From fac660c0e69c47272a149b1c09cff2d9f62fbc60 Mon Sep 17 00:00:00 2001
From: Krannich479 <krannich479@googlemail.com>
Date: Tue, 23 Apr 2024 11:14:08 +0200
Subject: [PATCH 01/47] new CI fundamental test

---
 .github/workflows/DryRun.yml           |  5 +++-
 .github/workflows/VariantCalling.yml   | 41 ++++++++++++++++++++++++++
 .github/workflows/pytest_workflows.yml |  4 ++-
 3 files changed, 48 insertions(+), 2 deletions(-)
 create mode 100644 .github/workflows/VariantCalling.yml

diff --git a/.github/workflows/DryRun.yml b/.github/workflows/DryRun.yml
index 0baf6cb..d9b4721 100644
--- a/.github/workflows/DryRun.yml
+++ b/.github/workflows/DryRun.yml
@@ -1,6 +1,9 @@
 name: DryRun
 
-on: [push]
+on:
+  push:
+    branches: [dhhgfgdsaashg]
+
 jobs:
   build:
     runs-on: ubuntu-latest
diff --git a/.github/workflows/VariantCalling.yml b/.github/workflows/VariantCalling.yml
new file mode 100644
index 0000000..59353aa
--- /dev/null
+++ b/.github/workflows/VariantCalling.yml
@@ -0,0 +1,41 @@
+name: Variantcalling
+
+on:
+  push:
+    branches: [main, dev, ci]
+  pull_request:
+    branches: [main]
+
+jobs:
+  Variantcalling:
+  
+    runs-on: ubuntu-latest
+    steps:
+    - name: Setup CovPipe2 and conda
+      uses: actions/checkout@v4
+      uses: conda-incubator/setup-miniconda@v3
+      with:
+        miniconda-version: "latest"
+        channels: defaults,bioconda,conda-forge
+        channel-priority: true
+        auto-activate-base: true
+
+    - name: Check conda installation
+      run: |
+        conda info
+        conda list
+        conda config --show-sources
+        conda config --show
+
+    - name: Install nextflow
+      run: |
+        conda install -c bioconda nextflow
+        nextflow -version
+
+    - name: Check CovPipe2 presence
+      run: nextflow run CoVpipe2.nf --help
+      
+#    - name: dry run
+#     run: |
+#         touch reads_1.fastq reads_2.fastq
+#         nextflow run CoVpipe2.nf --fastq reads_{1,2}.fastq --reference sars-cov-2 --cores 2 --max_cores 2 -stub -profile stub
diff --git a/.github/workflows/pytest_workflows.yml b/.github/workflows/pytest_workflows.yml
index 63c9fa5..b4ed1a6 100644
--- a/.github/workflows/pytest_workflows.yml
+++ b/.github/workflows/pytest_workflows.yml
@@ -1,6 +1,8 @@
 name: Pytest-workflow
 
-on: [push]
+on:
+  push:
+    branches: [dhhgfgdsaashg]
 
 jobs:
   test:

From a28896af383809fdce4576f5711b7855effea82d Mon Sep 17 00:00:00 2001
From: Krannich479 <krannich479@googlemail.com>
Date: Tue, 23 Apr 2024 11:20:10 +0200
Subject: [PATCH 02/47] the yaml grind chapter 1

---
 .github/workflows/VariantCalling.yml | 15 +++++++--------
 1 file changed, 7 insertions(+), 8 deletions(-)

diff --git a/.github/workflows/VariantCalling.yml b/.github/workflows/VariantCalling.yml
index 59353aa..28d4e36 100644
--- a/.github/workflows/VariantCalling.yml
+++ b/.github/workflows/VariantCalling.yml
@@ -11,14 +11,13 @@ jobs:
   
     runs-on: ubuntu-latest
     steps:
-    - name: Setup CovPipe2 and conda
-      uses: actions/checkout@v4
-      uses: conda-incubator/setup-miniconda@v3
-      with:
-        miniconda-version: "latest"
-        channels: defaults,bioconda,conda-forge
-        channel-priority: true
-        auto-activate-base: true
+      - uses: actions/checkout@v4
+      - uses: conda-incubator/setup-miniconda@v3
+        with:
+          miniconda-version: "latest"
+          channels: defaults,bioconda,conda-forge
+          channel-priority: true
+          auto-activate-base: true
 
     - name: Check conda installation
       run: |

From f62be3b3d62b2c3b17d8c039d5bd681eb32f01a5 Mon Sep 17 00:00:00 2001
From: Krannich479 <krannich479@googlemail.com>
Date: Tue, 23 Apr 2024 11:23:48 +0200
Subject: [PATCH 03/47] the yaml grind chapter 2

---
 .github/workflows/VariantCalling.yml | 5 ++++-
 1 file changed, 4 insertions(+), 1 deletion(-)

diff --git a/.github/workflows/VariantCalling.yml b/.github/workflows/VariantCalling.yml
index 28d4e36..325da8d 100644
--- a/.github/workflows/VariantCalling.yml
+++ b/.github/workflows/VariantCalling.yml
@@ -8,8 +8,11 @@ on:
 
 jobs:
   Variantcalling:
-  
+    name: Variantcalling CI
     runs-on: ubuntu-latest
+    defaults:
+      run:
+        shell: bash -el {0}
     steps:
       - uses: actions/checkout@v4
       - uses: conda-incubator/setup-miniconda@v3

From 921279e9a40b5fc586c499b7c6544e6760e80ca8 Mon Sep 17 00:00:00 2001
From: Krannich479 <krannich479@googlemail.com>
Date: Tue, 23 Apr 2024 11:25:30 +0200
Subject: [PATCH 04/47] the yaml grind chapter 3

---
 .github/workflows/VariantCalling.yml | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/.github/workflows/VariantCalling.yml b/.github/workflows/VariantCalling.yml
index 325da8d..e58a454 100644
--- a/.github/workflows/VariantCalling.yml
+++ b/.github/workflows/VariantCalling.yml
@@ -1,4 +1,4 @@
-name: Variantcalling
+name: VariantCalling
 
 on:
   push:
@@ -7,8 +7,8 @@ on:
     branches: [main]
 
 jobs:
-  Variantcalling:
-    name: Variantcalling CI
+  VariantCalling:
+    name: VariantCalling CI
     runs-on: ubuntu-latest
     defaults:
       run:

From ebf4b7b602bd819876a7877a48058d5f1bbaed1c Mon Sep 17 00:00:00 2001
From: Krannich479 <krannich479@googlemail.com>
Date: Tue, 23 Apr 2024 11:28:32 +0200
Subject: [PATCH 05/47] the yaml grind chapter 4

---
 .github/workflows/DryRun.yml           | 2 +-
 .github/workflows/VariantCalling.yml   | 4 ++--
 .github/workflows/pytest_workflows.yml | 2 +-
 3 files changed, 4 insertions(+), 4 deletions(-)

diff --git a/.github/workflows/DryRun.yml b/.github/workflows/DryRun.yml
index d9b4721..50785a1 100644
--- a/.github/workflows/DryRun.yml
+++ b/.github/workflows/DryRun.yml
@@ -2,7 +2,7 @@ name: DryRun
 
 on:
   push:
-    branches: [dhhgfgdsaashg]
+    branches: ["dhhgfgdsaashg"]
 
 jobs:
   build:
diff --git a/.github/workflows/VariantCalling.yml b/.github/workflows/VariantCalling.yml
index e58a454..e725fe9 100644
--- a/.github/workflows/VariantCalling.yml
+++ b/.github/workflows/VariantCalling.yml
@@ -2,9 +2,9 @@ name: VariantCalling
 
 on:
   push:
-    branches: [main, dev, ci]
+    branches: ["main", "dev", "ci"]
   pull_request:
-    branches: [main]
+    branches: ["main"]
 
 jobs:
   VariantCalling:
diff --git a/.github/workflows/pytest_workflows.yml b/.github/workflows/pytest_workflows.yml
index b4ed1a6..fd618c6 100644
--- a/.github/workflows/pytest_workflows.yml
+++ b/.github/workflows/pytest_workflows.yml
@@ -2,7 +2,7 @@ name: Pytest-workflow
 
 on:
   push:
-    branches: [dhhgfgdsaashg]
+    branches: ["dhhgfgdsaashg"]
 
 jobs:
   test:

From c36487d9e14b49c3627cb6080fcc2721dc047208 Mon Sep 17 00:00:00 2001
From: Krannich479 <krannich479@googlemail.com>
Date: Tue, 23 Apr 2024 11:32:28 +0200
Subject: [PATCH 06/47] the yaml grind chapter 5

---
 .github/workflows/VariantCalling.yml | 34 ++++++++++++++--------------
 1 file changed, 17 insertions(+), 17 deletions(-)

diff --git a/.github/workflows/VariantCalling.yml b/.github/workflows/VariantCalling.yml
index e725fe9..ca0c3f8 100644
--- a/.github/workflows/VariantCalling.yml
+++ b/.github/workflows/VariantCalling.yml
@@ -22,22 +22,22 @@ jobs:
           channel-priority: true
           auto-activate-base: true
 
-    - name: Check conda installation
-      run: |
-        conda info
-        conda list
-        conda config --show-sources
-        conda config --show
+      - name: Check conda installation
+        run: |
+          conda info
+          conda list
+          conda config --show-sources
+          conda config --show
 
-    - name: Install nextflow
-      run: |
-        conda install -c bioconda nextflow
-        nextflow -version
+      - name: Install nextflow
+        run: |
+          conda install -c bioconda nextflow
+          nextflow -version
 
-    - name: Check CovPipe2 presence
-      run: nextflow run CoVpipe2.nf --help
-      
-#    - name: dry run
-#     run: |
-#         touch reads_1.fastq reads_2.fastq
-#         nextflow run CoVpipe2.nf --fastq reads_{1,2}.fastq --reference sars-cov-2 --cores 2 --max_cores 2 -stub -profile stub
+      - name: Check CovPipe2 presence
+        run: nextflow run CoVpipe2.nf --help
+        
+  #    - name: dry run
+  #     run: |
+  #         touch reads_1.fastq reads_2.fastq
+  #         nextflow run CoVpipe2.nf --fastq reads_{1,2}.fastq --reference sars-cov-2 --cores 2 --max_cores 2 -stub -profile stub

From 2db097ab1126d719010de472c94d65b40d2c1efc Mon Sep 17 00:00:00 2001
From: Krannich479 <krannich479@googlemail.com>
Date: Tue, 23 Apr 2024 11:57:08 +0200
Subject: [PATCH 07/47] CI test cievad hap.nf

---
 .github/workflows/VariantCalling.yml | 9 +++++++++
 1 file changed, 9 insertions(+)

diff --git a/.github/workflows/VariantCalling.yml b/.github/workflows/VariantCalling.yml
index ca0c3f8..1d51c74 100644
--- a/.github/workflows/VariantCalling.yml
+++ b/.github/workflows/VariantCalling.yml
@@ -37,6 +37,15 @@ jobs:
       - name: Check CovPipe2 presence
         run: nextflow run CoVpipe2.nf --help
         
+      - name: Git checkout CIEVaD
+        run: |
+            git clone https://github.com/rki-mf1/cievad.git
+            pushd cievad
+            nextflow run hap.py -profile local,conda
+            ls -la results/simulated_hap*NGSWGS*.fastq
+            popd
+
+
   #    - name: dry run
   #     run: |
   #         touch reads_1.fastq reads_2.fastq

From 88a6e6d5562c7899d800a5f1206805e6be4518f9 Mon Sep 17 00:00:00 2001
From: Krannich479 <krannich479@googlemail.com>
Date: Tue, 23 Apr 2024 11:57:33 +0200
Subject: [PATCH 08/47] CI test hap.nf

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

diff --git a/.github/workflows/VariantCalling.yml b/.github/workflows/VariantCalling.yml
index 1d51c74..5787de7 100644
--- a/.github/workflows/VariantCalling.yml
+++ b/.github/workflows/VariantCalling.yml
@@ -41,7 +41,7 @@ jobs:
         run: |
             git clone https://github.com/rki-mf1/cievad.git
             pushd cievad
-            nextflow run hap.py -profile local,conda
+            nextflow run hap.nf -profile local,conda
             ls -la results/simulated_hap*NGSWGS*.fastq
             popd
 

From 06c3738f5d8c9f0a1e332bf00e38871fb36f8054 Mon Sep 17 00:00:00 2001
From: Krannich479 <krannich479@googlemail.com>
Date: Tue, 23 Apr 2024 12:53:48 +0200
Subject: [PATCH 09/47] manage deploy key for private repo access

---
 .github/workflows/VariantCalling.yml | 3 +++
 1 file changed, 3 insertions(+)

diff --git a/.github/workflows/VariantCalling.yml b/.github/workflows/VariantCalling.yml
index 5787de7..cf2c499 100644
--- a/.github/workflows/VariantCalling.yml
+++ b/.github/workflows/VariantCalling.yml
@@ -39,6 +39,9 @@ jobs:
         
       - name: Git checkout CIEVaD
         run: |
+            eval `ssh-agent -s`
+            ssh-add - <<< '${{ secrets.PRIVATE_SSH_KEY }}'
+            
             git clone https://github.com/rki-mf1/cievad.git
             pushd cievad
             nextflow run hap.nf -profile local,conda

From c3b2323674bcceb74c98e96b3203db6dda411ca5 Mon Sep 17 00:00:00 2001
From: Krannich479 <krannich479@googlemail.com>
Date: Tue, 23 Apr 2024 13:06:59 +0200
Subject: [PATCH 10/47] try SSH clone

---
 .github/workflows/VariantCalling.yml | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/.github/workflows/VariantCalling.yml b/.github/workflows/VariantCalling.yml
index cf2c499..8024de1 100644
--- a/.github/workflows/VariantCalling.yml
+++ b/.github/workflows/VariantCalling.yml
@@ -41,8 +41,8 @@ jobs:
         run: |
             eval `ssh-agent -s`
             ssh-add - <<< '${{ secrets.PRIVATE_SSH_KEY }}'
-            
-            git clone https://github.com/rki-mf1/cievad.git
+
+            git clone git@github.com:rki-mf1/cievad.git
             pushd cievad
             nextflow run hap.nf -profile local,conda
             ls -la results/simulated_hap*NGSWGS*.fastq

From f9e839267adac04a7e0f8848f70666e18ba6e31c Mon Sep 17 00:00:00 2001
From: Krannich479 <krannich479@googlemail.com>
Date: Tue, 23 Apr 2024 13:21:24 +0200
Subject: [PATCH 11/47] Add reference to CI

---
 .github/workflows/VariantCalling.yml | 5 +++--
 1 file changed, 3 insertions(+), 2 deletions(-)

diff --git a/.github/workflows/VariantCalling.yml b/.github/workflows/VariantCalling.yml
index 8024de1..d271d6d 100644
--- a/.github/workflows/VariantCalling.yml
+++ b/.github/workflows/VariantCalling.yml
@@ -41,10 +41,11 @@ jobs:
         run: |
             eval `ssh-agent -s`
             ssh-add - <<< '${{ secrets.PRIVATE_SSH_KEY }}'
-
             git clone git@github.com:rki-mf1/cievad.git
             pushd cievad
-            nextflow run hap.nf -profile local,conda
+            wget https://www.ebi.ac.uk/ena/browser/api/fasta/MN908947.3
+            sed 's/>ENA|MN908947|MN908947.3 Severe acute respiratory syndrome coronavirus 2 isolate Wuhan-Hu-1, complete genome./>MN908947.3/g' MN908947.3 > MN908947.3.fasta
+            nextflow run hap.nf -profile local,conda --reference MN908947.3.fasta
             ls -la results/simulated_hap*NGSWGS*.fastq
             popd
 

From 7eb2bd25c5cef94dc3d022bd3c1c497614fa50c7 Mon Sep 17 00:00:00 2001
From: Krannich479 <krannich479@googlemail.com>
Date: Tue, 23 Apr 2024 13:35:52 +0200
Subject: [PATCH 12/47] CI split and download and run of cievad

---
 .github/workflows/VariantCalling.yml | 7 ++++++-
 1 file changed, 6 insertions(+), 1 deletion(-)

diff --git a/.github/workflows/VariantCalling.yml b/.github/workflows/VariantCalling.yml
index d271d6d..4a805e2 100644
--- a/.github/workflows/VariantCalling.yml
+++ b/.github/workflows/VariantCalling.yml
@@ -37,7 +37,7 @@ jobs:
       - name: Check CovPipe2 presence
         run: nextflow run CoVpipe2.nf --help
         
-      - name: Git checkout CIEVaD
+      - name: Git checkout CIEVaD + REF
         run: |
             eval `ssh-agent -s`
             ssh-add - <<< '${{ secrets.PRIVATE_SSH_KEY }}'
@@ -45,6 +45,11 @@ jobs:
             pushd cievad
             wget https://www.ebi.ac.uk/ena/browser/api/fasta/MN908947.3
             sed 's/>ENA|MN908947|MN908947.3 Severe acute respiratory syndrome coronavirus 2 isolate Wuhan-Hu-1, complete genome./>MN908947.3/g' MN908947.3 > MN908947.3.fasta
+            popd
+
+      - name: Run CIEVaD hap
+        run: |
+            pushd cievad
             nextflow run hap.nf -profile local,conda --reference MN908947.3.fasta
             ls -la results/simulated_hap*NGSWGS*.fastq
             popd

From 5cf823bb6c11cdb7f932325741d4d181932333da Mon Sep 17 00:00:00 2001
From: Krannich479 <krannich479@googlemail.com>
Date: Tue, 23 Apr 2024 14:39:29 +0200
Subject: [PATCH 13/47] CI test unix variables across tasks

