Apply suggestions from code review

Co-authored-by: Matthias Hörtenhuber <mashehu@users.noreply.github.com>

.editorconfig

@@ -28,10 +28,6 @@ indent_style = unset
 [/assets/email*]
 indent_size = unset
 
-# ignore Readme
-[README.md]
-indent_style = unset
-
 # ignore python
 [*.{py,md}]
 indent_style = unset

.github/workflows/release-announcements.yml

@@ -12,7 +12,7 @@ jobs:
       - name: get topics and convert to hashtags
         id: get_topics
         run: |
-          curl -s https://nf-co.re/pipelines.json | jq -r '.remote_workflows[] | select(.full_name == "${{ github.repository }}") | .topics[]' | awk '{print "#"$0}' | tr '\n' ' ' >> $GITHUB_OUTPUT
+          echo "topics=$(curl -s https://nf-co.re/pipelines.json | jq -r '.remote_workflows[] | select(.full_name == "${{ github.repository }}") | .topics[]' | awk '{print "#"$0}' | tr '\n' ' ')"  >> $GITHUB_OUTPUT
 
       - uses: rzr/fediverse-action@master
         with:
@@ -25,7 +25,7 @@ jobs:
 
             Please see the changelog: ${{ github.event.release.html_url }}
 
-            ${{ steps.get_topics.outputs.GITHUB_OUTPUT }} #nfcore #openscience #nextflow #bioinformatics
+             ${{ steps.get_topics.outputs.topics }} #nfcore #openscience #nextflow #bioinformatics
 
   send-tweet:
     runs-on: ubuntu-latest

docs/usage.md

@@ -253,7 +253,7 @@ Instead of relying on one short amplicon, scaffolding multiple regions along a r
 
 For example, multiple variable regions of the 16S rRNA gene were sequenced with various primers and need to be unified. This leads to one unified abundance and taxonomy profile over all variable regions. However, ASV sequences are only available separately, there is no reconstruction of complete de-novo sequences feasible.
 
-Required is information about sequencing data via [`--input`](#samplesheet-input), region primers length information via [`--multiregion`](https://nf-co.re/ampliseq/parameters#multiregion), and a taxonomic database via [`--sidle_ref_taxonomy`](https://nf-co.re/ampliseq/parameters#sidle_ref_taxonomy) or [`--sidle_ref_tax_custom`](https://nf-co.re/ampliseq/parameters#sidle_ref_tax_custom).
+Information about sequencing data via [`--input`](#samplesheet-input), region primers length information via [`--multiregion`](https://nf-co.re/ampliseq/parameters#multiregion), and a taxonomic database via [`--sidle_ref_taxonomy`](https://nf-co.re/ampliseq/parameters#sidle_ref_taxonomy) or [`--sidle_ref_tax_custom`](https://nf-co.re/ampliseq/parameters#sidle_ref_tax_custom) is required.
 
 ```bash
 --input "samplesheet_multiregion.tsv"  --multiregion "regions_multiregion.tsv" --sidle_ref_taxonomy "silva=128"

modules/local/sidle_taxrecon.nf

@@ -29,7 +29,6 @@ process SIDLE_TAXRECON {
     export MPLCONFIGDIR="./mplconfigdir"
     export NUMBA_CACHE_DIR="./numbacache"
 
-    #CPU=1
     qiime sidle reconstruct-taxonomy \\
         --i-reconstruction-map ${reconstruction_map} \\
         --i-taxonomy ${tax} \\

modules/local/sidle_trim.nf

@@ -31,7 +31,6 @@ process SIDLE_TRIM {
     export MPLCONFIGDIR="./mplconfigdir"
     export NUMBA_CACHE_DIR="./numbacache"
 
-    #CPU=1
     qiime sidle trim-dada2-posthoc \\
         --i-table ${table} \\
         --i-representative-sequences ${seq} \\