From c81f8d3f9b57b934444bacf60c7a1e606f1d0f68 Mon Sep 17 00:00:00 2001 From: atrigila <18577080+atrigila@users.noreply.github.com> Date: Mon, 4 Nov 2024 18:31:00 +0000 Subject: [PATCH 1/6] update modules --- modules.json | 4 ++-- modules/nf-core/cellranger/mkfastq/main.nf | 4 ++-- modules/nf-core/samshee/meta.yml | 18 +++++++++--------- 3 files changed, 13 insertions(+), 13 deletions(-) diff --git a/modules.json b/modules.json index 65ceb04c..49c2cb41 100644 --- a/modules.json +++ b/modules.json @@ -22,7 +22,7 @@ }, "cellranger/mkfastq": { "branch": "master", - "git_sha": "a90a8863a3408e15d5a339b06413e57cf9ca9860", + "git_sha": "f7d2d43086b48d3cedd9e2df52bf098ee5a50542", "installed_by": ["modules"] }, "checkqc": { @@ -67,7 +67,7 @@ }, "samshee": { "branch": "master", - "git_sha": "3c464e75051db485c1b37ab9f1ea2182fb3d3533", + "git_sha": "467c202a876d26af544fa8c4b22a050a535462a7", "installed_by": ["modules"] }, "seqtk/sample": { diff --git a/modules/nf-core/cellranger/mkfastq/main.nf b/modules/nf-core/cellranger/mkfastq/main.nf index 09480345..89a1a824 100644 --- a/modules/nf-core/cellranger/mkfastq/main.nf +++ b/modules/nf-core/cellranger/mkfastq/main.nf @@ -10,8 +10,8 @@ process CELLRANGER_MKFASTQ { output: tuple val(meta), path("*_outs/outs/fastq_path/**/*.fastq.gz") , emit: fastq tuple val(meta), path("*_outs/outs/fastq_path/Undetermined*.fastq.gz") , optional:true, emit: undetermined_fastq - tuple val(meta), path("*_outs/outs/fastq_path/Reports") , emit: reports - tuple val(meta), path("*_outs/outs/fastq_path/Stats") , emit: stats + tuple val(meta), path("*_outs/outs/fastq_path/Reports") , optional:true, emit: reports + tuple val(meta), path("*_outs/outs/fastq_path/Stats") , optional:true, emit: stats tuple val(meta), path("*_outs/outs/interop_path/*.bin") , emit: interop path "versions.yml" , emit: versions diff --git a/modules/nf-core/samshee/meta.yml b/modules/nf-core/samshee/meta.yml index 50789dfb..4ff2ab9f 100644 --- a/modules/nf-core/samshee/meta.yml +++ b/modules/nf-core/samshee/meta.yml @@ -29,18 +29,18 @@ input: output: - samplesheet: - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', lane:1 ] + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', lane:1 ] - "*_formatted.csv": - type: file - description: "illumina v2 samplesheet" + type: file + description: "illumina v2 samplesheet" - versions: - versions.yml: - type: file - description: File containing software version - pattern: "versions.yml" + type: file + description: File containing software version + pattern: "versions.yml" authors: - "@nschcolnicov" maintainers: From 19b36463faf2e6f64be3459c831d592a49cb22a5 Mon Sep 17 00:00:00 2001 From: atrigila <18577080+atrigila@users.noreply.github.com> Date: Mon, 4 Nov 2024 18:31:17 +0000 Subject: [PATCH 2/6] update to latest nf-test --- .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 df00beb4..b9b76ddc 100644 --- a/.github/workflows/ci.yml +++ b/.github/workflows/ci.yml @@ -12,7 +12,7 @@ on: env: NFT_DIFF: "pdiff" NFT_DIFF_ARGS: "--line-numbers --expand-tabs=2" - NFT_VER: "0.9.0" + NFT_VER: "0.9.2" NFT_WORKDIR: "~" NXF_ANSI_LOG: false NXF_SINGULARITY_CACHEDIR: ${{ github.workspace }}/.singularity From e1b70352f4992c7b482b8f7936d3dc799bb5d8c7 Mon Sep 17 00:00:00 2001 From: atrigila <18577080+atrigila@users.noreply.github.com> Date: Mon, 4 Nov 2024 18:32:33 +0000 Subject: [PATCH 3/6] update subworkflows --- modules.json | 4 ++-- .../tests/main.workflow.nf.test | 10 ++++++---- .../nf-core/utils_nfschema_plugin/tests/main.nf.test | 4 ++-- 3 files changed, 10 insertions(+), 8 deletions(-) diff --git a/modules.json b/modules.json index 49c2cb41..326a8259 100644 --- a/modules.json +++ b/modules.json @@ -101,7 +101,7 @@ }, "utils_nextflow_pipeline": { "branch": "master", - "git_sha": "3aa0aec1d52d492fe241919f0c6100ebf0074082", + "git_sha": "56372688d8979092cafbe0c5c3895b491166ca1c", "installed_by": ["subworkflows"] }, "utils_nfcore_pipeline": { @@ -111,7 +111,7 @@ }, "utils_nfschema_plugin": { "branch": "master", - "git_sha": "bbd5a41f4535a8defafe6080e00ea74c45f4f96c", + "git_sha": "2fd2cd6d0e7b273747f32e465fdc6bcc3ae0814e", "installed_by": ["subworkflows"] } } diff --git a/subworkflows/nf-core/utils_nextflow_pipeline/tests/main.workflow.nf.test b/subworkflows/nf-core/utils_nextflow_pipeline/tests/main.workflow.nf.test index ca964ce8..02dbf094 100644 --- a/subworkflows/nf-core/utils_nextflow_pipeline/tests/main.workflow.nf.test +++ b/subworkflows/nf-core/utils_nextflow_pipeline/tests/main.workflow.nf.test @@ -52,10 +52,12 @@ nextflow_workflow { } then { - assertAll( - { assert workflow.success }, - { assert workflow.stdout.contains("nextflow_workflow v9.9.9") } - ) + expect { + with(workflow) { + assert success + assert "nextflow_workflow v9.9.9" in stdout + } + } } } diff --git a/subworkflows/nf-core/utils_nfschema_plugin/tests/main.nf.test b/subworkflows/nf-core/utils_nfschema_plugin/tests/main.nf.test index 842dc432..8fb30164 100644 --- a/subworkflows/nf-core/utils_nfschema_plugin/tests/main.nf.test +++ b/subworkflows/nf-core/utils_nfschema_plugin/tests/main.nf.test @@ -42,7 +42,7 @@ nextflow_workflow { params { test_data = '' - outdir = 1 + outdir = null } workflow { @@ -94,7 +94,7 @@ nextflow_workflow { params { test_data = '' - outdir = 1 + outdir = null } workflow { From 7dcfadb48474a209f8e19f745c2a017f883dae32 Mon Sep 17 00:00:00 2001 From: atrigila <18577080+atrigila@users.noreply.github.com> Date: Mon, 4 Nov 2024 19:05:01 +0000 Subject: [PATCH 4/6] update changelog --- CHANGELOG.md | 1 + 1 file changed, 1 insertion(+) diff --git a/CHANGELOG.md b/CHANGELOG.md index 6336efd8..294839d9 100755 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -11,6 +11,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 - [#275](https://github.com/nf-core/demultiplex/pull/275) Update samshee module from nf-core. - [#276](https://github.com/nf-core/demultiplex/pull/276) