From 7a74d2b378720fac2bff403ec7cdbd295bab8f6e Mon Sep 17 00:00:00 2001
From: Edmund Miller <20095261+edmundmiller@users.noreply.github.com>
Date: Tue, 5 Mar 2024 10:10:39 -0600
Subject: [PATCH] Apply suggestions from code review
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Co-authored-by: Matthias Hörtenhuber <mashehu@users.noreply.github.com>
---
 .github/workflows/download_pipeline.yml | 5 +++--
 README.md                               | 3 +--
 docs/output.md                          | 2 +-
 main.nf                                 | 3 ---
 4 files changed, 5 insertions(+), 8 deletions(-)

diff --git a/.github/workflows/download_pipeline.yml b/.github/workflows/download_pipeline.yml
index 8a330045..cd7a5bfe 100644
--- a/.github/workflows/download_pipeline.yml
+++ b/.github/workflows/download_pipeline.yml
@@ -42,7 +42,8 @@ jobs:
         run: |
           echo "REPO_LOWERCASE=${GITHUB_REPOSITORY,,}" >> ${GITHUB_ENV}
           echo "REPOTITLE_LOWERCASE=$(basename ${GITHUB_REPOSITORY,,})" >> ${GITHUB_ENV}
-          echo "REPO_BRANCH=${GITHUB_REF#refs/heads/}" >> ${GITHUB_ENV}
+         
+          echo "{% raw %}REPO_BRANCH=${{ github.event.inputs.testbranch || 'dev' }}" >> ${GITHUB_ENV}
 
       - name: Download the pipeline
         env:
@@ -64,4 +65,4 @@ jobs:
         env:
           NXF_SINGULARITY_CACHEDIR: ./
           NXF_SINGULARITY_HOME_MOUNT: true
-        run: nextflow run ./${{ env.REPOTITLE_LOWERCASE }}/$( sed 's/\W/_/g' <<< ${{ env.REPO_BRANCH }}) -stub -profile test,singularity --outdir ./results
+        run: nextflow run ./${{ env.REPOTITLE_LOWERCASE }}/$( sed 's/\W/_/g' <<< ${{ env.REPO_BRANCH }}) -stub -profile test,singularity --outdir ./results{% endraw %}
diff --git a/README.md b/README.md
index a998df32..107fac57 100644
--- a/README.md
+++ b/README.md
@@ -58,9 +58,8 @@ On release, automated continuous integration tests run the pipeline on a full-si
 
 First, prepare a samplesheet with your input data that looks as follows:
 
-`samplesheet.csv`:
 
-```csv
+```csv title="samplesheet.csv
 sample,fastq_1,fastq_2
 CONTROL_REP1,AEG588A1_S1_L002_R1_001.fastq.gz,AEG588A1_S1_L002_R2_001.fastq.gz
 ```
diff --git a/docs/output.md b/docs/output.md
index 027fb9a0..f6c1f784 100644
--- a/docs/output.md
+++ b/docs/output.md
@@ -370,7 +370,7 @@ They've also created some bed files that might be useful for analysis.
   - `bwa/`: Directory containing bwa indices.
   - `bwa-mem2/`: Directory containing bwa-mem2 indices.
   - `dragmap/`: Directory containing DRAGMAP indices.
-  - `bowtie2/`: Directory containing DRAGMAP indices.
+  - `bowtie2/`: Directory containing bowtie2 indices.
 
 </details>
 
diff --git a/main.nf b/main.nf
index 67bd7eb7..df61e5c2 100644
--- a/main.nf
+++ b/main.nf
@@ -17,9 +17,6 @@ nextflow.enable.dsl = 2
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 */
 
-// TODO nf-core: Remove this line if you don't need a FASTA file
-//   This is an example of how to use getGenomeAttribute() to fetch parameters
-//   from igenomes.config using `--genome`
 params.fasta = WorkflowMain.getGenomeAttribute(params, 'fasta')
 params.gtf = WorkflowMain.getGenomeAttribute(params, 'gtf')
 params.gff = WorkflowMain.getGenomeAttribute(params, 'gff')