---
 .github/workflows/VariantCalling.yml | 8 +++++++-
 1 file changed, 7 insertions(+), 1 deletion(-)

diff --git a/.github/workflows/VariantCalling.yml b/.github/workflows/VariantCalling.yml
index 4a805e2..7751c3a 100644
--- a/.github/workflows/VariantCalling.yml
+++ b/.github/workflows/VariantCalling.yml
@@ -49,11 +49,17 @@ jobs:
 
       - name: Run CIEVaD hap
         run: |
+            NB_SAMPLES=3
             pushd cievad
-            nextflow run hap.nf -profile local,conda --reference MN908947.3.fasta
+            nextflow run hap.nf -profile local,conda --n $NB_SAMPLES --reference MN908947.3.fasta
             ls -la results/simulated_hap*NGSWGS*.fastq
             popd
 
+      - name: Run CovPipe2
+        run: |
+            echo "sample,fastq_1,fastq_2" > samplesheet.csv
+            ech $NB_SAMPLES
+
 
   #    - name: dry run
   #     run: |

From 429350e68ac9ad8c8507f0f49c4cc7c11052f0c2 Mon Sep 17 00:00:00 2001
From: Krannich479 <krannich479@googlemail.com>
Date: Tue, 23 Apr 2024 14:40:17 +0200
Subject: [PATCH 14/47] -

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

diff --git a/.github/workflows/VariantCalling.yml b/.github/workflows/VariantCalling.yml
index 7751c3a..7110e73 100644
--- a/.github/workflows/VariantCalling.yml
+++ b/.github/workflows/VariantCalling.yml
@@ -58,7 +58,7 @@ jobs:
       - name: Run CovPipe2
         run: |
             echo "sample,fastq_1,fastq_2" > samplesheet.csv
-            ech $NB_SAMPLES
+            echo $NB_SAMPLES
 
 
   #    - name: dry run

From bb03c64af854ad381f7b439bcbf852f1008b7b6d Mon Sep 17 00:00:00 2001
From: Krannich479 <krannich479@googlemail.com>
Date: Tue, 23 Apr 2024 15:05:08 +0200
Subject: [PATCH 15/47] CI try run CovPipe2 on simulated data

---
 .github/workflows/VariantCalling.yml | 18 +++++++++++++++---
 1 file changed, 15 insertions(+), 3 deletions(-)

diff --git a/.github/workflows/VariantCalling.yml b/.github/workflows/VariantCalling.yml
index 7110e73..3ce4013 100644
--- a/.github/workflows/VariantCalling.yml
+++ b/.github/workflows/VariantCalling.yml
@@ -49,16 +49,28 @@ jobs:
 
       - name: Run CIEVaD hap
         run: |
-            NB_SAMPLES=3
             pushd cievad
-            nextflow run hap.nf -profile local,conda --n $NB_SAMPLES --reference MN908947.3.fasta
+            nextflow run hap.nf -profile local,conda --reference MN908947.3.fasta
             ls -la results/simulated_hap*NGSWGS*.fastq
             popd
 
       - name: Run CovPipe2
         run: |
+            # BECAUSE CIEVAD'S DEFAULT IS N=3 SAMPLES
+            NB_SAMPLES=3
             echo "sample,fastq_1,fastq_2" > samplesheet.csv
-            echo $NB_SAMPLES
+            for s in $(seq 1 $NB_SAMPLES); do echo "hap${s},cievad/results/simulated_hap${s}.NGSWGS.R1.fastq,cievad/results/simulated_hap${s}.NGSWGS.R2.fastq" >> samplesheet.csv; done
+            cat samplesheet.csv
+            nextflow run rki-mf1/CoVpipe2 \
+              -r v0.4.2 \
+              -profile local,conda \
+              -w work \
+              --output results \
+              --reference 'sars-cov-2' \
+              --fastq samplesheet.csv --list \
+              --primer_version V3
+            ls -la results/03-Variant-Calling/simulated_hap*/simulated_hap*.filtered.gt_adjust.filtered_indels.vcf.gz
+
 
 
   #    - name: dry run

From d4c42833c53a588c6eb3a065bebc22070d1a5b42 Mon Sep 17 00:00:00 2001
From: Krannich479 <krannich479@googlemail.com>
Date: Tue, 23 Apr 2024 15:17:55 +0200
Subject: [PATCH 16/47] CI retry with reformat

---
 .github/workflows/VariantCalling.yml | 9 +--------
 1 file changed, 1 insertion(+), 8 deletions(-)

diff --git a/.github/workflows/VariantCalling.yml b/.github/workflows/VariantCalling.yml
index 3ce4013..f0a9373 100644
--- a/.github/workflows/VariantCalling.yml
+++ b/.github/workflows/VariantCalling.yml
@@ -61,14 +61,7 @@ jobs:
             echo "sample,fastq_1,fastq_2" > samplesheet.csv
             for s in $(seq 1 $NB_SAMPLES); do echo "hap${s},cievad/results/simulated_hap${s}.NGSWGS.R1.fastq,cievad/results/simulated_hap${s}.NGSWGS.R2.fastq" >> samplesheet.csv; done
             cat samplesheet.csv
-            nextflow run rki-mf1/CoVpipe2 \
-              -r v0.4.2 \
-              -profile local,conda \
-              -w work \
-              --output results \
-              --reference 'sars-cov-2' \
-              --fastq samplesheet.csv --list \
-              --primer_version V3
+            nextflow run rki-mf1/CoVpipe2 -r v0.4.2 -profile local,conda -w work --output results --reference 'sars-cov-2' --fastq samplesheet.csv --list --primer_version V3
             ls -la results/03-Variant-Calling/simulated_hap*/simulated_hap*.filtered.gt_adjust.filtered_indels.vcf.gz
 
 

From a5aef6dd66f9adf1b9346bbc150e5729905fb25f Mon Sep 17 00:00:00 2001
From: Krannich479 <krannich479@googlemail.com>
Date: Tue, 23 Apr 2024 15:53:08 +0200
Subject: [PATCH 17/47] CI use CoVpipe2  version of auto-checkout

---
 .github/workflows/VariantCalling.yml | 8 +++++++-
 1 file changed, 7 insertions(+), 1 deletion(-)

diff --git a/.github/workflows/VariantCalling.yml b/.github/workflows/VariantCalling.yml
index f0a9373..0adb7d0 100644
--- a/.github/workflows/VariantCalling.yml
+++ b/.github/workflows/VariantCalling.yml
@@ -61,7 +61,13 @@ jobs:
             echo "sample,fastq_1,fastq_2" > samplesheet.csv
             for s in $(seq 1 $NB_SAMPLES); do echo "hap${s},cievad/results/simulated_hap${s}.NGSWGS.R1.fastq,cievad/results/simulated_hap${s}.NGSWGS.R2.fastq" >> samplesheet.csv; done
             cat samplesheet.csv
-            nextflow run rki-mf1/CoVpipe2 -r v0.4.2 -profile local,conda -w work --output results --reference 'sars-cov-2' --fastq samplesheet.csv --list --primer_version V3
+            nextflow run CoVpipe2.nf \
+              -profile local,conda \
+              -w work \
+              --output results \
+              --reference 'sars-cov-2' \
+              --fastq samplesheet.csv --list \
+              --primer_version V3
             ls -la results/03-Variant-Calling/simulated_hap*/simulated_hap*.filtered.gt_adjust.filtered_indels.vcf.gz
 
 

From d982643ce21b4fda1bebf73ce78856a0b6ca2223 Mon Sep 17 00:00:00 2001
From: Krannich479 <krannich479@googlemail.com>
Date: Tue, 23 Apr 2024 16:03:26 +0200
Subject: [PATCH 18/47] CI inspect  results

---
 .github/workflows/VariantCalling.yml | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/.github/workflows/VariantCalling.yml b/.github/workflows/VariantCalling.yml
index 0adb7d0..dbba2a4 100644
--- a/.github/workflows/VariantCalling.yml
+++ b/.github/workflows/VariantCalling.yml
@@ -68,7 +68,8 @@ jobs:
               --reference 'sars-cov-2' \
               --fastq samplesheet.csv --list \
               --primer_version V3
-            ls -la results/03-Variant-Calling/simulated_hap*/simulated_hap*.filtered.gt_adjust.filtered_indels.vcf.gz
+            ls -la results/
+            tree results
 
 
 

From 82182ce1b8fe30b1b91c02454900da0232736c98 Mon Sep 17 00:00:00 2001
From: Krannich479 <krannich479@googlemail.com>
Date: Tue, 23 Apr 2024 17:00:42 +0200
Subject: [PATCH 19/47] CI cievad eval

---
 .github/workflows/VariantCalling.yml | 17 ++++++++++-------
 1 file changed, 10 insertions(+), 7 deletions(-)

diff --git a/.github/workflows/VariantCalling.yml b/.github/workflows/VariantCalling.yml
index dbba2a4..a9fbc21 100644
--- a/.github/workflows/VariantCalling.yml
+++ b/.github/workflows/VariantCalling.yml
@@ -68,12 +68,15 @@ jobs:
               --reference 'sars-cov-2' \
               --fastq samplesheet.csv --list \
               --primer_version V3
-            ls -la results/
-            tree results
-
 
+      - name: Prep CIEVaD input
+            NB_SAMPLES=3
+            mkdir -p cievad/callsets
+            for s in $(seq 1 $NB_SAMPLES); do ln -s results/03-Variant-Calling/hap${s}/hap${s}.filtered.gt_adjust.filtered_indels.vcf.gz cievad/callsets/callset_${s}.vcf.gz; done
 
-  #    - name: dry run
-  #     run: |
-  #         touch reads_1.fastq reads_2.fastq
-  #         nextflow run CoVpipe2.nf --fastq reads_{1,2}.fastq --reference sars-cov-2 --cores 2 --max_cores 2 -stub -profile stub
+      - name: Run CIEVaD eval
+        run: |
+            pushd cievad
+            nextflow run eval.nf -profile local,conda --callsets_dir callsets
+            cat results/*sompy.stats.csv
+            popd

From da96a14b4db8a532d1cd43f46ba098f0a7334e3d Mon Sep 17 00:00:00 2001
From: Krannich479 <krannich479@googlemail.com>
Date: Tue, 23 Apr 2024 17:02:41 +0200
Subject: [PATCH 20/47] tiny fix

---
 .github/workflows/VariantCalling.yml | 1 +
 1 file changed, 1 insertion(+)

diff --git a/.github/workflows/VariantCalling.yml b/.github/workflows/VariantCalling.yml
index a9fbc21..50da9cf 100644
--- a/.github/workflows/VariantCalling.yml
+++ b/.github/workflows/VariantCalling.yml
@@ -70,6 +70,7 @@ jobs:
               --primer_version V3
 
       - name: Prep CIEVaD input
+        run: |
             NB_SAMPLES=3
             mkdir -p cievad/callsets
             for s in $(seq 1 $NB_SAMPLES); do ln -s results/03-Variant-Calling/hap${s}/hap${s}.filtered.gt_adjust.filtered_indels.vcf.gz cievad/callsets/callset_${s}.vcf.gz; done

From a21614bc8f3f3274b2fd0aaba5b18e4dc0e9dd6b Mon Sep 17 00:00:00 2001
From: Krannich479 <krannich479@googlemail.com>
Date: Tue, 23 Apr 2024 17:14:17 +0200
Subject: [PATCH 21/47] CI add ref to eval call

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

diff --git a/.github/workflows/VariantCalling.yml b/.github/workflows/VariantCalling.yml
index 50da9cf..5ee8e34 100644
--- a/.github/workflows/VariantCalling.yml
+++ b/.github/workflows/VariantCalling.yml
@@ -78,6 +78,6 @@ jobs:
       - name: Run CIEVaD eval
         run: |
             pushd cievad
-            nextflow run eval.nf -profile local,conda --callsets_dir callsets
+            nextflow run eval.nf -profile local,conda --callsets_dir callsets --reference MN908947.3.fasta
             cat results/*sompy.stats.csv
             popd

From 2dc989346869444b4e6e0b5c97654b6b0325e2e1 Mon Sep 17 00:00:00 2001
From: Krannich479 <krannich479@googlemail.com>
Date: Tue, 23 Apr 2024 17:25:32 +0200
Subject: [PATCH 22/47] CI check cievad  results

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

diff --git a/.github/workflows/VariantCalling.yml b/.github/workflows/VariantCalling.yml
index 5ee8e34..26399ff 100644
--- a/.github/workflows/VariantCalling.yml
+++ b/.github/workflows/VariantCalling.yml
@@ -79,5 +79,5 @@ jobs:
         run: |
             pushd cievad
             nextflow run eval.nf -profile local,conda --callsets_dir callsets --reference MN908947.3.fasta
-            cat results/*sompy.stats.csv
+            tree results
             popd

From 1a8fa1c99421079f3f83e0387e71a6f01d24755d Mon Sep 17 00:00:00 2001
From: Krannich479 <krannich479@googlemail.com>
Date: Tue, 23 Apr 2024 17:40:36 +0200
Subject: [PATCH 23/47] CI check folder structure

---
 .github/workflows/VariantCalling.yml | 1 +
 1 file changed, 1 insertion(+)

diff --git a/.github/workflows/VariantCalling.yml b/.github/workflows/VariantCalling.yml
index 26399ff..f54c4cf 100644
--- a/.github/workflows/VariantCalling.yml
+++ b/.github/workflows/VariantCalling.yml
@@ -74,6 +74,7 @@ jobs:
             NB_SAMPLES=3
             mkdir -p cievad/callsets
             for s in $(seq 1 $NB_SAMPLES); do ln -s results/03-Variant-Calling/hap${s}/hap${s}.filtered.gt_adjust.filtered_indels.vcf.gz cievad/callsets/callset_${s}.vcf.gz; done
+            tree .
 
       - name: Run CIEVaD eval
         run: |

From 262f9ec0d34d220b47ddaef6f9465e3100126c3e Mon Sep 17 00:00:00 2001
From: Krannich479 <krannich479@googlemail.com>
Date: Wed, 24 Apr 2024 10:56:07 +0200
Subject: [PATCH 24/47] CI better symbolic links

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

diff --git a/.github/workflows/VariantCalling.yml b/.github/workflows/VariantCalling.yml
index f54c4cf..6f72e53 100644
--- a/.github/workflows/VariantCalling.yml
+++ b/.github/workflows/VariantCalling.yml
@@ -73,7 +73,7 @@ jobs:
         run: |
             NB_SAMPLES=3
             mkdir -p cievad/callsets
-            for s in $(seq 1 $NB_SAMPLES); do ln -s results/03-Variant-Calling/hap${s}/hap${s}.filtered.gt_adjust.filtered_indels.vcf.gz cievad/callsets/callset_${s}.vcf.gz; done
+            for s in $(seq 1 $NB_SAMPLES); do ln -sr results/03-Variant-Calling/hap${s}/hap${s}.filtered.gt_adjust.filtered_indels.vcf.gz cievad/callsets/callset_${s}.vcf.gz; done
             tree .
 
       - name: Run CIEVaD eval

From c7b493e87308a8af32d8bd015cf47496cbf9c07c Mon Sep 17 00:00:00 2001
From: Krannich479 <krannich479@googlemail.com>
Date: Wed, 24 Apr 2024 12:53:32 +0200
Subject: [PATCH 25/47] CI debug

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

diff --git a/.github/workflows/VariantCalling.yml b/.github/workflows/VariantCalling.yml
index 6f72e53..052d4ce 100644
--- a/.github/workflows/VariantCalling.yml
+++ b/.github/workflows/VariantCalling.yml
@@ -74,11 +74,11 @@ jobs:
             NB_SAMPLES=3
             mkdir -p cievad/callsets
             for s in $(seq 1 $NB_SAMPLES); do ln -sr results/03-Variant-Calling/hap${s}/hap${s}.filtered.gt_adjust.filtered_indels.vcf.gz cievad/callsets/callset_${s}.vcf.gz; done
-            tree .
 
       - name: Run CIEVaD eval
         run: |
             pushd cievad
+            tree .
             nextflow run eval.nf -profile local,conda --callsets_dir callsets --reference MN908947.3.fasta
             tree results
             popd

From 335c584e6554259672b0fc431293b9dbd40f6966 Mon Sep 17 00:00:00 2001
From: Krannich479 <krannich479@googlemail.com>
Date: Wed, 24 Apr 2024 14:36:59 +0200
Subject: [PATCH 26/47] CI trying to fix dependencies

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

diff --git a/.github/workflows/VariantCalling.yml b/.github/workflows/VariantCalling.yml
index 052d4ce..9f18934 100644
--- a/.github/workflows/VariantCalling.yml
+++ b/.github/workflows/VariantCalling.yml
@@ -18,7 +18,7 @@ jobs:
       - uses: conda-incubator/setup-miniconda@v3
         with:
           miniconda-version: "latest"
-          channels: defaults,bioconda,conda-forge
+          channels: bioconda,conda-forge,defaults
           channel-priority: true
           auto-activate-base: true
 

From e59ddc05a7e0a6acd5aceb19492253b991808488 Mon Sep 17 00:00:00 2001
From: Krannich479 <krannich479@googlemail.com>
Date: Fri, 26 Apr 2024 12:32:49 +0200
Subject: [PATCH 27/47] test1 for auto-badge generation

---
 .github/workflows/VariantCalling.yml | 10 ++++++++++
 1 file changed, 10 insertions(+)

diff --git a/.github/workflows/VariantCalling.yml b/.github/workflows/VariantCalling.yml
index 9f18934..1a98934 100644
--- a/.github/workflows/VariantCalling.yml
+++ b/.github/workflows/VariantCalling.yml
@@ -82,3 +82,13 @@ jobs:
             nextflow run eval.nf -profile local,conda --callsets_dir callsets --reference MN908947.3.fasta
             tree results
             popd
+
+      - name: Create Badge
+        uses: schneegans/dynamic-badges-action@v1.7.0
+        with:
+          auth: ${{ secrets.GIST_SECRET_CIEVAD_GH_ACTIONS }}
+          gistID: 4a0fffafb6e8969ddb31b3100926e9cf
+          filename: cievad.json # Use test.svg if you want to use the SVG mode.
+          label: Hello
+          message: World
+          color: orange
\ No newline at end of file

From b44b6183efc5d4f89d674b9bd30f1ed5a14717dd Mon Sep 17 00:00:00 2001
From: Krannich479 <krannich479@googlemail.com>
Date: Fri, 26 Apr 2024 14:17:24 +0200
Subject: [PATCH 28/47] CI badge test pt2

---
 .github/workflows/VariantCalling.yml | 13 ++++++++++---
 1 file changed, 10 insertions(+), 3 deletions(-)

diff --git a/.github/workflows/VariantCalling.yml b/.github/workflows/VariantCalling.yml
index 1a98934..ed80842 100644
--- a/.github/workflows/VariantCalling.yml
+++ b/.github/workflows/VariantCalling.yml
@@ -83,12 +83,19 @@ jobs:
             tree results
             popd
 
+      - name: Create Badge variable for indels' average F1-score
+        run: |
+            INDELS_AVG_F1=$(cut -f 2,21 -d ',' cievad/results/summary.sompy.stats.csv | grep "indels" | sed 's/indels,//g')
+            INDELS_AVG_F1_ABS=$(echo $INDELS_AVG_F1*100 | bc)
       - name: Create Badge
         uses: schneegans/dynamic-badges-action@v1.7.0
         with:
           auth: ${{ secrets.GIST_SECRET_CIEVAD_GH_ACTIONS }}
           gistID: 4a0fffafb6e8969ddb31b3100926e9cf
           filename: cievad.json # Use test.svg if you want to use the SVG mode.
-          label: Hello
-          message: World
-          color: orange
\ No newline at end of file
+          label: Indels F1-score
+          message: ${{ env.INDELS_AVG_F1_ABS }}%
+          namedLogo: GitHub
+          minColorRange: 0
+          maxColorRange: 100
+          valColorRange: ${{ env.INDELS_AVG_F1_ABS }}
\ No newline at end of file

From 6e3a5deffb57c145d5c4f2a55cd753b209d7400e Mon Sep 17 00:00:00 2001
From: Krannich479 <krannich479@googlemail.com>
Date: Fri, 26 Apr 2024 14:41:57 +0200
Subject: [PATCH 29/47] CI badge test part3

---
 .github/workflows/VariantCalling.yml | 8 +++++---
 1 file changed, 5 insertions(+), 3 deletions(-)

diff --git a/.github/workflows/VariantCalling.yml b/.github/workflows/VariantCalling.yml
index ed80842..cb3e537 100644
--- a/.github/workflows/VariantCalling.yml
+++ b/.github/workflows/VariantCalling.yml
@@ -87,15 +87,17 @@ jobs:
         run: |
             INDELS_AVG_F1=$(cut -f 2,21 -d ',' cievad/results/summary.sompy.stats.csv | grep "indels" | sed 's/indels,//g')
             INDELS_AVG_F1_ABS=$(echo $INDELS_AVG_F1*100 | bc)
+            INDELS_AVG_F1_INT=$(echo $INDELS_AVG_F1_ABS | cut -f 1 -d '.')
+            echo "INDELS_SCORE=$INDELS_AVG_F1_INT" >> $GITHUB_ENV
       - name: Create Badge
         uses: schneegans/dynamic-badges-action@v1.7.0
         with:
           auth: ${{ secrets.GIST_SECRET_CIEVAD_GH_ACTIONS }}
           gistID: 4a0fffafb6e8969ddb31b3100926e9cf
           filename: cievad.json # Use test.svg if you want to use the SVG mode.
-          label: Indels F1-score
-          message: ${{ env.INDELS_AVG_F1_ABS }}%
           namedLogo: GitHub
+          label: Indels F1-score
+          message: ${{ env.INDELS_SCORE }}%
+          valColorRange: ${{ env.INDELS_SCORE }}
           minColorRange: 0
           maxColorRange: 100
-          valColorRange: ${{ env.INDELS_AVG_F1_ABS }}
\ No newline at end of file

From 7ae518500e675ab8ba855f910ad9c3ad2056c771 Mon Sep 17 00:00:00 2001
From: Thomas Krannich <Krannich479@users.noreply.github.com>
Date: Fri, 26 Apr 2024 15:05:14 +0200
Subject: [PATCH 30/47] Update README.md

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

diff --git a/README.md b/README.md
index e5be413..05dd026 100644
--- a/README.md
+++ b/README.md
@@ -8,6 +8,7 @@
 [![run with singularity](https://img.shields.io/badge/run%20with-singularity-1d355c.svg?labelColor=000000)](https://sylabs.io/docs/)
 ![](https://img.shields.io/badge/licence-GPL--3.0-lightgrey.svg)
 [![](https://img.shields.io/badge/awaiting%20peer%20review-F1000Research-ef8336.svg)](https://doi.org/10.12688/f1000research.136683.1)
+![badge](https://img.shields.io/endpoint?url=https://gist.githubusercontent.com/krannich479/4a0fffafb6e8969ddb31b3100926e9cf/raw/cievad.json)
 
 CoVpipe2 is a Nextflow pipeline for reference-based genome reconstruction of SARS-CoV-2 from NGS data. In principle it can be used also for other viruses.
 

From f1b9a24a4ae55c2a7dc99ee657008e260f3b7419 Mon Sep 17 00:00:00 2001
From: Thomas Krannich <Krannich479@users.noreply.github.com>
Date: Thu, 16 May 2024 11:29:55 +0200
Subject: [PATCH 31/47] Update VariantCalling.yml

---
 .github/workflows/VariantCalling.yml | 31 ++++++++++++++++++++++------
 1 file changed, 25 insertions(+), 6 deletions(-)

diff --git a/.github/workflows/VariantCalling.yml b/.github/workflows/VariantCalling.yml
index cb3e537..9e4d966 100644
--- a/.github/workflows/VariantCalling.yml
+++ b/.github/workflows/VariantCalling.yml
@@ -1,4 +1,4 @@
-name: VariantCalling
+name: VariantCallingBenchmark
 
 on:
   push:
@@ -7,8 +7,8 @@ on:
     branches: ["main"]
 
 jobs:
-  VariantCalling:
-    name: VariantCalling CI
+  VariantCallingBenchmark:
+    name: CIEVaD benchmarks
     runs-on: ubuntu-latest
     defaults:
       run:
@@ -83,21 +83,40 @@ jobs:
             tree results
             popd
 
-      - name: Create Badge variable for indels' average F1-score
+      - name: Create Badge variable for average indel F1-score
         run: |
             INDELS_AVG_F1=$(cut -f 2,21 -d ',' cievad/results/summary.sompy.stats.csv | grep "indels" | sed 's/indels,//g')
             INDELS_AVG_F1_ABS=$(echo $INDELS_AVG_F1*100 | bc)
             INDELS_AVG_F1_INT=$(echo $INDELS_AVG_F1_ABS | cut -f 1 -d '.')
             echo "INDELS_SCORE=$INDELS_AVG_F1_INT" >> $GITHUB_ENV
-      - name: Create Badge
+
+      - name: Create Indels Badge
         uses: schneegans/dynamic-badges-action@v1.7.0
         with:
           auth: ${{ secrets.GIST_SECRET_CIEVAD_GH_ACTIONS }}
           gistID: 4a0fffafb6e8969ddb31b3100926e9cf
-          filename: cievad.json # Use test.svg if you want to use the SVG mode.
+          filename: cievad_covpipe2_indels.json # Use test.svg if you want to use the SVG mode.
           namedLogo: GitHub
           label: Indels F1-score
           message: ${{ env.INDELS_SCORE }}%
           valColorRange: ${{ env.INDELS_SCORE }}
+
+      - name: Create Badge variable for average SNV F1-score
+        run: |
+            SNV_AVG_F1=$(cut -f 2,21 -d ',' cievad/results/summary.sompy.stats.csv | grep "SNVs" | sed 's/SNVs,//g')
+            SNV_AVG_F1_ABS=$(echo $SNV_AVG_F1*100 | bc)
+            SNV_AVG_F1_INT=$(echo $SNV_AVG_F1_ABS | cut -f 1 -d '.')
+            echo "SNV_SCORE=$SNV_AVG_F1_INT" >> $GITHUB_ENV
+
+      - name: Create SNV Badge
+        uses: schneegans/dynamic-badges-action@v1.7.0
+        with:
+          auth: ${{ secrets.GIST_SECRET_CIEVAD_GH_ACTIONS }}
+          gistID: 87db7a851147867bc3e8857dc643dd15
+          filename: cievad_covpipe2_SNV.json # Use test.svg if you want to use the SVG mode.
+          namedLogo: GitHub
+          label: Indels F1-score
+          message: ${{ env.SNV_SCORE }}%
+          valColorRange: ${{ env.SNV_SCORE }}
           minColorRange: 0
           maxColorRange: 100

From d643aee0aad380c6b6b571d76151ee775e73cab3 Mon Sep 17 00:00:00 2001
From: Thomas Krannich <Krannich479@users.noreply.github.com>
Date: Thu, 16 May 2024 11:47:45 +0200
Subject: [PATCH 32/47] Update VariantCalling.yml

---
 .github/workflows/VariantCalling.yml | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/.github/workflows/VariantCalling.yml b/.github/workflows/VariantCalling.yml
index 9e4d966..982a776 100644
--- a/.github/workflows/VariantCalling.yml
+++ b/.github/workflows/VariantCalling.yml
@@ -100,6 +100,8 @@ jobs:
           label: Indels F1-score
           message: ${{ env.INDELS_SCORE }}%
           valColorRange: ${{ env.INDELS_SCORE }}
+          minColorRange: 0
+          maxColorRange: 100
 
       - name: Create Badge variable for average SNV F1-score
         run: |

From 330f218ea3740855b88279c243c972852bba8f9b Mon Sep 17 00:00:00 2001
From: Thomas Krannich <Krannich479@users.noreply.github.com>
Date: Thu, 16 May 2024 12:15:47 +0200
Subject: [PATCH 33/47] Update README.md

---
 README.md | 4 +++-
 1 file changed, 3 insertions(+), 1 deletion(-)

diff --git a/README.md b/README.md
index 05dd026..fce7fcc 100644
--- a/README.md
+++ b/README.md
@@ -8,7 +8,9 @@
 [![run with singularity](https://img.shields.io/badge/run%20with-singularity-1d355c.svg?labelColor=000000)](https://sylabs.io/docs/)
 ![](https://img.shields.io/badge/licence-GPL--3.0-lightgrey.svg)
 [![](https://img.shields.io/badge/awaiting%20peer%20review-F1000Research-ef8336.svg)](https://doi.org/10.12688/f1000research.136683.1)
-![badge](https://img.shields.io/endpoint?url=https://gist.githubusercontent.com/krannich479/4a0fffafb6e8969ddb31b3100926e9cf/raw/cievad.json)
+![badge](https://img.shields.io/endpoint?url=https://gist.githubusercontent.com/krannich479/4a0fffafb6e8969ddb31b3100926e9cf/raw/cievad_covpipe2_indels.json)
+![badge](https://img.shields.io/endpoint?url=https://gist.githubusercontent.com/krannich479/87db7a851147867bc3e8857dc643dd15/raw/cievad_covpipe2_SNV.json)
+
 
 CoVpipe2 is a Nextflow pipeline for reference-based genome reconstruction of SARS-CoV-2 from NGS data. In principle it can be used also for other viruses.
 

From 074bcca88b4c846cf9c87d346c88947fbb95f376 Mon Sep 17 00:00:00 2001
From: Thomas Krannich <Krannich479@users.noreply.github.com>
Date: Thu, 16 May 2024 12:16:50 +0200
Subject: [PATCH 34/47] Update VariantCalling.yml

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

diff --git a/.github/workflows/VariantCalling.yml b/.github/workflows/VariantCalling.yml
index 982a776..0c996d9 100644
--- a/.github/workflows/VariantCalling.yml
+++ b/.github/workflows/VariantCalling.yml
@@ -117,7 +117,7 @@ jobs:
           gistID: 87db7a851147867bc3e8857dc643dd15
           filename: cievad_covpipe2_SNV.json # Use test.svg if you want to use the SVG mode.
           namedLogo: GitHub
-          label: Indels F1-score
+          label: SNV F1-score
           message: ${{ env.SNV_SCORE }}%
           valColorRange: ${{ env.SNV_SCORE }}
           minColorRange: 0

From 2fa3e1432c2282364eb19ae6ab943debf94b784c Mon Sep 17 00:00:00 2001
From: Thomas Krannich <Krannich479@users.noreply.github.com>
Date: Thu, 16 May 2024 12:43:31 +0200
Subject: [PATCH 35/47] Update DryRun.yml

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

diff --git a/.github/workflows/DryRun.yml b/.github/workflows/DryRun.yml
index 50785a1..1b66d2a 100644
--- a/.github/workflows/DryRun.yml
+++ b/.github/workflows/DryRun.yml
@@ -2,7 +2,7 @@ name: DryRun
 
 on:
   push:
-    branches: ["dhhgfgdsaashg"]
+    branches: ["main"]
 
 jobs:
   build:

From 814a63c0f8c91f008356479d4a0d7bc0b783249b Mon Sep 17 00:00:00 2001
From: Thomas Krannich <Krannich479@users.noreply.github.com>
Date: Thu, 16 May 2024 12:43:48 +0200
Subject: [PATCH 36/47] Update pytest_workflows.yml

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

diff --git a/.github/workflows/pytest_workflows.yml b/.github/workflows/pytest_workflows.yml
index fd618c6..6855275 100644
--- a/.github/workflows/pytest_workflows.yml
+++ b/.github/workflows/pytest_workflows.yml
@@ -2,7 +2,7 @@ name: Pytest-workflow
 
 on:
   push:
-    branches: ["dhhgfgdsaashg"]
+    branches: ["main"]
 
 jobs:
   test:

From 027d82f9e03323f3293dc0b5bb921e2306475b57 Mon Sep 17 00:00:00 2001
From: Thomas Krannich <Krannich479@users.noreply.github.com>
Date: Fri, 24 May 2024 15:07:04 +0200
Subject: [PATCH 37/47] Update README.md

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

diff --git a/README.md b/README.md
index fce7fcc..9417013 100644
--- a/README.md
+++ b/README.md
@@ -7,7 +7,7 @@
 [![run with docker](https://img.shields.io/badge/run%20with-docker-0db7ed?labelColor=000000&logo=docker)](https://www.docker.com/)
 [![run with singularity](https://img.shields.io/badge/run%20with-singularity-1d355c.svg?labelColor=000000)](https://sylabs.io/docs/)
 ![](https://img.shields.io/badge/licence-GPL--3.0-lightgrey.svg)
-[![](https://img.shields.io/badge/awaiting%20peer%20review-F1000Research-ef8336.svg)](https://doi.org/10.12688/f1000research.136683.1)
+[![](https://img.shields.io/badge/manuscript-F1000Research-ef8336.svg)](https://doi.org/10.12688/f1000research.136683.1)
 ![badge](https://img.shields.io/endpoint?url=https://gist.githubusercontent.com/krannich479/4a0fffafb6e8969ddb31b3100926e9cf/raw/cievad_covpipe2_indels.json)
 ![badge](https://img.shields.io/endpoint?url=https://gist.githubusercontent.com/krannich479/87db7a851147867bc3e8857dc643dd15/raw/cievad_covpipe2_SNV.json)
 

From 5a9b3c51a4ee928d326e122dc3a24593fd8e37bc Mon Sep 17 00:00:00 2001
From: Thomas Krannich <Krannich479@users.noreply.github.com>
Date: Wed, 29 May 2024 13:02:02 +0200
Subject: [PATCH 38/47] Remove ssh-key requirement from CI

---
 .github/workflows/VariantCalling.yml | 2 --
 1 file changed, 2 deletions(-)

diff --git a/.github/workflows/VariantCalling.yml b/.github/workflows/VariantCalling.yml
index 0c996d9..8c07486 100644
--- a/.github/workflows/VariantCalling.yml
+++ b/.github/workflows/VariantCalling.yml
@@ -39,8 +39,6 @@ jobs:
         
       - name: Git checkout CIEVaD + REF
         run: |
-            eval `ssh-agent -s`
-            ssh-add - <<< '${{ secrets.PRIVATE_SSH_KEY }}'
             git clone git@github.com:rki-mf1/cievad.git
             pushd cievad
             wget https://www.ebi.ac.uk/ena/browser/api/fasta/MN908947.3

From afb70c8a11d19c160920ed2c94011874131ebb98 Mon Sep 17 00:00:00 2001
From: Thomas Krannich <Krannich479@users.noreply.github.com>
Date: Wed, 29 May 2024 13:06:48 +0200
Subject: [PATCH 39/47] Update git clone strategy

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

diff --git a/.github/workflows/VariantCalling.yml b/.github/workflows/VariantCalling.yml
index 8c07486..efbce40 100644
--- a/.github/workflows/VariantCalling.yml
+++ b/.github/workflows/VariantCalling.yml
@@ -39,7 +39,7 @@ jobs:
         
       - name: Git checkout CIEVaD + REF
         run: |
-            git clone git@github.com:rki-mf1/cievad.git
+            git clone https://github.com/rki-mf1/cievad.git
             pushd cievad
             wget https://www.ebi.ac.uk/ena/browser/api/fasta/MN908947.3
             sed 's/>ENA|MN908947|MN908947.3 Severe acute respiratory syndrome coronavirus 2 isolate Wuhan-Hu-1, complete genome./>MN908947.3/g' MN908947.3 > MN908947.3.fasta

From a4f5d09151b6ac5faf367b82136284cc8d2108c6 Mon Sep 17 00:00:00 2001
From: Thomas Krannich <Krannich479@users.noreply.github.com>
Date: Wed, 29 May 2024 13:16:12 +0200
Subject: [PATCH 40/47] Update VariantCalling.yml

add running --help for principal check after download
---
 .github/workflows/VariantCalling.yml | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/.github/workflows/VariantCalling.yml b/.github/workflows/VariantCalling.yml
index efbce40..ad729c4 100644
--- a/.github/workflows/VariantCalling.yml
+++ b/.github/workflows/VariantCalling.yml
@@ -41,6 +41,8 @@ jobs:
         run: |
             git clone https://github.com/rki-mf1/cievad.git
             pushd cievad
+            nextflow run hap.nf --help
+            nextflow run eval.nf --help
             wget https://www.ebi.ac.uk/ena/browser/api/fasta/MN908947.3
             sed 's/>ENA|MN908947|MN908947.3 Severe acute respiratory syndrome coronavirus 2 isolate Wuhan-Hu-1, complete genome./>MN908947.3/g' MN908947.3 > MN908947.3.fasta
             popd

From dbc68b0edd2d619afb836265699f5be5ea27e752 Mon Sep 17 00:00:00 2001
From: Thomas Krannich <Krannich479@users.noreply.github.com>
Date: Wed, 29 May 2024 14:07:09 +0200
Subject: [PATCH 41/47] Remove external badge creation (via schneegans)

---
 .github/workflows/VariantCalling.yml | 48 ++++++++++++++--------------
 1 file changed, 24 insertions(+), 24 deletions(-)

diff --git a/.github/workflows/VariantCalling.yml b/.github/workflows/VariantCalling.yml
index ad729c4..48bef29 100644
--- a/.github/workflows/VariantCalling.yml
+++ b/.github/workflows/VariantCalling.yml
@@ -90,18 +90,18 @@ jobs:
             INDELS_AVG_F1_INT=$(echo $INDELS_AVG_F1_ABS | cut -f 1 -d '.')
             echo "INDELS_SCORE=$INDELS_AVG_F1_INT" >> $GITHUB_ENV
 
-      - name: Create Indels Badge
-        uses: schneegans/dynamic-badges-action@v1.7.0
-        with:
-          auth: ${{ secrets.GIST_SECRET_CIEVAD_GH_ACTIONS }}
-          gistID: 4a0fffafb6e8969ddb31b3100926e9cf
-          filename: cievad_covpipe2_indels.json # Use test.svg if you want to use the SVG mode.
-          namedLogo: GitHub
-          label: Indels F1-score
-          message: ${{ env.INDELS_SCORE }}%
-          valColorRange: ${{ env.INDELS_SCORE }}
-          minColorRange: 0
-          maxColorRange: 100
+      #- name: Create Indels Badge
+      #  uses: schneegans/dynamic-badges-action@v1.7.0
+      #  with:
+      #    auth: ${{ secrets.GIST_SECRET_CIEVAD_GH_ACTIONS }}
+      #    gistID: 4a0fffafb6e8969ddb31b3100926e9cf
+      #    filename: cievad_covpipe2_indels.json # Use test.svg if you want to use the SVG mode.
+      #    namedLogo: GitHub
+      #    label: Indels F1-score
+      #    message: ${{ env.INDELS_SCORE }}%
+      #    valColorRange: ${{ env.INDELS_SCORE }}
+      #    minColorRange: 0
+      #    maxColorRange: 100
 
       - name: Create Badge variable for average SNV F1-score
         run: |
@@ -110,15 +110,15 @@ jobs:
             SNV_AVG_F1_INT=$(echo $SNV_AVG_F1_ABS | cut -f 1 -d '.')
             echo "SNV_SCORE=$SNV_AVG_F1_INT" >> $GITHUB_ENV
 
-      - name: Create SNV Badge
-        uses: schneegans/dynamic-badges-action@v1.7.0
-        with:
-          auth: ${{ secrets.GIST_SECRET_CIEVAD_GH_ACTIONS }}
-          gistID: 87db7a851147867bc3e8857dc643dd15
-          filename: cievad_covpipe2_SNV.json # Use test.svg if you want to use the SVG mode.
-          namedLogo: GitHub
-          label: SNV F1-score
-          message: ${{ env.SNV_SCORE }}%
-          valColorRange: ${{ env.SNV_SCORE }}
-          minColorRange: 0
-          maxColorRange: 100
+      #- name: Create SNV Badge
+      #  uses: schneegans/dynamic-badges-action@v1.7.0
+      #  with:
+      #    auth: ${{ secrets.GIST_SECRET_CIEVAD_GH_ACTIONS }}
+      #    gistID: 87db7a851147867bc3e8857dc643dd15
+      #    filename: cievad_covpipe2_SNV.json # Use test.svg if you want to use the SVG mode.
+      #    namedLogo: GitHub
+      #    label: SNV F1-score
+      #    message: ${{ env.SNV_SCORE }}%
+      #    valColorRange: ${{ env.SNV_SCORE }}
+      #    minColorRange: 0
+      #    maxColorRange: 100

From 8846d32d1d663ef247e0da5b8a6824ef12fd2cfb Mon Sep 17 00:00:00 2001
From: Thomas Krannich <Krannich479@users.noreply.github.com>
Date: Wed, 29 May 2024 15:22:20 +0200
Subject: [PATCH 42/47] Update VariantCalling.yml

check thresholds for SNV and indel
---
 .github/workflows/VariantCalling.yml | 8 +++++++-
 1 file changed, 7 insertions(+), 1 deletion(-)

diff --git a/.github/workflows/VariantCalling.yml b/.github/workflows/VariantCalling.yml
index 48bef29..c171dbf 100644
--- a/.github/workflows/VariantCalling.yml
+++ b/.github/workflows/VariantCalling.yml
@@ -83,12 +83,15 @@ jobs:
             tree results
             popd
 
-      - name: Create Badge variable for average indel F1-score
+      - name: Create Badge variable for average indel F1-score # in personal (non-organisational) git repos the score can be visualized via schneegans' dynamic badge action
         run: |
             INDELS_AVG_F1=$(cut -f 2,21 -d ',' cievad/results/summary.sompy.stats.csv | grep "indels" | sed 's/indels,//g')
             INDELS_AVG_F1_ABS=$(echo $INDELS_AVG_F1*100 | bc)
             INDELS_AVG_F1_INT=$(echo $INDELS_AVG_F1_ABS | cut -f 1 -d '.')
             echo "INDELS_SCORE=$INDELS_AVG_F1_INT" >> $GITHUB_ENV
+            echo $INDELS_AVG_F1_ABS
+            echo $INDELS_AVG_F1_INT
+            exit $(( ($INDELS_AVG_F1_INT >= 94) 0 : 1 ))
 
       #- name: Create Indels Badge
       #  uses: schneegans/dynamic-badges-action@v1.7.0
@@ -109,6 +112,9 @@ jobs:
             SNV_AVG_F1_ABS=$(echo $SNV_AVG_F1*100 | bc)
             SNV_AVG_F1_INT=$(echo $SNV_AVG_F1_ABS | cut -f 1 -d '.')
             echo "SNV_SCORE=$SNV_AVG_F1_INT" >> $GITHUB_ENV
+            echo $SNV_AVG_F1_ABS
+            echo $SNV_AVG_F1_INT
+            exit $(( ($SNV_AVG_F1_INT >= 97) 0 : 1 ))
 
       #- name: Create SNV Badge
       #  uses: schneegans/dynamic-badges-action@v1.7.0

From 84e93bc290c972abb9bc002f9f3881c2c6588553 Mon Sep 17 00:00:00 2001
From: Thomas Krannich <Krannich479@users.noreply.github.com>
Date: Wed, 29 May 2024 15:36:43 +0200
Subject: [PATCH 43/47] Update VariantCalling.yml

---
 .github/workflows/VariantCalling.yml | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/.github/workflows/VariantCalling.yml b/.github/workflows/VariantCalling.yml
index c171dbf..f17ebdd 100644
--- a/.github/workflows/VariantCalling.yml
+++ b/.github/workflows/VariantCalling.yml
@@ -91,7 +91,7 @@ jobs:
             echo "INDELS_SCORE=$INDELS_AVG_F1_INT" >> $GITHUB_ENV
             echo $INDELS_AVG_F1_ABS
             echo $INDELS_AVG_F1_INT
-            exit $(( ($INDELS_AVG_F1_INT >= 94) 0 : 1 ))
+            exit $(( ($INDELS_AVG_F1_INT >= 94) ? 0 : 1 ))
 
       #- name: Create Indels Badge
       #  uses: schneegans/dynamic-badges-action@v1.7.0
@@ -114,7 +114,7 @@ jobs:
             echo "SNV_SCORE=$SNV_AVG_F1_INT" >> $GITHUB_ENV
             echo $SNV_AVG_F1_ABS
             echo $SNV_AVG_F1_INT
-            exit $(( ($SNV_AVG_F1_INT >= 97) 0 : 1 ))
+            exit $(( ($SNV_AVG_F1_INT >= 97) ? 0 : 1 ))
 
       #- name: Create SNV Badge
       #  uses: schneegans/dynamic-badges-action@v1.7.0

From c0335965b4f25a4fa0d84b214726a9cab5d88479 Mon Sep 17 00:00:00 2001
From: Thomas Krannich <Krannich479@users.noreply.github.com>
Date: Wed, 29 May 2024 16:03:42 +0200
Subject: [PATCH 44/47] Update VariantCalling.yml

---
 .github/workflows/VariantCalling.yml | 14 ++++++++++++--
 1 file changed, 12 insertions(+), 2 deletions(-)

diff --git a/.github/workflows/VariantCalling.yml b/.github/workflows/VariantCalling.yml
index f17ebdd..d750984 100644
--- a/.github/workflows/VariantCalling.yml
+++ b/.github/workflows/VariantCalling.yml
@@ -91,7 +91,12 @@ jobs:
             echo "INDELS_SCORE=$INDELS_AVG_F1_INT" >> $GITHUB_ENV
             echo $INDELS_AVG_F1_ABS
             echo $INDELS_AVG_F1_INT
-            exit $(( ($INDELS_AVG_F1_INT >= 94) ? 0 : 1 ))
+            if [ "$INDELS_AVG_F1_INT" -lt 94 ]; then
+              echo "Indels benchmark value decreased since last test! Exiting with status 1."
+              exit 1
+            else
+              echo "Indels benchmark did not drop since last test."
+            fi
 
       #- name: Create Indels Badge
       #  uses: schneegans/dynamic-badges-action@v1.7.0
@@ -114,7 +119,12 @@ jobs:
             echo "SNV_SCORE=$SNV_AVG_F1_INT" >> $GITHUB_ENV
             echo $SNV_AVG_F1_ABS
             echo $SNV_AVG_F1_INT
-            exit $(( ($SNV_AVG_F1_INT >= 97) ? 0 : 1 ))
+            if [ "$SNV_AVG_F1_INT" -lt 97 ]; then
+              echo "SNV benchmark value decreased since last test! Exiting with status 1."
+              exit 1
+            else
+              echo "SNV benchmark did not drop since last test."
+            fi
 
       #- name: Create SNV Badge
       #  uses: schneegans/dynamic-badges-action@v1.7.0

From 1cdc24ce254b2d9e489175fd2cee42ba55a2b90e Mon Sep 17 00:00:00 2001
From: Krannich479 <krannich479@googlemail.com>
Date: Wed, 29 May 2024 16:43:35 +0200
Subject: [PATCH 45/47] revert CI changes in previous tests; new status badge
 for variant calling tests

---
 .github/workflows/DryRun.yml           | 5 +----
 .github/workflows/pytest_workflows.yml | 4 +---
 README.md                              | 4 +---
 3 files changed, 3 insertions(+), 10 deletions(-)

diff --git a/.github/workflows/DryRun.yml b/.github/workflows/DryRun.yml
index 1b66d2a..0baf6cb 100644
--- a/.github/workflows/DryRun.yml
+++ b/.github/workflows/DryRun.yml
@@ -1,9 +1,6 @@
 name: DryRun
 
-on:
-  push:
-    branches: ["main"]
-
+on: [push]
 jobs:
   build:
     runs-on: ubuntu-latest
diff --git a/.github/workflows/pytest_workflows.yml b/.github/workflows/pytest_workflows.yml
index 6855275..63c9fa5 100644
--- a/.github/workflows/pytest_workflows.yml
+++ b/.github/workflows/pytest_workflows.yml
@@ -1,8 +1,6 @@
 name: Pytest-workflow
 
-on:
-  push:
-    branches: ["main"]
+on: [push]
 
 jobs:
   test:
diff --git a/README.md b/README.md
index 9417013..d36e63b 100644
--- a/README.md
+++ b/README.md
@@ -8,9 +8,7 @@
 [![run with singularity](https://img.shields.io/badge/run%20with-singularity-1d355c.svg?labelColor=000000)](https://sylabs.io/docs/)
 ![](https://img.shields.io/badge/licence-GPL--3.0-lightgrey.svg)
 [![](https://img.shields.io/badge/manuscript-F1000Research-ef8336.svg)](https://doi.org/10.12688/f1000research.136683.1)
-![badge](https://img.shields.io/endpoint?url=https://gist.githubusercontent.com/krannich479/4a0fffafb6e8969ddb31b3100926e9cf/raw/cievad_covpipe2_indels.json)
-![badge](https://img.shields.io/endpoint?url=https://gist.githubusercontent.com/krannich479/87db7a851147867bc3e8857dc643dd15/raw/cievad_covpipe2_SNV.json)
-
+[![VariantCallingBenchmark](https://github.com/rki-mf1/CoVpipe2/actions/workflows/VariantCalling.yml/badge.svg)](https://github.com/rki-mf1/CoVpipe2/actions/workflows/VariantCalling.yml)
 
 CoVpipe2 is a Nextflow pipeline for reference-based genome reconstruction of SARS-CoV-2 from NGS data. In principle it can be used also for other viruses.
 

From 2fdbdbaf4ee062b07a3aab207e6ecc932baccd4f Mon Sep 17 00:00:00 2001
From: Thomas Krannich <Krannich479@users.noreply.github.com>
Date: Mon, 10 Jun 2024 14:53:18 +0200
Subject: [PATCH 46/47] Update VariantCalling.yml

---
 .github/workflows/VariantCalling.yml | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/.github/workflows/VariantCalling.yml b/.github/workflows/VariantCalling.yml
index d750984..785572a 100644
--- a/.github/workflows/VariantCalling.yml
+++ b/.github/workflows/VariantCalling.yml
@@ -91,7 +91,7 @@ jobs:
             echo "INDELS_SCORE=$INDELS_AVG_F1_INT" >> $GITHUB_ENV
             echo $INDELS_AVG_F1_ABS
             echo $INDELS_AVG_F1_INT
-            if [ "$INDELS_AVG_F1_INT" -lt 94 ]; then
+            if [ "$INDELS_AVG_F1_INT" -lt 91 ]; then
               echo "Indels benchmark value decreased since last test! Exiting with status 1."
               exit 1
             else
@@ -119,7 +119,7 @@ jobs:
             echo "SNV_SCORE=$SNV_AVG_F1_INT" >> $GITHUB_ENV
             echo $SNV_AVG_F1_ABS
             echo $SNV_AVG_F1_INT
-            if [ "$SNV_AVG_F1_INT" -lt 97 ]; then
+            if [ "$SNV_AVG_F1_INT" -lt 96 ]; then
               echo "SNV benchmark value decreased since last test! Exiting with status 1."
               exit 1
             else

From c92deadda31ca9d0f5c67007f78e82a5fd421e97 Mon Sep 17 00:00:00 2001
From: Thomas Krannich <Krannich479@users.noreply.github.com>
Date: Wed, 12 Jun 2024 12:16:37 +0200
Subject: [PATCH 47/47] Update README.md

Co-authored-by: MarieLataretu <52002068+MarieLataretu@users.noreply.github.com>
---
 README.md | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/README.md b/README.md
index d36e63b..be3be67 100644
--- a/README.md
+++ b/README.md
@@ -7,7 +7,7 @@
 [![run with docker](https://img.shields.io/badge/run%20with-docker-0db7ed?labelColor=000000&logo=docker)](https://www.docker.com/)
 [![run with singularity](https://img.shields.io/badge/run%20with-singularity-1d355c.svg?labelColor=000000)](https://sylabs.io/docs/)
 ![](https://img.shields.io/badge/licence-GPL--3.0-lightgrey.svg)
-[![](https://img.shields.io/badge/manuscript-F1000Research-ef8336.svg)](https://doi.org/10.12688/f1000research.136683.1)
+[![](https://img.shields.io/badge/manuscript-F1000Research-ef8336.svg)](https://doi.org/10.12688/f1000research.136683.2)
 [![VariantCallingBenchmark](https://github.com/rki-mf1/CoVpipe2/actions/workflows/VariantCalling.yml/badge.svg)](https://github.com/rki-mf1/CoVpipe2/actions/workflows/VariantCalling.yml)
 
 CoVpipe2 is a Nextflow pipeline for reference-based genome reconstruction of SARS-CoV-2 from NGS data. In principle it can be used also for other viruses.