From 9dd4af7878a01aa7f601631c5a12daa16972a7eb Mon Sep 17 00:00:00 2001
From: Matthieu Muffato <mm49@sanger.ac.uk>
Date: Fri, 21 Jun 2024 17:28:40 +0100
Subject: [PATCH 1/5] Missing align flag

---
 conf/test_align.config      | 1 +
 conf/test_full_align.config | 1 +
 2 files changed, 2 insertions(+)

diff --git a/conf/test_align.config b/conf/test_align.config
index 8da6b65..f76a21b 100644
--- 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
index 79b9fd7..a29005a 100644
--- 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"

From ee637275963c0c967389cdb6531df0eb295ce1d0 Mon Sep 17 00:00:00 2001
From: Matthieu Muffato <mm49@sanger.ac.uk>
Date: Tue, 25 Jun 2024 09:51:44 +0100
Subject: [PATCH 2/5] Not needed if the profile includes the option

---
 .github/workflows/ci.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
index 567ac13..c8c1eca 100644
--- 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

From 0bd81bb066493eeda56c1c15fe8275244f5f9d4a Mon Sep 17 00:00:00 2001
From: Matthieu Muffato <mm49@sanger.ac.uk>
Date: Tue, 25 Jun 2024 09:52:15 +0100
Subject: [PATCH 3/5] 	 Not needed if the profile includes the option

---
 .github/workflows/sanger_test.yml | 3 +--
 1 file changed, 1 insertion(+), 2 deletions(-)

diff --git a/.github/workflows/sanger_test.yml b/.github/workflows/sanger_test.yml
index a4e5426..b8a382b 100644
--- 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
 

From 118a6a567e5c07ad46a9987af230e5fbb0313dd4 Mon Sep 17 00:00:00 2001
From: Matthieu Muffato <mm49@sanger.ac.uk>
Date: Tue, 25 Jun 2024 09:52:35 +0100
Subject: [PATCH 4/5] Not needed if the profile includes the option

---
 .github/workflows/sanger_test_full.yml | 3 +--
 1 file changed, 1 insertion(+), 2 deletions(-)

diff --git a/.github/workflows/sanger_test_full.yml b/.github/workflows/sanger_test_full.yml
index a552c63..4f4d5fc 100644
--- 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
 

From eaed3bd2e1b7b7c31491d75955f7389044d202f6 Mon Sep 17 00:00:00 2001
From: Guoying Qi <729395+gq1@users.noreply.github.com>
Date: Tue, 25 Jun 2024 10:17:03 +0100
Subject: [PATCH 5/5] Update README.md, remove align flag

---
 README.md | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/README.md b/README.md
index 3a344df..8722707 100644
--- 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>
 
    ```