-core/tools version 2.10. (by @jasmezz)
 
 ### `Dependencies`
 

diff --git a/assets/multiqc_config.yml b/assets/multiqc_config.yml
@@ -1,7 +1,7 @@
 report_comment: >
-  This report has been generated by the <a href="https://github.com/nf-core/funcscan/releases/tag/dev" target="_blank">nf-core/funcscan</a>
+  This report has been generated by the <a href="https://github.com/nf-core/funcscan/releases/tag/1.1.4" target="_blank">nf-core/funcscan</a>
   analysis pipeline. For information about how to interpret these results, please see the
-  <a href="https://nf-co.re/funcscan/dev/docs/output" target="_blank">documentation</a>.
+  <a href="https://nf-co.re/funcscan/1.1.4/docs/output" target="_blank">documentation</a>.
 report_section_order:
   "nf-core-funcscan-methods-description":
     order: -1000

diff --git a/docs/images/funcscan_metro_workflow.png b/docs/images/funcscan_metro_workflow.png
diff --git a/docs/images/funcscan_metro_workflow.svg b/docs/images/funcscan_metro_workflow.svg
diff --git a/docs/usage.md b/docs/usage.md
@@ -230,6 +230,8 @@ Note that the names of the supplied folders must differ from each other (e.g. `a
 
 ### DeepBGC
 
+> ⚠️ The dependencies for the deepBGC database download are currently broken. Until deepBGC gets fixed, users need to provide the database files themselves or just skip the tool (`--bgc_skip_deepbgc`). To provide the files yourself: The links for the database files can be found in [this script](https://github.com/Merck/deepbgc/blob/476934b61521d23c1122a1cfada176ee5e402741/deepbgc/data.py) from the deepBGC GitHub repository. The command `deepbgc download` as described below will not work at the moment.
+
 DeepBGC relies on trained models and Pfams to run its analysis. nf-core/funcscan will download these databases for you. If the flag `--save_databases` is set, the downloaded files will be stored in the output directory under `databases/deepbgc/`.
 
 Alternatively, if you already downloaded the database locally with `deepbgc download`, you can indicate the path to the database folder with `--bgc_deepbgc_database <path>/<to>/<deepbgc_db>/`. The folder has to contain the subfolders as in the database folder downloaded by `deepbgc download`:

diff --git a/modules.json b/modules.json
@@ -63,7 +63,7 @@
                     },
                     "custom/dumpsoftwareversions": {
                         "branch": "master",
-                        "git_sha": "05c280924b6c768d484c7c443dad5e605c4ff4b4",
+                        "git_sha": "1b372269755a5c4a13c23bc130ebada8cb9d4cd0",
                         "installed_by": ["modules"]
                     },
                     "deeparg/downloaddata": {

diff --git a/nextflow.config b/nextflow.config
@@ -391,7 +391,7 @@ manifest {
     description     = """Pipeline for screening for functional components of assembled contigs"""
     mainScript      = 'main.nf'
     nextflowVersion = '!>=23.04.0'
-    version         = '1.1.4dev'
+    version         = '1.1.4'
     doi             = '10.5281/zenodo.7643099'
 }