From 99419fdc4c1512ae47bacfbe8326095e0c0a7a04 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Sebastian=20Sch=C3=B6nherr?= <seb.schoenherr@gmail.com>
Date: Mon, 8 Dec 2025 21:30:56 +0100
Subject: [PATCH 1/4] Improve compression by writing no intermediate files

---
 modules/local/compression/compression_encryption_vcf.nf | 5 ++---
 1 file changed, 2 insertions(+), 3 deletions(-)

diff --git a/modules/local/compression/compression_encryption_vcf.nf b/modules/local/compression/compression_encryption_vcf.nf
index eb4a106..fb8dd2c 100644
--- a/modules/local/compression/compression_encryption_vcf.nf
+++ b/modules/local/compression/compression_encryption_vcf.nf
@@ -29,12 +29,11 @@ process COMPRESSION_ENCRYPTION_VCF {
     bcftools concat --threads ${task.cpus} -n ${info_joined} -o ${info_name} -Oz
 
     # concat dosage files and update header
-    bcftools concat --threads ${task.cpus} -n ${imputed_joined} -o intermediate_${imputed_name} -Oz
     echo "##mis_pipeline=${workflow.manifest.version}" > add_header.txt
     echo "##mis_phasing=${params.phasing.engine}" >> add_header.txt
     echo "##mis_panel=${panel_version}" >> add_header.txt
-    bcftools annotate --threads ${task.cpus} -h add_header.txt intermediate_${imputed_name} -o ${imputed_name} -Oz
-    rm intermediate_${imputed_name}
+    bcftools concat --threads ${task.cpus} -n ${imputed_joined} -Oz | \
+    bcftools annotate --threads ${task.cpus} -h add_header.txt -Oz -o ${imputed_name}
 
     # write meta files
     if [[ "${params.imputation.meta}" = true ]]

From c4bf0afc66289f23e32209fc8469c032353cdb59 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Sebastian=20Sch=C3=B6nherr?= <seb.schoenherr@gmail.com>
Date: Mon, 8 Dec 2025 21:55:54 +0100
Subject: [PATCH 2/4] Set tests to static Nextflow version

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

diff --git a/.github/workflows/ci-tests.yml b/.github/workflows/ci-tests.yml
index 19d6c5f..bb5d480 100644
--- a/.github/workflows/ci-tests.yml
+++ b/.github/workflows/ci-tests.yml
@@ -24,7 +24,7 @@ jobs:
       - name: Setup Nextflow
         uses: nf-core/setup-nextflow@v1
         with:
-          version: "latest-edge"
+          version: "25.10.0"
 
       - name: Install nf-test
         run: |

From 3ca4cd7c1f91c4bbcd7b0aa5f1006d5c1fd68d6b Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Sebastian=20Sch=C3=B6nherr?= <seb.schoenherr@gmail.com>
Date: Mon, 8 Dec 2025 22:03:20 +0100
Subject: [PATCH 3/4] Update 7zip to latest version

---
 environment.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/environment.yml b/environment.yml
index 2ca9f21..c7415af 100644
--- a/environment.yml
+++ b/environment.yml
@@ -24,5 +24,5 @@ dependencies:
  # - r-kernsmooth #use this?
   - csvtk=0.25.0
   - unzip=6.0
-  - P7Zip=15.09
+  - 7zip=25.01 
   - bcftools=1.20
\ No newline at end of file

From 736585ae0bb98d79695bd70883db5c9ca54b23e5 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Sebastian=20Sch=C3=B6nherr?= <seb.schoenherr@gmail.com>
Date: Tue, 9 Dec 2025 08:41:38 +0100
Subject: [PATCH 4/4] Revert change due to missing zip codecs

---
 environment.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/environment.yml b/environment.yml
index c7415af..2ca9f21 100644
--- a/environment.yml
+++ b/environment.yml
@@ -24,5 +24,5 @@ dependencies:
  # - r-kernsmooth #use this?
   - csvtk=0.25.0
   - unzip=6.0
-  - 7zip=25.01 
+  - P7Zip=15.09
   - bcftools=1.20
\ No newline at end of file