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 01/11] 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 02/11] 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 03/11] 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 04/11] 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 05/11] 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: | From 8a58aa866ccb21f47bf6805e652fb8ff90e1ba81 Mon Sep 17 00:00:00 2001 From: Nathan Weeks <1800812+nathanweeks@users.noreply.github.com> Date: Thu, 18 Jun 2026 11:33:34 -0400 Subject: [PATCH 06/11] Limit concurrent jobs on runner to 2 to address lack-of-space issue --- .github/workflows/nf-test.yml | 1 + 1 file changed, 1 insertion(+) diff --git a/.github/workflows/nf-test.yml b/.github/workflows/nf-test.yml index 9709f91..4c3d0e9 100644 --- a/.github/workflows/nf-test.yml +++ b/.github/workflows/nf-test.yml @@ -66,6 +66,7 @@ jobs: - runner=4cpu-linux-x64 strategy: fail-fast: false + max-parallel: 2 matrix: shard: ${{ fromJson(needs.nf-test-changes.outputs.shard) }} profile: [conda, docker, singularity] From 33a430e0a278e70bcabe3db667a7d8c670fa1ec8 Mon Sep 17 00:00:00 2001 From: Nathan Weeks <1800812+nathanweeks@users.noreply.github.com> Date: Mon, 6 Jul 2026 10:12:44 -0400 Subject: [PATCH 07/11] Revert max_shards to 7 & use 40gb volume on runner --- .github/workflows/nf-test.yml | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/.github/workflows/nf-test.yml b/.github/workflows/nf-test.yml index 4c3d0e9..5ecfec9 100644 --- a/.github/workflows/nf-test.yml +++ b/.github/workflows/nf-test.yml @@ -30,6 +30,7 @@ jobs: runs-on: # use self-hosted runners - runs-on=${{ github.run_id }}-nf-test-changes - runner=4cpu-linux-x64 + - volume=40gb outputs: shard: ${{ steps.set-shards.outputs.shard }} total_shards: ${{ steps.set-shards.outputs.total_shards }} @@ -50,7 +51,7 @@ jobs: env: NFT_VER: ${{ env.NFT_VER }} with: - max_shards: 30 + max_shards: 7 - name: debug run: | From 3d5131dbf55987c8f33f870afe057cb4e5f98bf6 Mon Sep 17 00:00:00 2001 From: Nathan Weeks <1800812+nathanweeks@users.noreply.github.com> Date: Mon, 6 Jul 2026 10:15:48 -0400 Subject: [PATCH 08/11] Remove max-parallel constraint --- .github/workflows/nf-test.yml | 1 - 1 file changed, 1 deletion(-) diff --git a/.github/workflows/nf-test.yml b/.github/workflows/nf-test.yml index 5ecfec9..f00d1bb 100644 --- a/.github/workflows/nf-test.yml +++ b/.github/workflows/nf-test.yml @@ -67,7 +67,6 @@ jobs: - runner=4cpu-linux-x64 strategy: fail-fast: false - max-parallel: 2 matrix: shard: ${{ fromJson(needs.nf-test-changes.outputs.shard) }} profile: [conda, docker, singularity] From c3bf14948604a22a34b992e3727535c82847fec7 Mon Sep 17 00:00:00 2001 From: Nathan Weeks <1800812+nathanweeks@users.noreply.github.com> Date: Mon, 6 Jul 2026 10:47:08 -0400 Subject: [PATCH 09/11] Increase runner volume size from 40GB to 60GB --- .github/workflows/nf-test.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/nf-test.yml b/.github/workflows/nf-test.yml index f00d1bb..181eb2d 100644 --- a/.github/workflows/nf-test.yml +++ b/.github/workflows/nf-test.yml @@ -30,7 +30,7 @@ jobs: runs-on: # use self-hosted runners - runs-on=${{ github.run_id }}-nf-test-changes - runner=4cpu-linux-x64 - - volume=40gb + - volume=60gb outputs: shard: ${{ steps.set-shards.outputs.shard }} total_shards: ${{ steps.set-shards.outputs.total_shards }} From cf3471c35718a6861b239ace13e2615ce23ee887 Mon Sep 17 00:00:00 2001 From: Nathan Weeks <1800812+nathanweeks@users.noreply.github.com> Date: Mon, 6 Jul 2026 11:36:26 -0400 Subject: [PATCH 10/11] Increase runner volume size from 60GB to 80GB --- .github/workflows/nf-test.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/nf-test.yml b/.github/workflows/nf-test.yml index 181eb2d..996cb53 100644 --- a/.github/workflows/nf-test.yml +++ b/.github/workflows/nf-test.yml @@ -30,7 +30,7 @@ jobs: runs-on: # use self-hosted runners - runs-on=${{ github.run_id }}-nf-test-changes - runner=4cpu-linux-x64 - - volume=60gb + - volume=80gb outputs: shard: ${{ steps.set-shards.outputs.shard }} total_shards: ${{ steps.set-shards.outputs.total_shards }} From 9bfcc3c3f3886887b9393f277a4df63106a118c5 Mon Sep 17 00:00:00 2001 From: Nathan Weeks <1800812+nathanweeks@users.noreply.github.com> Date: Mon, 6 Jul 2026 13:07:45 -0400 Subject: [PATCH 11/11] Move runner volume allocation to nf-test job; start at 40gb --- .github/workflows/nf-test.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/nf-test.yml b/.github/workflows/nf-test.yml index 996cb53..737d19b 100644 --- a/.github/workflows/nf-test.yml +++ b/.github/workflows/nf-test.yml @@ -30,7 +30,6 @@ jobs: runs-on: # use self-hosted runners - runs-on=${{ github.run_id }}-nf-test-changes - runner=4cpu-linux-x64 - - volume=80gb outputs: shard: ${{ steps.set-shards.outputs.shard }} total_shards: ${{ steps.set-shards.outputs.total_shards }} @@ -65,6 +64,7 @@ jobs: runs-on: # use self-hosted runners - runs-on=${{ github.run_id }}-nf-test - runner=4cpu-linux-x64 + - volume=40gb strategy: fail-fast: false matrix: