Merge pull request #84 from sanger-tol/align_flag

Missing align flag
sanger-tol · Jun 25, 2024 · d3743d3 · d3743d3
2 parents a94b5ad + eaed3bd
commit d3743d3
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Showing 6 changed files with 6 additions and 6 deletions.
diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
@@ -44,4 +44,4 @@ jobs:
 
       - name: Run pipeline with unaligned test data
         run: |
-          nextflow run ${GITHUB_WORKSPACE} -profile test_align,docker --outdir ./results --align
+          nextflow run ${GITHUB_WORKSPACE} -profile test_align,docker --outdir ./results
diff --git a/.github/workflows/sanger_test.yml b/.github/workflows/sanger_test.yml
@@ -18,8 +18,7 @@ jobs:
           workdir: ${{ secrets.TOWER_WORKDIR_PARENT }}/work/${{ github.repository }}/work-${{ github.sha }}
           parameters: |
             {
-              "outdir": "${{ secrets.TOWER_WORKDIR_PARENT }}/results/${{ github.repository }}/results-${{ github.sha }}",
-              "align":  true
+              "outdir": "${{ secrets.TOWER_WORKDIR_PARENT }}/results/${{ github.repository }}/results-${{ github.sha }}"
             }
           profiles: test_align,sanger,singularity,cleanup
 

diff --git a/.github/workflows/sanger_test_full.yml b/.github/workflows/sanger_test_full.yml
@@ -31,8 +31,7 @@ jobs:
           workdir: ${{ secrets.TOWER_WORKDIR_PARENT }}/work/${{ github.repository }}/work-${{ env.REVISION }}
           parameters: |
             {
-              "outdir": "${{ secrets.TOWER_WORKDIR_PARENT }}/results/${{ github.repository }}/results-${{ env.REVISION }}",
-              "align":  true,
+              "outdir": "${{ secrets.TOWER_WORKDIR_PARENT }}/results/${{ github.repository }}/results-${{ env.REVISION }}"
             }
           profiles: test_full_align,sanger,singularity,cleanup
 

diff --git a/README.md b/README.md
@@ -45,7 +45,7 @@ Steps involved:
    nextflow run sanger-tol/variantcalling -profile test,YOURPROFILE --outdir <OUTDIR>
 
    # for unaligned reads
-   nextflow run sanger-tol/variantcalling -profile test_align,YOURPROFILE --align --outdir <OUTDIR>
+   nextflow run sanger-tol/variantcalling -profile test_align,YOURPROFILE --outdir <OUTDIR>
 
    ```
 

diff --git a/conf/test_align.config b/conf/test_align.config
@@ -21,6 +21,7 @@ params {
 
     // Input data
     input  = "${projectDir}/assets/samplesheet_test_align.csv"
+    align  = true
 
     // Fasta references
     fasta = "https://tolit.cog.sanger.ac.uk/test-data/Cantharis_rufa/assembly/GCA_947369205.1_OX376310.1_CANBKR010000003.1.fasta.gz"

diff --git a/conf/test_full_align.config b/conf/test_full_align.config
@@ -18,6 +18,7 @@ params {
 
     // Input data for full size test
     input = "${projectDir}/assets/samplesheet_test_full_align.csv"
+    align = true
 
     // Fasta references
     fasta = "/lustre/scratch124/tol/projects/darwin/data/insects/Polyommatus_icarus/assembly/release/ilPolIcar1.1/insdc/GCA_937595015.1.fasta.gz"