From ee4731e3fca999436990822ddc0b8bac7d56cc7e Mon Sep 17 00:00:00 2001
From: fellen31 <felixlenner@gmail.com>
Date: Tue, 26 Mar 2024 16:15:13 +0100
Subject: [PATCH 1/4] add multisample test

---
 .github/workflows/ci.yml           | 3 ++-
 assets/samplesheet_multisample.csv | 3 +++
 2 files changed, 5 insertions(+), 1 deletion(-)
 create mode 100644 assets/samplesheet_multisample.csv

diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
index fae9a11d..cefedb8e 100644
--- a/.github/workflows/ci.yml
+++ b/.github/workflows/ci.yml
@@ -23,6 +23,7 @@ jobs:
     runs-on: ubuntu-latest
     strategy:
       matrix:
+        samplesheet: ["", "--input assets/samplesheet_multisample.csv"]
         NXF_VER:
           - "23.04.0"
           - "latest-everything"
@@ -43,4 +44,4 @@ jobs:
         # For example: adding multiple test runs with different parameters
         # Remember that you can parallelise this by using strategy.matrix
         run: |
-          nextflow run ${GITHUB_WORKSPACE} -profile test,docker --outdir ./results
+          nextflow run ${GITHUB_WORKSPACE} -profile test,docker --outdir ./results ${{ samplesheet }}
diff --git a/assets/samplesheet_multisample.csv b/assets/samplesheet_multisample.csv
new file mode 100644
index 00000000..9d8317c1
--- /dev/null
+++ b/assets/samplesheet_multisample.csv
@@ -0,0 +1,3 @@
+sample,file,family_id,paternal_id,maternal_id,sex,phenotype
+HG002_Revio_A,https://raw.githubusercontent.com/genomic-medicine-sweden/skierfe/dev/assets/test_data/HG002_PacBio_Revio.fastq.gz,FAM,XXX,YYY,1,1
+HG002_Revio_B,https://raw.githubusercontent.com/genomic-medicine-sweden/skierfe/dev/assets/test_data/HG002_PacBio_Revio.fastq.gz,FAM,XXX,YYY,1,1

From e732454cff61a414ab11a644c1024214f35dd649 Mon Sep 17 00:00:00 2001
From: fellen31 <felixlenner@gmail.com>
Date: Tue, 26 Mar 2024 16:17:25 +0100
Subject: [PATCH 2/4] fix variable

---
 .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 cefedb8e..8cd84c8a 100644
--- a/.github/workflows/ci.yml
+++ b/.github/workflows/ci.yml
@@ -44,4 +44,4 @@ jobs:
         # For example: adding multiple test runs with different parameters
         # Remember that you can parallelise this by using strategy.matrix
         run: |
-          nextflow run ${GITHUB_WORKSPACE} -profile test,docker --outdir ./results ${{ samplesheet }}
+          nextflow run ${GITHUB_WORKSPACE} -profile test,docker --outdir ./results ${{ matrix.samplesheet }}

From 0ece288aa26fcf30863ab11a4929662e6fc5da29 Mon Sep 17 00:00:00 2001
From: fellen31 <felixlenner@gmail.com>
Date: Tue, 26 Mar 2024 16:39:26 +0100
Subject: [PATCH 3/4] run split-alignment workflow and don't split deepvariant
 inputs

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

diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
index 8cd84c8a..b82beaf4 100644
--- a/.github/workflows/ci.yml
+++ b/.github/workflows/ci.yml
@@ -23,7 +23,7 @@ jobs:
     runs-on: ubuntu-latest
     strategy:
       matrix:
-        samplesheet: ["", "--input assets/samplesheet_multisample.csv"]
+        parameters: ["", "--input assets/samplesheet_multisample.csv --split_fastq 250 --parallel_snv 1"]
         NXF_VER:
           - "23.04.0"
           - "latest-everything"
@@ -44,4 +44,4 @@ jobs:
         # For example: adding multiple test runs with different parameters
         # Remember that you can parallelise this by using strategy.matrix
         run: |
-          nextflow run ${GITHUB_WORKSPACE} -profile test,docker --outdir ./results ${{ matrix.samplesheet }}
+          nextflow run ${GITHUB_WORKSPACE} -profile test,docker --outdir ./results ${{ matrix.parameters }}

From 245db2375ca69bb5d44fe37ee83e9d0d416fd163 Mon Sep 17 00:00:00 2001
From: fellen31 <felixlenner@gmail.com>
Date: Tue, 26 Mar 2024 17:08:40 +0100
Subject: [PATCH 4/4] formatting

---
 .github/workflows/ci.yml | 4 +++-
 1 file changed, 3 insertions(+), 1 deletion(-)

diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
index b82beaf4..af0ba787 100644
--- a/.github/workflows/ci.yml
+++ b/.github/workflows/ci.yml
@@ -23,7 +23,9 @@ jobs:
     runs-on: ubuntu-latest
     strategy:
       matrix:
-        parameters: ["", "--input assets/samplesheet_multisample.csv --split_fastq 250 --parallel_snv 1"]
+        parameters:
+          - ""
+          - "--input assets/samplesheet_multisample.csv --split_fastq 250 --parallel_snv 1"
         NXF_VER:
           - "23.04.0"
           - "latest-everything"