From b64ac504c79d648fbb0842ebf42c2f1351ace962 Mon Sep 17 00:00:00 2001 From: Young Date: Tue, 11 Feb 2025 12:43:02 -0700 Subject: [PATCH 01/20] Change to ubuntu-latest --- .github/workflows/check_versions.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/check_versions.yml b/.github/workflows/check_versions.yml index a5b6e93..f51e85e 100644 --- a/.github/workflows/check_versions.yml +++ b/.github/workflows/check_versions.yml @@ -7,7 +7,7 @@ on: jobs: check: - runs-on: ubuntu-20.04 + runs-on: ubuntu-latest steps: - name: Checkout uses: actions/checkout@master From cc60d97c566780390200030049fa33faa9b7af39 Mon Sep 17 00:00:00 2001 From: Young Date: Tue, 11 Feb 2025 12:43:58 -0700 Subject: [PATCH 02/20] Update to ubuntu-latest --- .github/workflows/test.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/test.yml b/.github/workflows/test.yml index d86744f..1574848 100644 --- a/.github/workflows/test.yml +++ b/.github/workflows/test.yml @@ -6,7 +6,7 @@ run-name: Download fastq and fasta and run jobs: test: - runs-on: ubuntu-20.04 + runs-on: ubuntu-latest steps: - name: Checkout uses: actions/checkout@master From bad962d325dfe856c2c46e309e7f224432a0a787 Mon Sep 17 00:00:00 2001 From: Young Date: Tue, 11 Feb 2025 12:44:27 -0700 Subject: [PATCH 03/20] Update to ubuntu-latest --- .github/workflows/test_kraken2.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/test_kraken2.yml b/.github/workflows/test_kraken2.yml index 4005e12..1ae54f8 100755 --- a/.github/workflows/test_kraken2.yml +++ b/.github/workflows/test_kraken2.yml @@ -6,7 +6,7 @@ run-name: Test profile jobs: test: - runs-on: ubuntu-20.04 + runs-on: ubuntu-latest steps: - name: Checkout uses: actions/checkout@master From 07f8b6c8ec8f63402b866b4d24d443007bde9ae7 Mon Sep 17 00:00:00 2001 From: Young Date: Tue, 11 Feb 2025 12:44:53 -0700 Subject: [PATCH 04/20] Update to ubuntu-latest --- .github/workflows/test_mpx.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/test_mpx.yml b/.github/workflows/test_mpx.yml index 859340c..1c71d5a 100644 --- a/.github/workflows/test_mpx.yml +++ b/.github/workflows/test_mpx.yml @@ -6,7 +6,7 @@ run-name: MPX jobs: test: - runs-on: ubuntu-20.04 + runs-on: ubuntu-latest steps: - name: Checkout uses: actions/checkout@master From a84595b41f954fb1a927198a50d3962c155f582c Mon Sep 17 00:00:00 2001 From: Young Date: Tue, 11 Feb 2025 12:45:15 -0700 Subject: [PATCH 05/20] Update to ubuntu-latest --- .github/workflows/test_mpx_idt.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/test_mpx_idt.yml b/.github/workflows/test_mpx_idt.yml index 9901311..9661f81 100644 --- a/.github/workflows/test_mpx_idt.yml +++ b/.github/workflows/test_mpx_idt.yml @@ -6,7 +6,7 @@ run-name: MPX with IDT Primers jobs: mpx_idt: - runs-on: ubuntu-20.04 + runs-on: ubuntu-latest steps: - name: Checkout uses: actions/checkout@master From 996564dac41d040966e54405a38ad43645f95583 Mon Sep 17 00:00:00 2001 From: Young Date: Tue, 11 Feb 2025 12:45:34 -0700 Subject: [PATCH 06/20] Update to ubuntu-latest --- .github/workflows/test_mpx_primalseq.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/test_mpx_primalseq.yml b/.github/workflows/test_mpx_primalseq.yml index 516576a..62db83f 100644 --- a/.github/workflows/test_mpx_primalseq.yml +++ b/.github/workflows/test_mpx_primalseq.yml @@ -6,7 +6,7 @@ run-name: mpx_primalseq jobs: test: - runs-on: ubuntu-20.04 + runs-on: ubuntu-latest steps: - name: Checkout uses: actions/checkout@master From 88a466efff44ba6753bd156bd5fc81f9a0d6c781 Mon Sep 17 00:00:00 2001 From: Young Date: Tue, 11 Feb 2025 12:45:59 -0700 Subject: [PATCH 07/20] Update to ubuntu-latest --- .github/workflows/test_mpx_yale.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/test_mpx_yale.yml b/.github/workflows/test_mpx_yale.yml index 2cc7266..94e6c53 100755 --- a/.github/workflows/test_mpx_yale.yml +++ b/.github/workflows/test_mpx_yale.yml @@ -6,7 +6,7 @@ run-name: mpx_yale jobs: test: - runs-on: ubuntu-20.04 + runs-on: ubuntu-latest steps: - name: Checkout uses: actions/checkout@master From f1d9671ae52a77e645c0dcd9d2cc191743d0e67a Mon Sep 17 00:00:00 2001 From: Young Date: Tue, 11 Feb 2025 12:46:16 -0700 Subject: [PATCH 08/20] Update to ubuntu-latest --- .github/workflows/test_nanopore.