From 192360eb1a6b5ee7940058c5aa0abe662d556ae8 Mon Sep 17 00:00:00 2001
From: Nathan Weeks <1800812+nathanweeks@users.noreply.github.com>
Date: Thu, 21 May 2026 10:38:20 -0400
Subject: [PATCH 1/5] Update nf-schema plugin version to 2.7.2

Fixes CLI parameter type casting with Nextflow parser v2
---
 nextflow.config | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/nextflow.config b/nextflow.config
index ecf3509..337a41d 100644
--- a/nextflow.config
+++ b/nextflow.config
@@ -348,7 +348,7 @@ manifest {
 
 // Nextflow plugins
 plugins {
-    id 'nf-schema@2.5.1' // Validation of pipeline parameters and creation of an input channel from a sample sheet
+    id 'nf-schema@2.7.2' // Validation of pipeline parameters and creation of an input channel from a sample sheet
 }
 
 validation {

From ce00c5b04816ee5f9f569dcc47ef41dce01a49d0 Mon Sep 17 00:00:00 2001
From: Nathan Weeks <1800812+nathanweeks@users.noreply.github.com>
Date: Thu, 21 May 2026 15:08:21 -0400
Subject: [PATCH 2/5] Bump max_shards from 7 to 10

Attempt to address no-space-left-on-device errors
---
 .github/workflows/nf-test.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/nf-test.yml b/.github/workflows/nf-test.yml
index efd72d6..3f04ed2 100644
--- a/.github/workflows/nf-test.yml
+++ b/.github/workflows/nf-test.yml
@@ -50,7 +50,7 @@ jobs:
         env:
           NFT_VER: ${{ env.NFT_VER }}
         with:
-          max_shards: 7
+          max_shards: 10
 
       - name: debug
         run: |

From b7c1402ff4580e39bdfb0de35feff81c76c2c8fc Mon Sep 17 00:00:00 2001
From: Nathan Weeks <1800812+nathanweeks@users.noreply.github.com>
Date: Thu, 21 May 2026 15:24:47 -0400
Subject: [PATCH 3/5] Increase max_shards from 10 to 15

Still encountering no space left on device errors at 10 shards
---
 .github/workflows/nf-test.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/nf-test.yml b/.github/workflows/nf-test.yml
index 3f04ed2..c989d68 100644
--- a/.github/workflows/nf-test.yml
+++ b/.github/workflows/nf-test.yml
@@ -50,7 +50,7 @@ jobs:
         env:
           NFT_VER: ${{ env.NFT_VER }}
         with:
-          max_shards: 10
+          max_shards: 15
 
       - name: debug
         run: |

From cb55298da313269ee77e295cacd61a36d9652a9e Mon Sep 17 00:00:00 2001
From: Nathan Weeks <1800812+nathanweeks@users.noreply.github.com>
Date: Thu, 21 May 2026 15:56:24 -0400
Subject: [PATCH 4/5] Bump max_shards from 15 to 20

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

diff --git a/.github/workflows/nf-test.yml b/.github/workflows/nf-test.yml
index c989d68..82def55 100644
--- a/.github/workflows/nf-test.yml
+++ b/.github/workflows/nf-test.yml
@@ -50,7 +50,7 @@ jobs:
         env:
           NFT_VER: ${{ env.NFT_VER }}
         with:
-          max_shards: 15
+          max_shards: 20
 
       - name: debug
         run: |

From 0371f579808b71e114f2384f5d47e2c363d86484 Mon Sep 17 00:00:00 2001
From: Nathan Weeks <1800812+nathanweeks@users.noreply.github.com>
Date: Thu, 21 May 2026 16:21:20 -0400
Subject: [PATCH 5/5] Bump max_shards from 20 to 30

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

diff --git a/.github/workflows/nf-test.yml b/.github/workflows/nf-test.yml
index 82def55..9709f91 100644
--- a/.github/workflows/nf-test.yml
+++ b/.github/workflows/nf-test.yml
@@ -50,7 +50,7 @@ jobs:
         env:
           NFT_VER: ${{ env.NFT_VER }}
         with:
-          max_shards: 20
+          max_shards: 30
 
       - name: debug
         run: |