From 7878df41a319d44965d9085272feb9de640016e7 Mon Sep 17 00:00:00 2001 From: Ariel Erijman Date: Tue, 1 Sep 2026 14:14:13 -0400 Subject: [PATCH 1/9] Update tasmanian-mismatch to 2.0.4 --- modules/tasmanian.nf | 12 ++++++++---- 1 file changed, 8 insertions(+), 4 deletions(-) diff --git a/modules/tasmanian.nf b/modules/tasmanian.nf index 9441c36..5c89d6e 100644 --- a/modules/tasmanian.nf +++ b/modules/tasmanian.nf @@ -2,7 +2,7 @@ process tasmanian { label 'medium_cpu' tag { library } publishDir "${params.outputDir}/stats/tasmanian" - conda "bioconda::samtools=1.22 bioconda::tasmanian-mismatch=1.0.9" + conda "bioconda::tasmanian-mismatch=2.0.3" errorStrategy { task.attempt <= 1 ? 'retry' : 'terminate' } maxRetries 1 @@ -15,14 +15,18 @@ process tasmanian { output: tuple val(library), path("${library}.tasmanian.csv"), emit: for_agg - tuple val("${task.process}"), val('samtools'), eval('samtools --version | head -n 1 | sed \'s/^samtools //\''), topic: versions - tuple val("${task.process}"), val('tasmanian'), val('*should be* 1.0.9'), topic: versions + tuple val("${task.process}"), val('tasmanian-mismatch'), val('*should be* 2.0.3'), topic: versions script: """ set +e set +o pipefail - samtools view -q 30 -F 3840 ${bam} | head -n 2000000 | run_tasmanian -r ${genome_fa} > ${library}.tasmanian.csv + tasmanian-mismatch ${bam} ${genome_fa} \ + --position-mode read \ + --min-base-quality 20 \ + --min-map-quality 30 \ + -F 3840 \ + -o ${library}.tasmanian.csv """ } From 6dcc911a32f03c8664f4099bfbf06259b758d52f Mon Sep 17 00:00:00 2001 From: Brad Langhorst Date: Wed, 2 Sep 2026 21:19:28 +0000 Subject: [PATCH 2/9] Updates ref CpG and Genome Links --- README.md | 7 ++++--- 1 file changed, 4 insertions(+), 3 deletions(-) diff --git a/README.md b/README.md index 7f79415..deac315 100644 --- a/README.md +++ b/README.md @@ -104,9 +104,10 @@ Modify the conf/references.config file to specify your genome files ## Reference Genomes -Pre-built reference genomes with methylation spike-in controls: -- **T2T CHM13**: https://neb-em-seq-sra.s3.amazonaws.com/T2T_chm13v2.0%2Bbs_controls.fa -- **GRCh38**: https://neb-em-seq-sra.s3.amazonaws.com/grch38_core%2Bbs_controls.fa +Pre-built reference genomes with methylation spike-in controls + CpG Island Annotation files: +- **T2T CHM13**: [T2T_chm13v2.0+ meth_controls](https://neb-em-seq-sra.s3.us-east-1.amazonaws.com/T2T_chm13v2.0%2Bmeth_controls.fa.gz) [CpG Islands](https://neb-em-seq-sra.s3.us-east-1.amazonaws.com/human_t2t_cpg_islands.gtf) +- **GRCh38**: [GRCh39 + meth controls](https://neb-em-seq-sra.s3.us-east-1.amazonaws.com/grch38_core%2Bmeth_controls.fa.gz) [CpG Islands](https://neb-em-seq-sra.s3.us-east-1.amazonaws.com/human_grch38_cpg_islands.gtf) +- **GRCm39**: [GRCm39 + meth_controls](https://neb-em-seq-sra.s3.us-east-1.amazonaws.com/grcm39%2Bmeth_controls.fa.gz) [CpG Islands](https://neb-em-seq-sra.s3.us-east-1.amazonaws.com/grcm39_cpg_islands.gtf) - Create your own reference by appending the [control sequences](assets/methylation_controls.fa) to your preferred genome fasta (e.g. `cat genome.fa methylation_controls.fa > genome+methylation_controls.fa`) | Sequence | Methylation State | Purpose | |----------|--------------------------------------------------|---------| From ea72baf6aabe0b78c39b01a17255c7122dbd4244 Mon Sep 17 00:00:00 2001 From: Ariel Erijman Date: Thu, 3 Sep 2026 08:13:27 -0400 Subject: [PATCH 3/9] preview topic is contingent on nextflow version --- README.md | 8 +++++--- main.nf | 5 ++++- 2 files changed, 9 insertions(+), 4 deletions(-) diff --git a/README.md b/README.md index deac315..b7e7f43 100644 --- a/README.md +++ b/README.md @@ -157,6 +157,8 @@ nf-test test --updateSnapshot ``` ## Upgrade -As of July, 2026, Nextflow v24 or older is not supported anymore. -If using Nextlfow version 24 is your only option, -please add `nextflow.preview.topic = true` as the top line in *main.nf* +This pipeline uses topic channels, which became a stable Nextflow feature in v25.04. +On older versions (including v24.x), topic channels are only available as a preview +feature behind `nextflow.preview.topic = true`. `main.nf` checks the running Nextflow +version at startup and sets that flag automatically when needed — no manual edits +required, on any version. diff --git a/main.nf b/main.nf index 68c3ed9..ae54eb8 100644 --- a/main.nf +++ b/main.nf @@ -1,4 +1,7 @@ -nextflow.preview.topic = true +if (nextflow.version.matches('<25.04')) { + nextflow.preview.topic = true +} + include { registerEmailNotifications } from './lib/notifications.nf' include { createVersionsFile } from './lib/versions.nf' include { format_ngs_agg_opts } from './modules/aggregate_results' From eb7d0aa3af501f1dff0e6218663cd7a67d738355 Mon Sep 17 00:00:00 2001 From: Ariel Erijman Date: Thu, 3 Sep 2026 08:21:31 -0400 Subject: [PATCH 4/9] Revert "preview topic is contingent on nextflow version" This reverts commit d93555ea3b72f2259adddfde6f38efef41448812. --- README.md | 8 +++----- main.nf | 5 +---- 2 files changed, 4 insertions(+), 9 deletions(-) diff --git a/README.md b/README.md index b7e7f43..deac315 100644 --- a/README.md +++ b/README.md @@ -157,8 +157,6 @@ nf-test test --updateSnapshot ``` ## Upgrade -This pipeline uses topic channels, which became a stable Nextflow feature in v25.04. -On older versions (including v24.x), topic channels are only available as a preview -feature behind `nextflow.preview.topic = true`. `main.nf` checks the running Nextflow -version at startup and sets that flag automatically when needed — no manual edits -required, on any version. +As of July, 2026, Nextflow v24 or older is not supported anymore. +If using Nextlfow version 24 is your only option, +please add `nextflow.preview.topic = true` as the top line in *main.nf* diff --git a/main.nf b/main.nf index ae54eb8..68c3ed9 100644 --- a/main.nf +++ b/main.nf @@ -1,7 +1,4 @@ -if (nextflow.version.matches('<25.04')) { - nextflow.preview.topic = true -} - +nextflow.preview.topic = true include { registerEmailNotifications } from './lib/notifications.nf' include { createVersionsFile } from './lib/versions.nf' include { format_ngs_agg_opts } from './modules/aggregate_results' From 978969925bf381d400b398030e2752d09f2b1d88 Mon Sep 17 00:00:00 2001 From: Ariel Erijman Date: Thu, 3 Sep 2026 08:38:22 -0400 Subject: [PATCH 5/9] preview is commented. --- README.md | 2 +- main.nf | 3 ++- 2 files changed, 3 insertions(+), 2 deletions(-) diff --git a/README.md b/README.md index deac315..d6107a2 100644 --- a/README.md +++ b/README.md @@ -159,4 +159,4 @@ nf-test test --updateSnapshot ## Upgrade As of July, 2026, Nextflow v24 or older is not supported anymore. If using Nextlfow version 24 is your only option, -please add `nextflow.preview.topic = true` as the top line in *main.nf* +please uncomment `nextflow.preview.topic = true` as the top line in *main.nf* diff --git a/main.nf b/main.nf index 68c3ed9..0b15f53 100644 --- a/main.nf +++ b/main.nf @@ -1,4 +1,5 @@ -nextflow.preview.topic = true +// nextflow.preview.topic = true + include { registerEmailNotifications } from './lib/notifications.nf' include { createVersionsFile } from './lib/versions.nf' include { format_ngs_agg_opts } from './modules/aggregate_results' From 547d73a186b031febdd714b4cdf3179f0ffdd888 Mon Sep 17 00:00:00 2001 From: Ariel Erijman Date: Thu, 3 Sep 2026 09:27:31 -0400 Subject: [PATCH 6/9] nf-test to 0.95 and sort tests as in snapshot --- tests/main.nf.test.snap | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/tests/main.nf.test.snap b/tests/main.nf.test.snap index 6bfe7b2..fbf1058 100644 --- a/tests/main.nf.test.snap +++ b/tests/main.nf.test.snap @@ -2,8 +2,8 @@ "EM-seq workflow uBam - single-end": { "content": [ { - "tasksFailed": 0, "tasksCount": 47, + "tasksFailed": 0, "tasksSucceeded": 47 }, [ @@ -313,7 +313,7 @@ ] ], "meta": { - "nf-test": "0.9.0", + "nf-test": "0.9.5", "nextflow": "24.10.5" }, "timestamp": "2026-08-20T15:14:15.067200906" @@ -321,8 +321,8 @@ "EM-seq workflow uBam": { "content": [ { - "tasksFailed": 0, "tasksCount": 49, + "tasksFailed": 0, "tasksSucceeded": 49 }, [ @@ -675,7 +675,7 @@ ] ], "meta": { - "nf-test": "0.9.0", + "nf-test": "0.9.5", "nextflow": "24.10.5" }, "timestamp": "2026-08-20T15:13:32.113269349" From 0adea48498b12307794bb811309222fd6da22632 Mon Sep 17 00:00:00 2001 From: Ariel Erijman Date: Thu, 3 Sep 2026 09:31:50 -0400 Subject: [PATCH 7/9] nextflow versions small issue --- main.nf | 1 + 1 file changed, 1 insertion(+) diff --git a/main.nf b/main.nf index 0b15f53..6b65c16 100644 --- a/main.nf +++ b/main.nf @@ -1,3 +1,4 @@ +// Nextflow v24 or older only: uncomment the line below (see README's Upgrade section) // nextflow.preview.topic = true include { registerEmailNotifications } from './lib/notifications.nf' From 609753c3f787e616c6626338314f400175842d68 Mon Sep 17 00:00:00 2001 From: Ariel Erijman Date: Thu, 3 Sep 2026 09:40:46 -0400 Subject: [PATCH 8/9] type in genomes --- README.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/README.md b/README.md index d6107a2..50d937d 100644 --- a/README.md +++ b/README.md @@ -106,7 +106,7 @@ Modify the conf/references.config file to specify your genome files ## Reference Genomes Pre-built reference genomes with methylation spike-in controls + CpG Island Annotation files: - **T2T CHM13**: [T2T_chm13v2.0+ meth_controls](https://neb-em-seq-sra.s3.us-east-1.amazonaws.com/T2T_chm13v2.0%2Bmeth_controls.fa.gz) [CpG Islands](https://neb-em-seq-sra.s3.us-east-1.amazonaws.com/human_t2t_cpg_islands.gtf) -- **GRCh38**: [GRCh39 + meth controls](https://neb-em-seq-sra.s3.us-east-1.amazonaws.com/grch38_core%2Bmeth_controls.fa.gz) [CpG Islands](https://neb-em-seq-sra.s3.us-east-1.amazonaws.com/human_grch38_cpg_islands.gtf) +- **GRCh38**: [GRCh38 + meth controls](https://neb-em-seq-sra.s3.us-east-1.amazonaws.com/grch38_core%2Bmeth_controls.fa.gz) [CpG Islands](https://neb-em-seq-sra.s3.us-east-1.amazonaws.com/human_grch38_cpg_islands.gtf) - **GRCm39**: [GRCm39 + meth_controls](https://neb-em-seq-sra.s3.us-east-1.amazonaws.com/grcm39%2Bmeth_controls.fa.gz) [CpG Islands](https://neb-em-seq-sra.s3.us-east-1.amazonaws.com/grcm39_cpg_islands.gtf) - Create your own reference by appending the [control sequences](assets/methylation_controls.fa) to your preferred genome fasta (e.g. `cat genome.fa methylation_controls.fa > genome+methylation_controls.fa`) | Sequence | Methylation State | Purpose | From 461c69d02a54ce8167bca513313a82bfb4d39f69 Mon Sep 17 00:00:00 2001 From: Ariel Erijman Date: Fri, 4 Sep 2026 10:10:46 -0400 Subject: [PATCH 9/9] tasmanian version updated --- modules/tasmanian.nf | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/modules/tasmanian.nf b/modules/tasmanian.nf index 5c89d6e..d0e8ec5 100644 --- a/modules/tasmanian.nf +++ b/modules/tasmanian.nf @@ -2,7 +2,7 @@ process tasmanian { label 'medium_cpu' tag { library } publishDir "${params.outputDir}/stats/tasmanian" - conda "bioconda::tasmanian-mismatch=2.0.3" + conda "bioconda::tasmanian-mismatch=2.0.5" errorStrategy { task.attempt <= 1 ? 'retry' : 'terminate' } maxRetries 1 @@ -15,7 +15,7 @@ process tasmanian { output: tuple val(library), path("${library}.tasmanian.csv"), emit: for_agg - tuple val("${task.process}"), val('tasmanian-mismatch'), val('*should be* 2.0.3'), topic: versions + tuple val("${task.process}"), val('tasmanian-mismatch'), val('2.0.5'), topic: versions script: """