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/test_nanopore.yml b/.github/workflows/test_nanopore.yml index f90e785..b07b410 100644 --- a/.github/workflows/test_nanopore.yml +++ b/.github/workflows/test_nanopore.yml @@ -6,7 +6,7 @@ run-name: nanopore jobs: test: - runs-on: ubuntu-20.04 + runs-on: ubuntu-latest steps: - name: Checkout uses: actions/checkout@master From 3cd78494bec2d8f1b75983a5ef8ea7be736b8227 Mon Sep 17 00:00:00 2001 From: Young Date: Tue, 11 Feb 2025 12:46:54 -0700 Subject: [PATCH 09/20] Update to ubuntu-latest --- .github/workflows/test_primers.yml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/.github/workflows/test_primers.yml b/.github/workflows/test_primers.yml index 9a95c76..518a71f 100644 --- a/.github/workflows/test_primers.yml +++ b/.github/workflows/test_primers.yml @@ -6,11 +6,11 @@ run-name: primers jobs: test: - runs-on: ubuntu-20.04 + runs-on: ubuntu-latest strategy: matrix: primer: - [ + [ "midnight_idt_V1", "midnight_ont_V1", "midnight_ont_V2", From 17091d076de3eef140d2f6653cb052410126e23f Mon Sep 17 00:00:00 2001 From: Young Date: Tue, 11 Feb 2025 12:47:14 -0700 Subject: [PATCH 10/20] Update to ubuntu-latest --- .github/workflows/test_profile.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/test_profile.yml b/.github/workflows/test_profile.yml index 3a72f59..48aa145 100644 --- a/.github/workflows/test_profile.yml +++ b/.github/workflows/test_profile.yml @@ -6,7 +6,7 @@ run-name: Test profile jobs: test: - runs-on: ubuntu-20.04 + runs-on: ubuntu-latest steps: - name: Checkout uses: actions/checkout@master From 2deb35f659c5c522008ba7e52eb152ba37fe43eb Mon Sep 17 00:00:00 2001 From: Young Date: Tue, 11 Feb 2025 12:47:33 -0700 Subject: [PATCH 11/20] Update to ubuntu-latest --- .github/workflows/test_profile1.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/test_profile1.yml b/.github/workflows/test_profile1.yml index 47a4bad..ad44f98 100644 --- a/.github/workflows/test_profile1.yml +++ b/.github/workflows/test_profile1.yml @@ -6,7 +6,7 @@ run-name: Profile 1 jobs: test: - runs-on: ubuntu-20.04 + runs-on: ubuntu-latest steps: - name: Checkout uses: actions/checkout@master From 8f5c6f22f0bde9c7eb40f7b8fbb542f776de67ef Mon Sep 17 00:00:00 2001 From: Young Date: Tue, 11 Feb 2025 12:47:49 -0700 Subject: [PATCH 12/20] Update to ubuntu-latest --- .github/workflows/test_profile2.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/test_profile2.yml b/.github/workflows/test_profile2.yml index ca8be12..af06fab 100644 --- a/.github/workflows/test_profile2.yml +++ b/.github/workflows/test_profile2.yml @@ -6,7 +6,7 @@ run-name: Profile 2 jobs: test: - runs-on: ubuntu-20.04 + runs-on: ubuntu-latest steps: - name: Checkout uses: actions/checkout@master From fd1dd8e904b2057afa9672da63eb0e2495fbb6cf Mon Sep 17 00:00:00 2001 From: Young Date: Tue, 11 Feb 2025 12:48:09 -0700 Subject: [PATCH 13/20] Update to ubuntu-latest --- .github/workflows/test_profile3.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/test_profile3.yml b/.github/workflows/test_profile3.yml index c020d63..ee73191 100755 --- a/.github/workflows/test_profile3.yml +++ b/.github/workflows/test_profile3.yml @@ -6,7 +6,7 @@ run-name: Profile 3 jobs: test: - runs-on: ubuntu-20.04 + runs-on: ubuntu-latest steps: - name: Checkout uses: actions/checkout@master From be5fb1f462484ab39d1abd82f3b5d38a6da3d659 Mon Sep 17 00:00:00 2001 From: Young Date: Tue, 11 Feb 2025 12:48:26 -0700 Subject: [PATCH 14/20] Update to ubuntu-latest --- .github/workflows/test_relatedness.