From c08e19b61a941c2c804bc1d99548635c2aaadacd Mon Sep 17 00:00:00 2001 From: Sateesh Date: Fri, 25 Oct 2024 06:25:40 +0000 Subject: [PATCH 01/13] post-release version bump --- .nf-core.yml | 10 +++++----- assets/multiqc_config.yml | 7 ++++--- nextflow.config | 2 +- tests/bismark_emseq_clip_r1.nf.test.snap | 4 ++-- tests/bismark_hisat.nf.test.snap | 4 ++-- tests/bismark_hisat_rrbs.nf.test.snap | 4 ++-- ...at_save_reference_save_align_intermeds.nf.test.snap | 4 ++-- tests/bismark_nomeseq.nf.test.snap | 4 ++-- tests/bismark_rrbs.nf.test.snap | 4 ++-- ...rk_save_reference_save_align_intermeds.nf.test.snap | 4 ++-- tests/bismark_skip_deduplication.nf.test.snap | 4 ++-- tests/bismark_skip_multiqc.nf.test.snap | 4 ++-- tests/bismark_skip_trimming.nf.test.snap | 4 ++-- tests/bwameth.nf.test.snap | 4 ++-- tests/bwameth_rrbs.nf.test.snap | 6 +++--- ...th_save_reference_save_align_intermeds.nf.test.snap | 4 ++-- tests/bwameth_skip_deduplication.nf.test.snap | 6 +++--- tests/bwameth_skip_trimming.nf.test.snap | 4 ++-- tests/default.nf.test.snap | 4 ++-- 19 files changed, 44 insertions(+), 43 deletions(-) diff --git a/.nf-core.yml b/.nf-core.yml index 1eee6001..d9717653 100644 --- a/.nf-core.yml +++ b/.nf-core.yml @@ -1,4 +1,4 @@ -bump_version: null +bump_version: lint: actions_ci: false files_exist: @@ -6,7 +6,7 @@ lint: - conf/modules.config modules_config: false nf_core_version: 3.0.2 -org_path: null +org_path: repository_type: pipeline template: author: Phil Ewels, Sateesh Peri @@ -17,6 +17,6 @@ template: name: methylseq org: nf-core outdir: . - skip_features: null - version: 2.7.0 -update: null + skip_features: + version: 2.8.0dev +update: diff --git a/assets/multiqc_config.yml b/assets/multiqc_config.yml index 37078f04..0639e2fa 100644 --- a/assets/multiqc_config.yml +++ b/assets/multiqc_config.yml @@ -1,7 +1,8 @@ report_comment: > - This report has been generated by the nf-core/methylseq - analysis pipeline. For information about how to interpret these results, please see the - documentation. + This report has been generated by the nf-core/methylseq analysis pipeline. For information about how + to interpret these results, please see the documentation. report_section_order: "nf-core-methylseq-methods-description": order: -1000 diff --git a/nextflow.config b/nextflow.config index af2a040e..4cf66cba 100644 --- a/nextflow.config +++ b/nextflow.config @@ -289,7 +289,7 @@ manifest { description = """Methylation (Bisulfite-Sequencing) Best Practice analysis pipeline, part of the nf-core community.""" mainScript = 'main.nf' nextflowVersion = '!>=24.04.2' - version = '2.7.0' + version = '2.8.0dev' doi = '10.5281/zenodo.1343417' } diff --git a/tests/bismark_emseq_clip_r1.nf.test.snap b/tests/bismark_emseq_clip_r1.nf.test.snap index 0f82b86b..a4ce459c 100644 --- a/tests/bismark_emseq_clip_r1.nf.test.snap +++ b/tests/bismark_emseq_clip_r1.nf.test.snap @@ -20,7 +20,7 @@ "cutadapt": 4.2 }, "Workflow": { - "nf-core/methylseq": "v2.7.0" + "nf-core/methylseq": "v2.8.0dev" } }, [ @@ -576,4 +576,4 @@ }, "timestamp": "2024-10-21T17:43:14.505236122" } -} \ No newline at end of file +} diff --git a/tests/bismark_hisat.nf.test.snap b/tests/bismark_hisat.nf.test.snap index 0e92c1eb..4e24adb7 100644 --- a/tests/bismark_hisat.nf.test.snap +++ b/tests/bismark_hisat.nf.test.snap @@ -30,7 +30,7 @@ "cutadapt": 4.2 }, "Workflow": { - "nf-core/methylseq": "v2.7.0" + "nf-core/methylseq": "v2.8.0dev" } }, [ @@ -588,4 +588,4 @@ }, "timestamp": "2024-10-21T17:44:48.196812536" } -} \ No newline at end of file +} diff --git a/tests/bismark_hisat_rrbs.nf.test.snap b/tests/bismark_hisat_rrbs.nf.test.snap index 0eb368cc..8b7edc34 100644 --- a/tests/bismark_hisat_rrbs.nf.test.snap +++ b/tests/bismark_hisat_rrbs.nf.test.snap @@ -20,7 +20,7 @@ "cutadapt": 4.2 }, "Workflow": { - "nf-core/methylseq": "v2.7.0" + "nf-core/methylseq": "v2.8.0dev" } }, [ @@ -581,4 +581,4 @@ }, "timestamp": "2024-10-21T17:48:05.852952347" } -} \ No newline at end of file +} diff --git a/tests/bismark_hisat_save_reference_save_align_intermeds.nf.test.snap b/tests/bismark_hisat_save_reference_save_align_intermeds.nf.test.snap index c70f3bb4..22c75d3f 100644 --- a/tests/bismark_hisat_save_reference_save_align_intermeds.nf.test.snap +++ b/tests/bismark_hisat_save_reference_save_align_intermeds.nf.test.snap @@ -20,7 +20,7 @@ "cutadapt": 4.2 }, "Workflow": { - "nf-core/methylseq": "v2.7.0" + "nf-core/methylseq": "v2.8.0dev" } }, [ @@ -659,4 +659,4 @@ }, "timestamp": "2024-10-21T17:49:33.437253199" } -} \ No newline at end of file +} diff --git a/tests/bismark_nomeseq.nf.test.snap b/tests/bismark_nomeseq.nf.test.snap index d23aa5fe..e644ef56 100644 --- a/tests/bismark_nomeseq.nf.test.snap +++ b/tests/bismark_nomeseq.nf.test.snap @@ -20,7 +20,7 @@ "cutadapt": 4.2 }, "Workflow": { - "nf-core/methylseq": "v2.7.0" + "nf-core/methylseq": "v2.8.0dev" } }, [ @@ -622,4 +622,4 @@ }, "timestamp": "2024-10-21T17:50:56.499718354" } -} \ No newline at end of file +} diff --git a/tests/bismark_rrbs.nf.test.snap b/tests/bismark_rrbs.nf.test.snap index fb7cc545..1af56bf7 100644 --- a/tests/bismark_rrbs.nf.test.snap +++ b/tests/bismark_rrbs.nf.test.snap @@ -20,7 +20,7 @@ "cutadapt": 4.2 }, "Workflow": { - "nf-core/methylseq": "v2.7.0" + "nf-core/methylseq": "v2.8.0dev" } }, [ @@ -581,4 +581,4 @@ }, "timestamp": "2024-10-21T17:52:32.475797707" } -} \ No newline at end of file +} diff --git a/tests/bismark_save_reference_save_align_intermeds.nf.test.snap b/tests/bismark_save_reference_save_align_intermeds.nf.test.snap index 8ec9d79e..1bfad2d9 100644 --- a/tests/bismark_save_reference_save_align_intermeds.nf.test.snap +++ b/tests/bismark_save_reference_save_align_intermeds.nf.test.snap @@ -20,7 +20,7 @@ "cutadapt": 4.2 }, "Workflow": { - "nf-core/methylseq": "v2.7.0" + "nf-core/methylseq": "v2.8.0dev" } }, [ @@ -651,4 +651,4 @@ }, "timestamp": "2024-10-21T18:10:42.065837136" } -} \ No newline at end of file +} diff --git a/tests/bismark_skip_deduplication.nf.test.snap b/tests/bismark_skip_deduplication.nf.test.snap index 13bf50eb..5edc5c6a 100644 --- a/tests/bismark_skip_deduplication.nf.test.snap +++ b/tests/bismark_skip_deduplication.nf.test.snap @@ -20,7 +20,7 @@ "cutadapt": 4.2 }, "Workflow": { - "nf-core/methylseq": "v2.7.0" + "nf-core/methylseq": "v2.8.0dev" } }, [ @@ -583,4 +583,4 @@ }, "timestamp": "2024-10-21T17:54:28.816433456" } -} \ No newline at end of file +} diff --git a/tests/bismark_skip_multiqc.nf.test.snap b/tests/bismark_skip_multiqc.nf.test.snap index 84d72c00..5ad46fb1 100644 --- a/tests/bismark_skip_multiqc.nf.test.snap +++ b/tests/bismark_skip_multiqc.nf.test.snap @@ -20,7 +20,7 @@ "cutadapt": 4.2 }, "Workflow": { - "nf-core/methylseq": "v2.7.0" + "nf-core/methylseq": "v2.8.0dev" } }, [ @@ -578,4 +578,4 @@ }, "timestamp": "2024-10-21T17:55:48.550138313" } -} \ No newline at end of file +} diff --git a/tests/bismark_skip_trimming.nf.test.snap b/tests/bismark_skip_trimming.nf.test.snap index 97e616c6..65b700f2 100644 --- a/tests/bismark_skip_trimming.nf.test.snap +++ b/tests/bismark_skip_trimming.nf.test.snap @@ -16,7 +16,7 @@ "qualimap": 2.3 }, "Workflow": { - "nf-core/methylseq": "v2.7.0" + "nf-core/methylseq": "v2.8.0dev" } }, [ @@ -535,4 +535,4 @@ }, "timestamp": "2024-10-17T11:09:41.623493366" } -} \ No newline at end of file +} diff --git a/tests/bwameth.nf.test.snap b/tests/bwameth.nf.test.snap index 6ce8c6d3..edc9b679 100644 --- a/tests/bwameth.nf.test.snap +++ b/tests/bwameth.nf.test.snap @@ -20,7 +20,7 @@ "cutadapt": 4.2 }, "Workflow": { - "nf-core/methylseq": "v2.7.0" + "nf-core/methylseq": "v2.8.0dev" } }, [ @@ -450,4 +450,4 @@ }, "timestamp": "2024-10-12T07:40:41.336750081" } -} \ No newline at end of file +} diff --git a/tests/bwameth_rrbs.nf.test.snap b/tests/bwameth_rrbs.nf.test.snap index 59f497d9..5dff4559 100644 --- a/tests/bwameth_rrbs.nf.test.snap +++ b/tests/bwameth_rrbs.nf.test.snap @@ -20,7 +20,7 @@ "cutadapt": 4.2 }, "Workflow": { - "nf-core/methylseq": "v2.7.0" + "nf-core/methylseq": "v2.8.0dev" } }, [ @@ -386,7 +386,7 @@ "genome_results.txt:md5,58d212848ac7b7650e3bd6812a4064af" ], [ - + ] ], "meta": { @@ -395,4 +395,4 @@ }, "timestamp": "2024-10-21T18:00:44.344954074" } -} \ No newline at end of file +} diff --git a/tests/bwameth_save_reference_save_align_intermeds.nf.test.snap b/tests/bwameth_save_reference_save_align_intermeds.nf.test.snap index 546c1371..672786fb 100644 --- a/tests/bwameth_save_reference_save_align_intermeds.nf.test.snap +++ b/tests/bwameth_save_reference_save_align_intermeds.nf.test.snap @@ -20,7 +20,7 @@ "cutadapt": 4.2 }, "Workflow": { - "nf-core/methylseq": "v2.7.0" + "nf-core/methylseq": "v2.8.0dev" } }, [ @@ -498,4 +498,4 @@ }, "timestamp": "2024-10-21T18:01:53.259560408" } -} \ No newline at end of file +} diff --git a/tests/bwameth_skip_deduplication.nf.test.snap b/tests/bwameth_skip_deduplication.nf.test.snap index f73c18ae..d113ef44 100644 --- a/tests/bwameth_skip_deduplication.nf.test.snap +++ b/tests/bwameth_skip_deduplication.nf.test.snap @@ -20,7 +20,7 @@ "cutadapt": 4.2 }, "Workflow": { - "nf-core/methylseq": "v2.7.0" + "nf-core/methylseq": "v2.8.0dev" } }, [ @@ -386,7 +386,7 @@ "genome_results.txt:md5,478f711b8ef22e094e4d0ff7fa0dfda0" ], [ - + ] ], "meta": { @@ -395,4 +395,4 @@ }, "timestamp": "2024-10-21T18:02:51.160774031" } -} \ No newline at end of file +} diff --git a/tests/bwameth_skip_trimming.nf.test.snap b/tests/bwameth_skip_trimming.nf.test.snap index 7603b462..5aeed3ce 100644 --- a/tests/bwameth_skip_trimming.nf.test.snap +++ b/tests/bwameth_skip_trimming.nf.test.snap @@ -16,7 +16,7 @@ "qualimap": 2.3 }, "Workflow": { - "nf-core/methylseq": "v2.7.0" + "nf-core/methylseq": "v2.8.0dev" } }, [ @@ -397,4 +397,4 @@ }, "timestamp": "2024-10-17T10:43:35.237760512" } -} \ No newline at end of file +} diff --git a/tests/default.nf.test.snap b/tests/default.nf.test.snap index 675f4e67..e3241084 100644 --- a/tests/default.nf.test.snap +++ b/tests/default.nf.test.snap @@ -30,7 +30,7 @@ "cutadapt": 4.2 }, "Workflow": { - "nf-core/methylseq": "v2.7.0" + "nf-core/methylseq": "v2.8.0dev" } }, [ @@ -588,4 +588,4 @@ }, "timestamp": "2024-10-21T18:05:06.16706255" } -} \ No newline at end of file +} From f00692ce976b1790b021f5b51214b682a2f11744 Mon Sep 17 00:00:00 2001 From: Sateesh Date: Fri, 25 Oct 2024 06:32:34 +0000 Subject: [PATCH 02/13] update changelog --- CHANGELOG.md | 6 ++++++ 1 file changed, 6 insertions(+) diff --git a/CHANGELOG.md b/CHANGELOG.md index 22560fce..6de89b31 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -1,5 +1,11 @@ # nf-core/methylseq +## [v2.8.0](https://github.com/nf-core/methylseq/releases/tag/2.8.0) - [] + +### Bug fixes & refactoring + +### Pipeline Updates + ## [v2.7.0](https://github.com/nf-core/methylseq/releases/tag/2.7.0) - [2024-10-25] ### Bug fixes & refactoring From 8419ad348bd1ebb464b282e96d9a5e82452840a3 Mon Sep 17 00:00:00 2001 From: Sateesh_Peri <33637490+sateeshperi@users.noreply.github.com> Date: Fri, 25 Oct 2024 12:19:48 +0530 Subject: [PATCH 03/13] Update .nf-core.yml MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit Co-authored-by: Matthias Hörtenhuber --- .nf-core.yml | 1 - 1 file changed, 1 deletion(-) diff --git a/.nf-core.yml b/.nf-core.yml index d9717653..3cd4bf46 100644 --- a/.nf-core.yml +++ b/.nf-core.yml @@ -1,4 +1,3 @@ -bump_version: lint: actions_ci: false files_exist: From 8fc3130cf87b5798d8069f1def37b6e37daab801 Mon Sep 17 00:00:00 2001 From: Sateesh Date: Fri, 25 Oct 2024 14:51:41 +0000 Subject: [PATCH 04/13] update modules with bismark, bwameth symlink fix --- modules/nf-core/bismark/align/main.nf | 4 +-- .../nf-core/bismark/align/tests/main.nf.test | 25 +++++++++++++++---- .../align/tests/nextflow_bowtie2.config | 8 ------ .../align/tests/nextflow_hisat2.config | 8 ------ .../align/tests/nextflow_minimap2.config | 8 ------ modules/nf-core/bismark/summary/main.nf | 2 +- modules/nf-core/bwameth/align/main.nf | 4 +-- modules/nf-core/trimgalore/environment.yml | 2 +- modules/nf-core/trimgalore/main.nf | 4 +-- .../trimgalore/tests/main.nf.test.snap | 20 +++++++-------- 10 files changed, 36 insertions(+), 49 deletions(-) delete mode 100644 modules/nf-core/bismark/align/tests/nextflow_bowtie2.config delete mode 100644 modules/nf-core/bismark/align/tests/nextflow_hisat2.config delete mode 100644 modules/nf-core/bismark/align/tests/nextflow_minimap2.config diff --git a/modules/nf-core/bismark/align/main.nf b/modules/nf-core/bismark/align/main.nf index d8ce3d01..1de78f32 100644 --- a/modules/nf-core/bismark/align/main.nf +++ b/modules/nf-core/bismark/align/main.nf @@ -56,9 +56,7 @@ process BISMARK_ALIGN { } } """ - if [ ! -f $index/$fasta ]; then - ln -s \$(readlink $fasta) $index/$fasta; - fi + ln -sf \$(readlink $fasta) $index/$fasta bismark \\ $fastq \\ diff --git a/modules/nf-core/bismark/align/tests/main.nf.test b/modules/nf-core/bismark/align/tests/main.nf.test index fcd693c8..059057d3 100644 --- a/modules/nf-core/bismark/align/tests/main.nf.test +++ b/modules/nf-core/bismark/align/tests/main.nf.test @@ -25,9 +25,12 @@ nextflow_process { } test("bowtie2 single-end / sarscov2 genome [fasta]") { - config './nextflow_bowtie2.config' + config './nextflow.config' when { + params { + bismark_args = '--bowtie2' + } process { """ input[0] = Channel.of([ @@ -55,9 +58,12 @@ nextflow_process { } test("bowtie2 paired-end / sarscov2 genome [fasta]") { - config './nextflow_bowtie2.config' + config './nextflow.config' when { + params { + bismark_args = '--bowtie2' + } process { """ input[0] = Channel.of([ @@ -88,9 +94,12 @@ nextflow_process { } test("hisat2 single-end / sarscov2 genome [fasta]") { - config './nextflow_hisat2.config' + config './nextflow.config' when { + params { + bismark_args = '--hisat2' + } process { """ input[0] = Channel.of([ @@ -118,9 +127,12 @@ nextflow_process { } test("hisat2 paired-end / sarscov2 genome [fasta]") { - config './nextflow_hisat2.config' + config './nextflow.config' when { + params { + bismark_args = '--hisat2' + } process { """ input[0] = Channel.of([ @@ -151,9 +163,12 @@ nextflow_process { } test("minimap2 single-end / sarscov2 genome [fasta]") { - config './nextflow_minimap2.config' + config './nextflow.config' when { + params { + bismark_args = '--minimap2' + } process { """ input[0] = Channel.of([ diff --git a/modules/nf-core/bismark/align/tests/nextflow_bowtie2.config b/modules/nf-core/bismark/align/tests/nextflow_bowtie2.config deleted file mode 100644 index cf0357e2..00000000 --- a/modules/nf-core/bismark/align/tests/nextflow_bowtie2.config +++ /dev/null @@ -1,8 +0,0 @@ -process { - withName: BISMARK_ALIGN { - ext.args = '--bowtie2' - } - withName: BISMARK_GENOMEPREPARATION { - ext.args = '--bowtie2' - } -} \ No newline at end of file diff --git a/modules/nf-core/bismark/align/tests/nextflow_hisat2.config b/modules/nf-core/bismark/align/tests/nextflow_hisat2.config deleted file mode 100644 index 5b962ae0..00000000 --- a/modules/nf-core/bismark/align/tests/nextflow_hisat2.config +++ /dev/null @@ -1,8 +0,0 @@ -process { - withName: BISMARK_ALIGN { - ext.args = '--hisat2' - } - withName: BISMARK_GENOMEPREPARATION { - ext.args = '--hisat2' - } -} \ No newline at end of file diff --git a/modules/nf-core/bismark/align/tests/nextflow_minimap2.config b/modules/nf-core/bismark/align/tests/nextflow_minimap2.config deleted file mode 100644 index dd46fe26..00000000 --- a/modules/nf-core/bismark/align/tests/nextflow_minimap2.config +++ /dev/null @@ -1,8 +0,0 @@ -process { - withName: BISMARK_ALIGN { - ext.args = '--minimap2' - } - withName: BISMARK_GENOMEPREPARATION { - ext.args = '--minimap2' - } -} \ No newline at end of file diff --git a/modules/nf-core/bismark/summary/main.nf b/modules/nf-core/bismark/summary/main.nf index 2aadfc03..94533c40 100644 --- a/modules/nf-core/bismark/summary/main.nf +++ b/modules/nf-core/bismark/summary/main.nf @@ -33,7 +33,7 @@ process BISMARK_SUMMARY { stub: def args = task.ext.args ?: '' - def prefix = task.ext.prefix ?: "${meta.id}" + def prefix = task.ext.prefix ?: "${bam.baseName()}" """ touch ${prefix}.report.txt touch ${prefix}.report.html diff --git a/modules/nf-core/bwameth/align/main.nf b/modules/nf-core/bwameth/align/main.nf index 2e6ff2d0..99f5f63a 100644 --- a/modules/nf-core/bwameth/align/main.nf +++ b/modules/nf-core/bwameth/align/main.nf @@ -29,9 +29,7 @@ process BWAMETH_ALIGN { # See https://github.com/nf-core/methylseq/pull/217 touch -c $index/* - if [ ! -f $index/$fasta ]; then - ln -s \$(readlink $fasta) $index/$fasta; - fi + ln -sf \$(readlink $fasta) $index/$fasta bwameth.py \\ $args \\ diff --git a/modules/nf-core/trimgalore/environment.yml b/modules/nf-core/trimgalore/environment.yml index 910ffa88..622407ed 100644 --- a/modules/nf-core/trimgalore/environment.yml +++ b/modules/nf-core/trimgalore/environment.yml @@ -3,5 +3,5 @@ channels: - bioconda dependencies: - - bioconda::cutadapt=4.2 + - bioconda::cutadapt=4.9 - bioconda::trim-galore=0.6.10 diff --git a/modules/nf-core/trimgalore/main.nf b/modules/nf-core/trimgalore/main.nf index 30d17edc..8a2fc54b 100644 --- a/modules/nf-core/trimgalore/main.nf +++ b/modules/nf-core/trimgalore/main.nf @@ -4,8 +4,8 @@ process TRIMGALORE { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/trim-galore:0.6.10--hdfd78af_0' : - 'biocontainers/trim-galore:0.6.10--hdfd78af_0' }" + 'https://depot.galaxyproject.org/singularity/trim-galore%3A0.6.10--hdfd78af_1' : + 'biocontainers/trim-galore:0.6.10--hdfd78af_1' }" input: tuple val(meta), path(reads) diff --git a/modules/nf-core/trimgalore/tests/main.nf.test.snap b/modules/nf-core/trimgalore/tests/main.nf.test.snap index 61b3504a..21da8493 100644 --- a/modules/nf-core/trimgalore/tests/main.nf.test.snap +++ b/modules/nf-core/trimgalore/tests/main.nf.test.snap @@ -2,14 +2,14 @@ "test_trimgalore_single_end": { "content": [ [ - "versions.yml:md5,0376fafd6096035de5c7ca6cb4e5e119" + "versions.yml:md5,81a0b49f3a9e1315fe564f9946eb8c50" ] ], "meta": { "nf-test": "0.9.0", "nextflow": "24.04.4" }, - "timestamp": "2024-10-18T12:50:36.440264431" + "timestamp": "2024-10-22T19:23:17.969056957" }, "test_trimgalore_single_end - stub": { "content": [ @@ -42,7 +42,7 @@ ], "5": [ - "versions.yml:md5,0376fafd6096035de5c7ca6cb4e5e119" + "versions.yml:md5,81a0b49f3a9e1315fe564f9946eb8c50" ], "html": [ @@ -69,7 +69,7 @@ ], "versions": [ - "versions.yml:md5,0376fafd6096035de5c7ca6cb4e5e119" + "versions.yml:md5,81a0b49f3a9e1315fe564f9946eb8c50" ], "zip": [ @@ -80,7 +80,7 @@ "nf-test": "0.9.0", "nextflow": "24.04.4" }, - "timestamp": "2024-10-18T12:50:51.25902234" + "timestamp": "2024-10-22T19:23:28.617831159" }, "test_trimgalore_paired_end - stub": { "content": [ @@ -119,7 +119,7 @@ ], "5": [ - "versions.yml:md5,0376fafd6096035de5c7ca6cb4e5e119" + "versions.yml:md5,81a0b49f3a9e1315fe564f9946eb8c50" ], "html": [ @@ -152,7 +152,7 @@ ], "versions": [ - "versions.yml:md5,0376fafd6096035de5c7ca6cb4e5e119" + "versions.yml:md5,81a0b49f3a9e1315fe564f9946eb8c50" ], "zip": [ @@ -163,18 +163,18 @@ "nf-test": "0.9.0", "nextflow": "24.04.4" }, - "timestamp": "2024-10-18T12:51:19.024228479" + "timestamp": "2024-10-22T19:23:51.539787731" }, "test_trimgalore_paired_end": { "content": [ [ - "versions.yml:md5,0376fafd6096035de5c7ca6cb4e5e119" + "versions.yml:md5,81a0b49f3a9e1315fe564f9946eb8c50" ] ], "meta": { "nf-test": "0.9.0", "nextflow": "24.04.4" }, - "timestamp": "2024-10-18T12:51:02.471703095" + "timestamp": "2024-10-22T19:23:41.16485915" } } \ No newline at end of file From 6de1c1b999313cb9ffe98844d22712466e807b9d Mon Sep 17 00:00:00 2001 From: Sateesh Date: Fri, 25 Oct 2024 14:52:44 +0000 Subject: [PATCH 05/13] minor fixes from vscode nextflow extension --- modules.json | 8 ++++---- subworkflows/local/bwameth/main.nf | 2 +- 2 files changed, 5 insertions(+), 5 deletions(-) diff --git a/modules.json b/modules.json index 53e3c295..0174a44b 100644 --- a/modules.json +++ b/modules.json @@ -7,7 +7,7 @@ "nf-core": { "bismark/align": { "branch": "master", - "git_sha": "9c4438173b1fcbf3f9004080e3af74af19d5f56e", + "git_sha": "dfd89399e3c6e2422c4cdcf0aaa8cf2393dc51c9", "installed_by": ["modules"] }, "bismark/coverage2cytosine": { @@ -37,12 +37,12 @@ }, "bismark/summary": { "branch": "master", - "git_sha": "0755c617637d21b2c290b26d225debe3070aa109", + "git_sha": "dfd89399e3c6e2422c4cdcf0aaa8cf2393dc51c9", "installed_by": ["modules"] }, "bwameth/align": { "branch": "master", - "git_sha": "9c4438173b1fcbf3f9004080e3af74af19d5f56e", + "git_sha": "dfd89399e3c6e2422c4cdcf0aaa8cf2393dc51c9", "installed_by": ["modules"] }, "bwameth/index": { @@ -127,7 +127,7 @@ }, "trimgalore": { "branch": "master", - "git_sha": "49f4e50534fe4b64101e62ea41d5dc43b1324358", + "git_sha": "8c5eeedd45e295fc9a4f164631da6a8b37e6b9c6", "installed_by": ["modules"] }, "untar": { diff --git a/subworkflows/local/bwameth/main.nf b/subworkflows/local/bwameth/main.nf index 11c60eae..04608995 100644 --- a/subworkflows/local/bwameth/main.nf +++ b/subworkflows/local/bwameth/main.nf @@ -80,7 +80,7 @@ workflow BWAMETH { PICARD_MARKDUPLICATES ( SAMTOOLS_SORT.out.bam, fasta, - fasta_index.map{ fasta_index -> [[:], fasta_index]}, + fasta_index.map{ index -> [[:], index]}, ) PICARD_MARKDUPLICATES.out.bam.dump(tag: 'BWAMETH/PICARD_MARKDUPLICATES: bam') /* From 6cdbb40f59cd66e720b6adef92c42bfd4778efca Mon Sep 17 00:00:00 2001 From: Sateesh Date: Fri, 25 Oct 2024 14:53:45 +0000 Subject: [PATCH 06/13] update modules with bismark, bwameth symlink fix --- modules/nf-core/bismark/align/tests/nextflow.config | 8 ++++++++ 1 file changed, 8 insertions(+) create mode 100644 modules/nf-core/bismark/align/tests/nextflow.config diff --git a/modules/nf-core/bismark/align/tests/nextflow.config b/modules/nf-core/bismark/align/tests/nextflow.config new file mode 100644 index 00000000..3313dfa8 --- /dev/null +++ b/modules/nf-core/bismark/align/tests/nextflow.config @@ -0,0 +1,8 @@ +process { + withName: BISMARK_ALIGN { + ext.args = params.bismark_args + } + withName: BISMARK_GENOMEPREPARATION { + ext.args = params.bismark_args + } +} From 2741d6c8ebb33f23c9f8eb07c3d1d17291ae27c9 Mon Sep 17 00:00:00 2001 From: Sateesh Date: Fri, 25 Oct 2024 14:54:12 +0000 Subject: [PATCH 07/13] update snaps after module updates --- tests/bismark_emseq_clip_r1.nf.test.snap | 12 +++--- tests/bismark_hisat.nf.test.snap | 12 +++--- tests/bismark_hisat_rrbs.nf.test.snap | 12 +++--- ...eference_save_align_intermeds.nf.test.snap | 12 +++--- tests/bismark_nomeseq.nf.test.snap | 38 +++---------------- tests/bismark_rrbs.nf.test.snap | 12 +++--- ...eference_save_align_intermeds.nf.test.snap | 12 +++--- tests/bismark_skip_deduplication.nf.test.snap | 12 +++--- tests/bismark_skip_multiqc.nf.test.snap | 12 +++--- tests/bismark_skip_trimming.nf.test.snap | 2 +- tests/bwameth.nf.test.snap | 12 +++--- tests/bwameth_rrbs.nf.test.snap | 14 +++---- ...eference_save_align_intermeds.nf.test.snap | 12 +++--- tests/bwameth_skip_deduplication.nf.test.snap | 14 +++---- tests/bwameth_skip_trimming.nf.test.snap | 2 +- tests/default.nf.test.snap | 12 +++--- 16 files changed, 88 insertions(+), 114 deletions(-) diff --git a/tests/bismark_emseq_clip_r1.nf.test.snap b/tests/bismark_emseq_clip_r1.nf.test.snap index a4ce459c..2cff8aea 100644 --- a/tests/bismark_emseq_clip_r1.nf.test.snap +++ b/tests/bismark_emseq_clip_r1.nf.test.snap @@ -17,10 +17,10 @@ }, "TRIMGALORE": { "trimgalore": "0.6.10", - "cutadapt": 4.2 + "cutadapt": 4.9 }, "Workflow": { - "nf-core/methylseq": "v2.8.0dev" + "nf-core/methylseq": "v2.7.1" } }, [ @@ -541,7 +541,7 @@ "multiqc_bismark_dedup.txt:md5,16e464f5bf2f1851a571ec87cbc1a0d9", "multiqc_bismark_methextract.txt:md5,ef3c68247a6254ae5e11e26052e3229e", "multiqc_citations.txt:md5,b9d42869faad581bd963d3d3bb490026", - "multiqc_cutadapt.txt:md5,f7a61369244b1e040d264e6913b8a839", + "multiqc_cutadapt.txt:md5,883891ac4901385102be053212068732", "qualimap_coverage_histogram.txt:md5,7d321d1eb204be4c3661364cf928c3e3", "qualimap_gc_content.txt:md5,d914dc3ae413deb1db307910d9907ea9", "qualimap_genome_fraction.txt:md5,2f6d7ae8cfdafc69358ce6a6800bef54", @@ -571,9 +571,9 @@ ] ], "meta": { - "nf-test": "0.9.0", + "nf-test": "0.9.1", "nextflow": "24.04.4" }, - "timestamp": "2024-10-21T17:43:14.505236122" + "timestamp": "2024-10-25T14:26:16.42655233" } -} +} \ No newline at end of file diff --git a/tests/bismark_hisat.nf.test.snap b/tests/bismark_hisat.nf.test.snap index 4e24adb7..7672c433 100644 --- a/tests/bismark_hisat.nf.test.snap +++ b/tests/bismark_hisat.nf.test.snap @@ -27,10 +27,10 @@ }, "TRIMGALORE": { "trimgalore": "0.6.10", - "cutadapt": 4.2 + "cutadapt": 4.9 }, "Workflow": { - "nf-core/methylseq": "v2.8.0dev" + "nf-core/methylseq": "v2.7.1" } }, [ @@ -553,7 +553,7 @@ "multiqc_bismark_dedup.txt:md5,5e58032548eda3c39384495cf0cfaa3d", "multiqc_bismark_methextract.txt:md5,5ce6739f6daa34276200f303c240e4b1", "multiqc_citations.txt:md5,b9d42869faad581bd963d3d3bb490026", - "multiqc_cutadapt.txt:md5,f7a61369244b1e040d264e6913b8a839", + "multiqc_cutadapt.txt:md5,883891ac4901385102be053212068732", "qualimap_coverage_histogram.txt:md5,b78964924f4985d97f6dff7ced688d29", "qualimap_gc_content.txt:md5,ad345dd40fe367f2138776c8ea2b257f", "qualimap_genome_fraction.txt:md5,9a1c3d3f7349cf1c2af1c5878dac4185", @@ -583,9 +583,9 @@ ] ], "meta": { - "nf-test": "0.9.0", + "nf-test": "0.9.1", "nextflow": "24.04.4" }, - "timestamp": "2024-10-21T17:44:48.196812536" + "timestamp": "2024-10-25T14:27:35.247058389" } -} +} \ No newline at end of file diff --git a/tests/bismark_hisat_rrbs.nf.test.snap b/tests/bismark_hisat_rrbs.nf.test.snap index 8b7edc34..7f48a90d 100644 --- a/tests/bismark_hisat_rrbs.nf.test.snap +++ b/tests/bismark_hisat_rrbs.nf.test.snap @@ -17,10 +17,10 @@ }, "TRIMGALORE": { "trimgalore": "0.6.10", - "cutadapt": 4.2 + "cutadapt": 4.9 }, "Workflow": { - "nf-core/methylseq": "v2.8.0dev" + "nf-core/methylseq": "v2.7.1" } }, [ @@ -530,7 +530,7 @@ "multiqc_bismark_alignment.txt:md5,75a6ccfb5b5bff3a5b3d3e2174929fc3", "multiqc_bismark_methextract.txt:md5,d1312f03f47d7cc07ac18254cda720bd", "multiqc_citations.txt:md5,b9d42869faad581bd963d3d3bb490026", - "multiqc_cutadapt.txt:md5,b376b3816764859cfc345bf13cda536f", + "multiqc_cutadapt.txt:md5,8752cce2e7320f49516e897c60487831", "qualimap_coverage_histogram.txt:md5,938111519a9ad1b2580f8f944fb659aa", "qualimap_gc_content.txt:md5,3263a2edb88dcbddf5654df1b233f66d", "qualimap_genome_fraction.txt:md5,5490f57857141d3e31a1f978bf1f7ead", @@ -576,9 +576,9 @@ ] ], "meta": { - "nf-test": "0.9.0", + "nf-test": "0.9.1", "nextflow": "24.04.4" }, - "timestamp": "2024-10-21T17:48:05.852952347" + "timestamp": "2024-10-25T14:30:16.774897867" } -} +} \ No newline at end of file diff --git a/tests/bismark_hisat_save_reference_save_align_intermeds.nf.test.snap b/tests/bismark_hisat_save_reference_save_align_intermeds.nf.test.snap index 22c75d3f..ce353067 100644 --- a/tests/bismark_hisat_save_reference_save_align_intermeds.nf.test.snap +++ b/tests/bismark_hisat_save_reference_save_align_intermeds.nf.test.snap @@ -17,10 +17,10 @@ }, "TRIMGALORE": { "trimgalore": "0.6.10", - "cutadapt": 4.2 + "cutadapt": 4.9 }, "Workflow": { - "nf-core/methylseq": "v2.8.0dev" + "nf-core/methylseq": "v2.7.1" } }, [ @@ -592,7 +592,7 @@ "multiqc_bismark_dedup.txt:md5,5e58032548eda3c39384495cf0cfaa3d", "multiqc_bismark_methextract.txt:md5,5ce6739f6daa34276200f303c240e4b1", "multiqc_citations.txt:md5,b9d42869faad581bd963d3d3bb490026", - "multiqc_cutadapt.txt:md5,f7a61369244b1e040d264e6913b8a839", + "multiqc_cutadapt.txt:md5,883891ac4901385102be053212068732", "qualimap_coverage_histogram.txt:md5,b78964924f4985d97f6dff7ced688d29", "qualimap_gc_content.txt:md5,ad345dd40fe367f2138776c8ea2b257f", "qualimap_genome_fraction.txt:md5,9a1c3d3f7349cf1c2af1c5878dac4185", @@ -654,9 +654,9 @@ ] ], "meta": { - "nf-test": "0.9.0", + "nf-test": "0.9.1", "nextflow": "24.04.4" }, - "timestamp": "2024-10-21T17:49:33.437253199" + "timestamp": "2024-10-25T14:31:35.562277469" } -} +} \ No newline at end of file diff --git a/tests/bismark_nomeseq.nf.test.snap b/tests/bismark_nomeseq.nf.test.snap index e644ef56..329bcb47 100644 --- a/tests/bismark_nomeseq.nf.test.snap +++ b/tests/bismark_nomeseq.nf.test.snap @@ -17,10 +17,10 @@ }, "TRIMGALORE": { "trimgalore": "0.6.10", - "cutadapt": 4.2 + "cutadapt": 4.9 }, "Workflow": { - "nf-core/methylseq": "v2.8.0dev" + "nf-core/methylseq": "v2.7.1" } }, [ @@ -41,20 +41,6 @@ "bismark/coverage2cytosine/coverage/SRR389222_sub2.NOMe.GpC.cov.gz", "bismark/coverage2cytosine/coverage/SRR389222_sub3.NOMe.CpG.cov.gz", "bismark/coverage2cytosine/coverage/SRR389222_sub3.NOMe.GpC.cov.gz", - "bismark/coverage2cytosine/reports", - "bismark/coverage2cytosine/reports/Ecoli_10K_methylated.NOMe.CpG_report.txt.gz", - "bismark/coverage2cytosine/reports/Ecoli_10K_methylated.NOMe.GpC_report.txt.gz", - "bismark/coverage2cytosine/reports/SRR389222_sub1.NOMe.CpG_report.txt.gz", - "bismark/coverage2cytosine/reports/SRR389222_sub1.NOMe.GpC_report.txt.gz", - "bismark/coverage2cytosine/reports/SRR389222_sub2.NOMe.CpG_report.txt.gz", - "bismark/coverage2cytosine/reports/SRR389222_sub2.NOMe.GpC_report.txt.gz", - "bismark/coverage2cytosine/reports/SRR389222_sub3.NOMe.CpG_report.txt.gz", - "bismark/coverage2cytosine/reports/SRR389222_sub3.NOMe.GpC_report.txt.gz", - "bismark/coverage2cytosine/summaries", - "bismark/coverage2cytosine/summaries/Ecoli_10K_methylated.cytosine_context_summary.txt", - "bismark/coverage2cytosine/summaries/SRR389222_sub1.cytosine_context_summary.txt", - "bismark/coverage2cytosine/summaries/SRR389222_sub2.cytosine_context_summary.txt", - "bismark/coverage2cytosine/summaries/SRR389222_sub3.cytosine_context_summary.txt", "bismark/deduplicated", "bismark/deduplicated/Ecoli_10K_methylated.deduplicated.sorted.bam", "bismark/deduplicated/Ecoli_10K_methylated.deduplicated.sorted.bam.bai", @@ -507,18 +493,6 @@ "SRR389222_sub2.NOMe.GpC.cov.gz:md5,10837f6099f63dc4aae2895d821a582e", "SRR389222_sub3.NOMe.CpG.cov.gz:md5,85098361910f7398528dcbb0e46a7561", "SRR389222_sub3.NOMe.GpC.cov.gz:md5,8005a9dad4d0f5562a3c7cf215a18908", - "Ecoli_10K_methylated.NOMe.CpG_report.txt.gz:md5,f766e73a44789a40dffce322ec599007", - "Ecoli_10K_methylated.NOMe.GpC_report.txt.gz:md5,a8126d4d596cfb6e696cdb808451840c", - "SRR389222_sub1.NOMe.CpG_report.txt.gz:md5,731e940264ca803ca48842a1fc9402ad", - "SRR389222_sub1.NOMe.GpC_report.txt.gz:md5,96c3f1c2f3d334baafb55f0805eaf52c", - "SRR389222_sub2.NOMe.CpG_report.txt.gz:md5,2ec3a32d0e8239ba50c079e1519aaf00", - "SRR389222_sub2.NOMe.GpC_report.txt.gz:md5,bcde6f7e90831604368ae6430e5695f0", - "SRR389222_sub3.NOMe.CpG_report.txt.gz:md5,f9793efc46ecdf413a84338e9f9f42dd", - "SRR389222_sub3.NOMe.GpC_report.txt.gz:md5,e4ab9e9c4d4ea2fe3ca2378f3802f6f6", - "Ecoli_10K_methylated.cytosine_context_summary.txt:md5,482eac2bc68ca28545bab71c0c414c3a", - "SRR389222_sub1.cytosine_context_summary.txt:md5,1d4c33ccf5e249907ca2ba50a37c7697", - "SRR389222_sub2.cytosine_context_summary.txt:md5,8f7684582aa75b24197866138e6d1a4c", - "SRR389222_sub3.cytosine_context_summary.txt:md5,7ba71718c6556e8b3019e1704948d562", "Ecoli_10K_methylated_1_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz:md5,88e599178b08907aab7d248302b7d37e", "SRR389222_sub1_trimmed_bismark_bt2.deduplicated.bedGraph.gz:md5,ccf9537924fa4aa1db2f4462d2b9bc8e", "SRR389222_sub2_trimmed_bismark_bt2.deduplicated.bedGraph.gz:md5,c352886f5d59592bc679843548ca5eef", @@ -587,7 +561,7 @@ "multiqc_bismark_dedup.txt:md5,d09a5de4d81a3207efb6a8937d060e46", "multiqc_bismark_methextract.txt:md5,825f57cdf45203406e583beb495afccc", "multiqc_citations.txt:md5,b9d42869faad581bd963d3d3bb490026", - "multiqc_cutadapt.txt:md5,f7a61369244b1e040d264e6913b8a839", + "multiqc_cutadapt.txt:md5,883891ac4901385102be053212068732", "qualimap_coverage_histogram.txt:md5,7cd194077fe839edf034b44cc73dd024", "qualimap_gc_content.txt:md5,4f6ec70d9fb71ffe5f2f99f44fe5ef0c", "qualimap_genome_fraction.txt:md5,3e528946a376ae752b57adaaa73f5cdf", @@ -617,9 +591,9 @@ ] ], "meta": { - "nf-test": "0.9.0", + "nf-test": "0.9.1", "nextflow": "24.04.4" }, - "timestamp": "2024-10-21T17:50:56.499718354" + "timestamp": "2024-10-25T14:33:03.212223004" } -} +} \ No newline at end of file diff --git a/tests/bismark_rrbs.nf.test.snap b/tests/bismark_rrbs.nf.test.snap index 1af56bf7..61dc63a1 100644 --- a/tests/bismark_rrbs.nf.test.snap +++ b/tests/bismark_rrbs.nf.test.snap @@ -17,10 +17,10 @@ }, "TRIMGALORE": { "trimgalore": "0.6.10", - "cutadapt": 4.2 + "cutadapt": 4.9 }, "Workflow": { - "nf-core/methylseq": "v2.8.0dev" + "nf-core/methylseq": "v2.7.1" } }, [ @@ -530,7 +530,7 @@ "multiqc_bismark_alignment.txt:md5,f9f3e888d5176131440f6a8a6d1abccc", "multiqc_bismark_methextract.txt:md5,1a2967a22fa1522f9e8d672fc43ca78d", "multiqc_citations.txt:md5,b9d42869faad581bd963d3d3bb490026", - "multiqc_cutadapt.txt:md5,b376b3816764859cfc345bf13cda536f", + "multiqc_cutadapt.txt:md5,8752cce2e7320f49516e897c60487831", "qualimap_coverage_histogram.txt:md5,22c70e761489597e34a3d71d036ff190", "qualimap_gc_content.txt:md5,c872803a08b92b36c136e2ba3bee96d4", "qualimap_genome_fraction.txt:md5,393f86423cc89983ab66fa29f93dd710", @@ -576,9 +576,9 @@ ] ], "meta": { - "nf-test": "0.9.0", + "nf-test": "0.9.1", "nextflow": "24.04.4" }, - "timestamp": "2024-10-21T17:52:32.475797707" + "timestamp": "2024-10-25T14:34:25.708997835" } -} +} \ No newline at end of file diff --git a/tests/bismark_save_reference_save_align_intermeds.nf.test.snap b/tests/bismark_save_reference_save_align_intermeds.nf.test.snap index 1bfad2d9..2f145429 100644 --- a/tests/bismark_save_reference_save_align_intermeds.nf.test.snap +++ b/tests/bismark_save_reference_save_align_intermeds.nf.test.snap @@ -17,10 +17,10 @@ }, "TRIMGALORE": { "trimgalore": "0.6.10", - "cutadapt": 4.2 + "cutadapt": 4.9 }, "Workflow": { - "nf-core/methylseq": "v2.8.0dev" + "nf-core/methylseq": "v2.7.1" } }, [ @@ -584,7 +584,7 @@ "multiqc_bismark_dedup.txt:md5,d09a5de4d81a3207efb6a8937d060e46", "multiqc_bismark_methextract.txt:md5,825f57cdf45203406e583beb495afccc", "multiqc_citations.txt:md5,b9d42869faad581bd963d3d3bb490026", - "multiqc_cutadapt.txt:md5,f7a61369244b1e040d264e6913b8a839", + "multiqc_cutadapt.txt:md5,883891ac4901385102be053212068732", "qualimap_coverage_histogram.txt:md5,7cd194077fe839edf034b44cc73dd024", "qualimap_gc_content.txt:md5,4f6ec70d9fb71ffe5f2f99f44fe5ef0c", "qualimap_genome_fraction.txt:md5,3e528946a376ae752b57adaaa73f5cdf", @@ -646,9 +646,9 @@ ] ], "meta": { - "nf-test": "0.9.0", + "nf-test": "0.9.1", "nextflow": "24.04.4" }, - "timestamp": "2024-10-21T18:10:42.065837136" + "timestamp": "2024-10-25T14:35:51.348052183" } -} +} \ No newline at end of file diff --git a/tests/bismark_skip_deduplication.nf.test.snap b/tests/bismark_skip_deduplication.nf.test.snap index 5edc5c6a..6f4ff1ed 100644 --- a/tests/bismark_skip_deduplication.nf.test.snap +++ b/tests/bismark_skip_deduplication.nf.test.snap @@ -17,10 +17,10 @@ }, "TRIMGALORE": { "trimgalore": "0.6.10", - "cutadapt": 4.2 + "cutadapt": 4.9 }, "Workflow": { - "nf-core/methylseq": "v2.8.0dev" + "nf-core/methylseq": "v2.7.1" } }, [ @@ -532,7 +532,7 @@ "multiqc_bismark_alignment.txt:md5,40ab86041f508d3f1a63bde20cab5440", "multiqc_bismark_methextract.txt:md5,374ad746b0cfa5143fc3606f77f53283", "multiqc_citations.txt:md5,b9d42869faad581bd963d3d3bb490026", - "multiqc_cutadapt.txt:md5,f7a61369244b1e040d264e6913b8a839", + "multiqc_cutadapt.txt:md5,883891ac4901385102be053212068732", "qualimap_coverage_histogram.txt:md5,dfd099755c43854826eb71acca153a33", "qualimap_gc_content.txt:md5,55baed387d09b5a0583ce2b5abfc0d12", "qualimap_genome_fraction.txt:md5,bde4b1a12ad8ad0420b44fa3f1ed0512", @@ -578,9 +578,9 @@ ] ], "meta": { - "nf-test": "0.9.0", + "nf-test": "0.9.1", "nextflow": "24.04.4" }, - "timestamp": "2024-10-21T17:54:28.816433456" + "timestamp": "2024-10-25T14:37:11.98959127" } -} +} \ No newline at end of file diff --git a/tests/bismark_skip_multiqc.nf.test.snap b/tests/bismark_skip_multiqc.nf.test.snap index 5ad46fb1..6f1e9301 100644 --- a/tests/bismark_skip_multiqc.nf.test.snap +++ b/tests/bismark_skip_multiqc.nf.test.snap @@ -17,10 +17,10 @@ }, "TRIMGALORE": { "trimgalore": "0.6.10", - "cutadapt": 4.2 + "cutadapt": 4.9 }, "Workflow": { - "nf-core/methylseq": "v2.8.0dev" + "nf-core/methylseq": "v2.7.1" } }, [ @@ -543,7 +543,7 @@ "multiqc_bismark_dedup.txt:md5,d09a5de4d81a3207efb6a8937d060e46", "multiqc_bismark_methextract.txt:md5,825f57cdf45203406e583beb495afccc", "multiqc_citations.txt:md5,b9d42869faad581bd963d3d3bb490026", - "multiqc_cutadapt.txt:md5,f7a61369244b1e040d264e6913b8a839", + "multiqc_cutadapt.txt:md5,883891ac4901385102be053212068732", "qualimap_coverage_histogram.txt:md5,7cd194077fe839edf034b44cc73dd024", "qualimap_gc_content.txt:md5,4f6ec70d9fb71ffe5f2f99f44fe5ef0c", "qualimap_genome_fraction.txt:md5,3e528946a376ae752b57adaaa73f5cdf", @@ -573,9 +573,9 @@ ] ], "meta": { - "nf-test": "0.9.0", + "nf-test": "0.9.1", "nextflow": "24.04.4" }, - "timestamp": "2024-10-21T17:55:48.550138313" + "timestamp": "2024-10-25T14:38:34.022258124" } -} +} \ No newline at end of file diff --git a/tests/bismark_skip_trimming.nf.test.snap b/tests/bismark_skip_trimming.nf.test.snap index 65b700f2..b0a9958c 100644 --- a/tests/bismark_skip_trimming.nf.test.snap +++ b/tests/bismark_skip_trimming.nf.test.snap @@ -16,7 +16,7 @@ "qualimap": 2.3 }, "Workflow": { - "nf-core/methylseq": "v2.8.0dev" + "nf-core/methylseq": "v2.7.1" } }, [ diff --git a/tests/bwameth.nf.test.snap b/tests/bwameth.nf.test.snap index edc9b679..5d804e01 100644 --- a/tests/bwameth.nf.test.snap +++ b/tests/bwameth.nf.test.snap @@ -17,10 +17,10 @@ }, "TRIMGALORE": { "trimgalore": "0.6.10", - "cutadapt": 4.2 + "cutadapt": 4.9 }, "Workflow": { - "nf-core/methylseq": "v2.8.0dev" + "nf-core/methylseq": "v2.7.1" } }, [ @@ -394,7 +394,7 @@ "fastqc_sequence_duplication_levels_plot.txt:md5,9e5712db9aa39b5754ea1e0c49cfff15", "fastqc_top_overrepresented_sequences_table.txt:md5,6dfc5334a09c05392ea17369aa742d01", "multiqc_citations.txt:md5,581df5b266851d0244e7cfb213351ffb", - "multiqc_cutadapt.txt:md5,f7a61369244b1e040d264e6913b8a839", + "multiqc_cutadapt.txt:md5,883891ac4901385102be053212068732", "multiqc_picard_dups.txt:md5,82eaab96189f22fd93db38bb516ba6a5", "multiqc_samtools_flagstat.txt:md5,a8f5b45b8b3412a9adc3dd0d35208c73", "multiqc_samtools_stats.txt:md5,e24271a8111b06c1f545b6b1a077a4a7", @@ -435,10 +435,10 @@ ] ], "meta": { - "nf-test": "0.9.0", + "nf-test": "0.9.1", "nextflow": "24.04.4" }, - "timestamp": "2024-10-21T17:58:28.435328799" + "timestamp": "2024-10-25T14:41:20.919214758" }, "Params: bwameth with bwameth-index": { "content": [ @@ -450,4 +450,4 @@ }, "timestamp": "2024-10-12T07:40:41.336750081" } -} +} \ No newline at end of file diff --git a/tests/bwameth_rrbs.nf.test.snap b/tests/bwameth_rrbs.nf.test.snap index 5dff4559..f2c5c583 100644 --- a/tests/bwameth_rrbs.nf.test.snap +++ b/tests/bwameth_rrbs.nf.test.snap @@ -17,10 +17,10 @@ }, "TRIMGALORE": { "trimgalore": "0.6.10", - "cutadapt": 4.2 + "cutadapt": 4.9 }, "Workflow": { - "nf-core/methylseq": "v2.8.0dev" + "nf-core/methylseq": "v2.7.1" } }, [ @@ -369,7 +369,7 @@ "fastqc_sequence_duplication_levels_plot.txt:md5,9e5712db9aa39b5754ea1e0c49cfff15", "fastqc_top_overrepresented_sequences_table.txt:md5,6dfc5334a09c05392ea17369aa742d01", "multiqc_citations.txt:md5,581df5b266851d0244e7cfb213351ffb", - "multiqc_cutadapt.txt:md5,b376b3816764859cfc345bf13cda536f", + "multiqc_cutadapt.txt:md5,8752cce2e7320f49516e897c60487831", "multiqc_samtools_flagstat.txt:md5,4389e377eb1db8dde26b0e8db6589c2d", "multiqc_samtools_stats.txt:md5,3843eed6fb6ec8d27729a8b901ada0cf", "qualimap_coverage_histogram.txt:md5,c5354816b9ce0a18d633506e2dd4e4ac", @@ -386,13 +386,13 @@ "genome_results.txt:md5,58d212848ac7b7650e3bd6812a4064af" ], [ - + ] ], "meta": { - "nf-test": "0.9.0", + "nf-test": "0.9.1", "nextflow": "24.04.4" }, - "timestamp": "2024-10-21T18:00:44.344954074" + "timestamp": "2024-10-25T14:43:36.391049268" } -} +} \ No newline at end of file diff --git a/tests/bwameth_save_reference_save_align_intermeds.nf.test.snap b/tests/bwameth_save_reference_save_align_intermeds.nf.test.snap index 672786fb..19d1a27e 100644 --- a/tests/bwameth_save_reference_save_align_intermeds.nf.test.snap +++ b/tests/bwameth_save_reference_save_align_intermeds.nf.test.snap @@ -17,10 +17,10 @@ }, "TRIMGALORE": { "trimgalore": "0.6.10", - "cutadapt": 4.2 + "cutadapt": 4.9 }, "Workflow": { - "nf-core/methylseq": "v2.8.0dev" + "nf-core/methylseq": "v2.7.1" } }, [ @@ -420,7 +420,7 @@ "fastqc_sequence_duplication_levels_plot.txt:md5,9e5712db9aa39b5754ea1e0c49cfff15", "fastqc_top_overrepresented_sequences_table.txt:md5,6dfc5334a09c05392ea17369aa742d01", "multiqc_citations.txt:md5,581df5b266851d0244e7cfb213351ffb", - "multiqc_cutadapt.txt:md5,f7a61369244b1e040d264e6913b8a839", + "multiqc_cutadapt.txt:md5,883891ac4901385102be053212068732", "multiqc_picard_dups.txt:md5,82eaab96189f22fd93db38bb516ba6a5", "multiqc_samtools_flagstat.txt:md5,a8f5b45b8b3412a9adc3dd0d35208c73", "multiqc_samtools_stats.txt:md5,e24271a8111b06c1f545b6b1a077a4a7", @@ -493,9 +493,9 @@ ] ], "meta": { - "nf-test": "0.9.0", + "nf-test": "0.9.1", "nextflow": "24.04.4" }, - "timestamp": "2024-10-21T18:01:53.259560408" + "timestamp": "2024-10-25T14:44:54.756005023" } -} +} \ No newline at end of file diff --git a/tests/bwameth_skip_deduplication.nf.test.snap b/tests/bwameth_skip_deduplication.nf.test.snap index d113ef44..a646e5d7 100644 --- a/tests/bwameth_skip_deduplication.nf.test.snap +++ b/tests/bwameth_skip_deduplication.nf.test.snap @@ -17,10 +17,10 @@ }, "TRIMGALORE": { "trimgalore": "0.6.10", - "cutadapt": 4.2 + "cutadapt": 4.9 }, "Workflow": { - "nf-core/methylseq": "v2.8.0dev" + "nf-core/methylseq": "v2.7.1" } }, [ @@ -369,7 +369,7 @@ "fastqc_sequence_duplication_levels_plot.txt:md5,9e5712db9aa39b5754ea1e0c49cfff15", "fastqc_top_overrepresented_sequences_table.txt:md5,6dfc5334a09c05392ea17369aa742d01", "multiqc_citations.txt:md5,581df5b266851d0244e7cfb213351ffb", - "multiqc_cutadapt.txt:md5,f7a61369244b1e040d264e6913b8a839", + "multiqc_cutadapt.txt:md5,883891ac4901385102be053212068732", "multiqc_samtools_flagstat.txt:md5,a8f5b45b8b3412a9adc3dd0d35208c73", "multiqc_samtools_stats.txt:md5,e24271a8111b06c1f545b6b1a077a4a7", "qualimap_coverage_histogram.txt:md5,c7c932e4d84b735bd434c1aaa713b6e6", @@ -386,13 +386,13 @@ "genome_results.txt:md5,478f711b8ef22e094e4d0ff7fa0dfda0" ], [ - + ] ], "meta": { - "nf-test": "0.9.0", + "nf-test": "0.9.1", "nextflow": "24.04.4" }, - "timestamp": "2024-10-21T18:02:51.160774031" + "timestamp": "2024-10-25T14:46:02.99245907" } -} +} \ No newline at end of file diff --git a/tests/bwameth_skip_trimming.nf.test.snap b/tests/bwameth_skip_trimming.nf.test.snap index 5aeed3ce..8e890b74 100644 --- a/tests/bwameth_skip_trimming.nf.test.snap +++ b/tests/bwameth_skip_trimming.nf.test.snap @@ -16,7 +16,7 @@ "qualimap": 2.3 }, "Workflow": { - "nf-core/methylseq": "v2.8.0dev" + "nf-core/methylseq": "v2.7.1" } }, [ diff --git a/tests/default.nf.test.snap b/tests/default.nf.test.snap index e3241084..f38b3782 100644 --- a/tests/default.nf.test.snap +++ b/tests/default.nf.test.snap @@ -27,10 +27,10 @@ }, "TRIMGALORE": { "trimgalore": "0.6.10", - "cutadapt": 4.2 + "cutadapt": 4.9 }, "Workflow": { - "nf-core/methylseq": "v2.8.0dev" + "nf-core/methylseq": "v2.7.1" } }, [ @@ -553,7 +553,7 @@ "multiqc_bismark_dedup.txt:md5,d09a5de4d81a3207efb6a8937d060e46", "multiqc_bismark_methextract.txt:md5,825f57cdf45203406e583beb495afccc", "multiqc_citations.txt:md5,b9d42869faad581bd963d3d3bb490026", - "multiqc_cutadapt.txt:md5,f7a61369244b1e040d264e6913b8a839", + "multiqc_cutadapt.txt:md5,883891ac4901385102be053212068732", "qualimap_coverage_histogram.txt:md5,7cd194077fe839edf034b44cc73dd024", "qualimap_gc_content.txt:md5,4f6ec70d9fb71ffe5f2f99f44fe5ef0c", "qualimap_genome_fraction.txt:md5,3e528946a376ae752b57adaaa73f5cdf", @@ -583,9 +583,9 @@ ] ], "meta": { - "nf-test": "0.9.0", + "nf-test": "0.9.1", "nextflow": "24.04.4" }, - "timestamp": "2024-10-21T18:05:06.16706255" + "timestamp": "2024-10-25T14:48:27.537789856" } -} +} \ No newline at end of file From 4cdb8b57cd8fc0aabde121a35a7425eb8e92e752 Mon Sep 17 00:00:00 2001 From: Sateesh Date: Fri, 25 Oct 2024 14:54:41 +0000 Subject: [PATCH 08/13] update nf-test 0.9.1 --- .github/workflows/ci.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml index 468812a9..21409c6c 100644 --- a/.github/workflows/ci.yml +++ b/.github/workflows/ci.yml @@ -11,7 +11,7 @@ on: env: NXF_ANSI_LOG: false - NFT_VER: "0.9.0" + NFT_VER: "0.9.1" NFT_WORKDIR: "~" NFT_DIFF: "pdiff" NFT_DIFF_ARGS: "--line-numbers --width 120 --expand-tabs=2" From 3ee6d0d13877ced7e85e3d95a00e7df9f9520292 Mon Sep 17 00:00:00 2001 From: Sateesh Date: Fri, 25 Oct 2024 14:55:57 +0000 Subject: [PATCH 09/13] release version bump 2.7.1 --- .nf-core.yml | 2 +- assets/multiqc_config.yml | 4 ++-- nextflow.config | 2 +- 3 files changed, 4 insertions(+), 4 deletions(-) diff --git a/.nf-core.yml b/.nf-core.yml index 3cd4bf46..b7f57a7a 100644 --- a/.nf-core.yml +++ b/.nf-core.yml @@ -17,5 +17,5 @@ template: org: nf-core outdir: . skip_features: - version: 2.8.0dev + version: 2.7.1 update: diff --git a/assets/multiqc_config.yml b/assets/multiqc_config.yml index 0639e2fa..f9552e53 100644 --- a/assets/multiqc_config.yml +++ b/assets/multiqc_config.yml @@ -1,7 +1,7 @@ report_comment: > - This report has been generated by the nf-core/methylseq analysis pipeline. For information about how - to interpret these results, please see the documentation. report_section_order: "nf-core-methylseq-methods-description": diff --git a/nextflow.config b/nextflow.config index 4cf66cba..4821c55b 100644 --- a/nextflow.config +++ b/nextflow.config @@ -289,7 +289,7 @@ manifest { description = """Methylation (Bisulfite-Sequencing) Best Practice analysis pipeline, part of the nf-core community.""" mainScript = 'main.nf' nextflowVersion = '!>=24.04.2' - version = '2.8.0dev' + version = '2.7.1' doi = '10.5281/zenodo.1343417' } From 6847d5e461ed000c5add8a83bfda21db70957829 Mon Sep 17 00:00:00 2001 From: Sateesh Date: Fri, 25 Oct 2024 15:00:47 +0000 Subject: [PATCH 10/13] update changelog --- CHANGELOG.md | 5 ++++- 1 file changed, 4 insertions(+), 1 deletion(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index 6de89b31..43c51c94 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -1,9 +1,12 @@ # nf-core/methylseq -## [v2.8.0](https://github.com/nf-core/methylseq/releases/tag/2.8.0) - [] +## [v2.7.1](https://github.com/nf-core/methylseq/releases/tag/2.7.1) - [2024-10-27] ### Bug fixes & refactoring +- 🐛 fix fasta symlink in bismark & bwameth align modules [#448](https://github.com/nf-core/methylseq/pull/448) +- 🐛 apply few new vscode nextflow extension [#448](https://github.com/nf-core/methylseq/pull/448) + ### Pipeline Updates ## [v2.7.0](https://github.com/nf-core/methylseq/releases/tag/2.7.0) - [2024-10-25] From 9c2a4820a15df1af14c0a484d8a812f437b6b9be Mon Sep 17 00:00:00 2001 From: Sateesh Date: Fri, 25 Oct 2024 16:38:56 +0000 Subject: [PATCH 11/13] fix back publish of coveragetocytosine module --- .../bismark/coverage2cytosine/nextflow.config | 6 ++-- tests/bismark_nomeseq.nf.test.snap | 28 ++++++++++++++++++- 2 files changed, 31 insertions(+), 3 deletions(-) diff --git a/modules/nf-core/bismark/coverage2cytosine/nextflow.config b/modules/nf-core/bismark/coverage2cytosine/nextflow.config index f593a1d1..dc39a610 100644 --- a/modules/nf-core/bismark/coverage2cytosine/nextflow.config +++ b/modules/nf-core/bismark/coverage2cytosine/nextflow.config @@ -1,20 +1,22 @@ process { withName: BISMARK_COVERAGE2CYTOSINE { ext.args = params.nomeseq ? '--nome-seq' : '' + publishDir = [ publishDir = [ path: { "${params.outdir}/bismark/coverage2cytosine/summaries" }, mode: params.publish_dir_mode, pattern: "*_summary.txt" - ] + ], publishDir = [ path: { "${params.outdir}/bismark/coverage2cytosine/reports" }, mode: params.publish_dir_mode, pattern: "*_report.txt.gz" - ] + ], publishDir = [ path: { "${params.outdir}/bismark/coverage2cytosine/coverage" }, mode: params.publish_dir_mode, pattern: "*cov.gz" ] + ] } } \ No newline at end of file diff --git a/tests/bismark_nomeseq.nf.test.snap b/tests/bismark_nomeseq.nf.test.snap index 329bcb47..1a0dfae7 100644 --- a/tests/bismark_nomeseq.nf.test.snap +++ b/tests/bismark_nomeseq.nf.test.snap @@ -41,6 +41,20 @@ "bismark/coverage2cytosine/coverage/SRR389222_sub2.NOMe.GpC.cov.gz", "bismark/coverage2cytosine/coverage/SRR389222_sub3.NOMe.CpG.cov.gz", "bismark/coverage2cytosine/coverage/SRR389222_sub3.NOMe.GpC.cov.gz", + "bismark/coverage2cytosine/reports", + "bismark/coverage2cytosine/reports/Ecoli_10K_methylated.NOMe.CpG_report.txt.gz", + "bismark/coverage2cytosine/reports/Ecoli_10K_methylated.NOMe.GpC_report.txt.gz", + "bismark/coverage2cytosine/reports/SRR389222_sub1.NOMe.CpG_report.txt.gz", + "bismark/coverage2cytosine/reports/SRR389222_sub1.NOMe.GpC_report.txt.gz", + "bismark/coverage2cytosine/reports/SRR389222_sub2.NOMe.CpG_report.txt.gz", + "bismark/coverage2cytosine/reports/SRR389222_sub2.NOMe.GpC_report.txt.gz", + "bismark/coverage2cytosine/reports/SRR389222_sub3.NOMe.CpG_report.txt.gz", + "bismark/coverage2cytosine/reports/SRR389222_sub3.NOMe.GpC_report.txt.gz", + "bismark/coverage2cytosine/summaries", + "bismark/coverage2cytosine/summaries/Ecoli_10K_methylated.cytosine_context_summary.txt", + "bismark/coverage2cytosine/summaries/SRR389222_sub1.cytosine_context_summary.txt", + "bismark/coverage2cytosine/summaries/SRR389222_sub2.cytosine_context_summary.txt", + "bismark/coverage2cytosine/summaries/SRR389222_sub3.cytosine_context_summary.txt", "bismark/deduplicated", "bismark/deduplicated/Ecoli_10K_methylated.deduplicated.sorted.bam", "bismark/deduplicated/Ecoli_10K_methylated.deduplicated.sorted.bam.bai", @@ -493,6 +507,18 @@ "SRR389222_sub2.NOMe.GpC.cov.gz:md5,10837f6099f63dc4aae2895d821a582e", "SRR389222_sub3.NOMe.CpG.cov.gz:md5,85098361910f7398528dcbb0e46a7561", "SRR389222_sub3.NOMe.GpC.cov.gz:md5,8005a9dad4d0f5562a3c7cf215a18908", + "Ecoli_10K_methylated.NOMe.CpG_report.txt.gz:md5,f766e73a44789a40dffce322ec599007", + "Ecoli_10K_methylated.NOMe.GpC_report.txt.gz:md5,a8126d4d596cfb6e696cdb808451840c", + "SRR389222_sub1.NOMe.CpG_report.txt.gz:md5,731e940264ca803ca48842a1fc9402ad", + "SRR389222_sub1.NOMe.GpC_report.txt.gz:md5,96c3f1c2f3d334baafb55f0805eaf52c", + "SRR389222_sub2.NOMe.CpG_report.txt.gz:md5,2ec3a32d0e8239ba50c079e1519aaf00", + "SRR389222_sub2.NOMe.GpC_report.txt.gz:md5,bcde6f7e90831604368ae6430e5695f0", + "SRR389222_sub3.NOMe.CpG_report.txt.gz:md5,f9793efc46ecdf413a84338e9f9f42dd", + "SRR389222_sub3.NOMe.GpC_report.txt.gz:md5,e4ab9e9c4d4ea2fe3ca2378f3802f6f6", + "Ecoli_10K_methylated.cytosine_context_summary.txt:md5,482eac2bc68ca28545bab71c0c414c3a", + "SRR389222_sub1.cytosine_context_summary.txt:md5,1d4c33ccf5e249907ca2ba50a37c7697", + "SRR389222_sub2.cytosine_context_summary.txt:md5,8f7684582aa75b24197866138e6d1a4c", + "SRR389222_sub3.cytosine_context_summary.txt:md5,7ba71718c6556e8b3019e1704948d562", "Ecoli_10K_methylated_1_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz:md5,88e599178b08907aab7d248302b7d37e", "SRR389222_sub1_trimmed_bismark_bt2.deduplicated.bedGraph.gz:md5,ccf9537924fa4aa1db2f4462d2b9bc8e", "SRR389222_sub2_trimmed_bismark_bt2.deduplicated.bedGraph.gz:md5,c352886f5d59592bc679843548ca5eef", @@ -594,6 +620,6 @@ "nf-test": "0.9.1", "nextflow": "24.04.4" }, - "timestamp": "2024-10-25T14:33:03.212223004" + "timestamp": "2024-10-25T16:37:19.615304198" } } \ No newline at end of file From a85eb4c0248bedfec201a6222eaf925ed8545039 Mon Sep 17 00:00:00 2001 From: Sateesh Date: Fri, 25 Oct 2024 16:47:46 +0000 Subject: [PATCH 12/13] fix coverage2cytosine publishDirs --- modules/nf-core/bismark/coverage2cytosine/nextflow.config | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/modules/nf-core/bismark/coverage2cytosine/nextflow.config b/modules/nf-core/bismark/coverage2cytosine/nextflow.config index dc39a610..f1a83fb7 100644 --- a/modules/nf-core/bismark/coverage2cytosine/nextflow.config +++ b/modules/nf-core/bismark/coverage2cytosine/nextflow.config @@ -2,17 +2,17 @@ process { withName: BISMARK_COVERAGE2CYTOSINE { ext.args = params.nomeseq ? '--nome-seq' : '' publishDir = [ - publishDir = [ + [ path: { "${params.outdir}/bismark/coverage2cytosine/summaries" }, mode: params.publish_dir_mode, pattern: "*_summary.txt" ], - publishDir = [ + [ path: { "${params.outdir}/bismark/coverage2cytosine/reports" }, mode: params.publish_dir_mode, pattern: "*_report.txt.gz" ], - publishDir = [ + [ path: { "${params.outdir}/bismark/coverage2cytosine/coverage" }, mode: params.publish_dir_mode, pattern: "*cov.gz" From 07ec67a404b97b89a856d6ef14d3755f574f368f Mon Sep 17 00:00:00 2001 From: Sateesh_Peri <33637490+sateeshperi@users.noreply.github.com> Date: Sun, 27 Oct 2024 13:12:34 +0530 Subject: [PATCH 13/13] Update CHANGELOG.md Co-authored-by: James A. Fellows Yates --- CHANGELOG.md | 1 - 1 file changed, 1 deletion(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index 43c51c94..437105c1 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -5,7 +5,6 @@ ### Bug fixes & refactoring - 🐛 fix fasta symlink in bismark & bwameth align modules [#448](https://github.com/nf-core/methylseq/pull/448) -- 🐛 apply few new vscode nextflow extension [#448](https://github.com/nf-core/methylseq/pull/448) ### Pipeline Updates