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/test_relatedness.yml b/.github/workflows/test_relatedness.yml index 785926a..cbd0a95 100644 --- a/.github/workflows/test_relatedness.yml +++ b/.github/workflows/test_relatedness.yml @@ -6,7 +6,7 @@ run-name: Test MSA jobs: msa: - runs-on: ubuntu-20.04 + runs-on: ubuntu-latest steps: - name: Checkout uses: actions/checkout@master From 275442f5ba8a3cdfb3404a9157214bd725508568 Mon Sep 17 00:00:00 2001 From: Young Date: Tue, 11 Feb 2025 12:49:26 -0700 Subject: [PATCH 15/20] Update to ubuntu-latest --- .github/workflows/test_samplesheet.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/test_samplesheet.yml b/.github/workflows/test_samplesheet.yml index 6f929a2..2e324fa 100755 --- a/.github/workflows/test_samplesheet.yml +++ b/.github/workflows/test_samplesheet.yml @@ -6,7 +6,7 @@ run-name: Download fastq and fasta and run jobs: test: - runs-on: ubuntu-20.04 + runs-on: ubuntu-latest steps: - name: Checkout uses: actions/checkout@master From 4e475e033efe3fcd4491cbd1f4d846d43eec9ff0 Mon Sep 17 00:00:00 2001 From: Young Date: Tue, 11 Feb 2025 12:49:41 -0700 Subject: [PATCH 16/20] Update to ubuntu-latest --- .github/workflows/test_wastewater.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/test_wastewater.yml b/.github/workflows/test_wastewater.yml index f8840aa..1b463fc 100644 --- a/.github/workflows/test_wastewater.yml +++ b/.github/workflows/test_wastewater.yml @@ -6,7 +6,7 @@ run-name: Download wastewater fastq jobs: test: - runs-on: ubuntu-20.04 + runs-on: ubuntu-latest steps: - name: Checkout uses: actions/checkout@master From 5894325ede8401058df3d37a2dd73a571a9afab4 Mon Sep 17 00:00:00 2001 From: Young Date: Tue, 11 Feb 2025 12:50:02 -0700 Subject: [PATCH 17/20] Update to ubuntu-latest --- .github/workflows/update_nextclade.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/update_nextclade.yml b/.github/workflows/update_nextclade.yml index aecb2c4..abe0ad4 100644 --- a/.github/workflows/update_nextclade.yml +++ b/.github/workflows/update_nextclade.yml @@ -7,7 +7,7 @@ on: jobs: update-nextclade-dataset: - runs-on: ubuntu-20.04 + runs-on: ubuntu-latest steps: - name: Checkout uses: actions/checkout@master From d55907121e5e390baaf1252e66986b522410d806 Mon Sep 17 00:00:00 2001 From: Young Date: Tue, 11 Feb 2025 12:51:04 -0700 Subject: [PATCH 18/20] Update to 3.26.25042 --- nextflow.config | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/nextflow.config b/nextflow.config index 2cc3581..11e0eb5 100644 --- a/nextflow.config +++ b/nextflow.config @@ -263,7 +263,7 @@ manifest { name = 'UPHL-BioNGS/Cecret' author = 'Erin Young' homePage = 'https://github.com/UPHL-BioNGS/Cecret' - version = 'v3.26.25034' + version = 'v3.26.25042' defaultBranch = 'master' recurseSubmodules = false description = 'Reference-based consensus creation' From b48da5b56d170702d661b8228fe9ac2e723a1c34 Mon Sep 17 00:00:00 2001 From: Young Date: Tue, 11 Feb 2025 12:52:28 -0700 Subject: [PATCH 19/20] Update freyja to 1.5.2-02_10_2025-01-52-2025-02-10 --- modules/local/freyja.nf | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/modules/local/freyja.nf b/modules/local/freyja.nf index 258e7a0..627a7b6 100644 --- a/modules/local/freyja.nf +++ b/modules/local/freyja.nf @@ -1,7 +1,7 @@ process FREYJA { tag "${meta.id}" label "process_medium" - container 'staphb/freyja:1.5.2-02_03_2025-02-26-2025-02-03' + container 'staphb/freyja:1.5.2-02_10_2025-01-52-2025-02-10' input: tuple val(meta), file(bam), file(reference_genome) From 940357a2553d7fc177217bdabf444ddc61c76af0 Mon Sep 17 00:00:00 2001 From: Young Date: Tue, 11 Feb 2025 12:56:19 -0700 Subject: [PATCH 20/20] Added apptainer --- nextflow.config | 11 +++++++++++ 1 file changed, 11 insertions(+) diff --git a/nextflow.config b/nextflow.config index 11e0eb5..d09aa66 100644 --- a/nextflow.config +++ b/nextflow.config @@ -166,6 +166,17 @@ profiles { apptainer.enabled = false docker.runOptions = '-u $(id -u):$(id -g)' } + apptainer { + singularity.enabled = false + singularity.autoMounts = false + conda.enabled = false + docker.enabled = false + podman.enabled = false + shifter.enabled = false + charliecloud.enabled = false + apptainer.enabled = true + apptainer.autoMounts = true + } singularity { singularity.enabled = true singularity.autoMounts = true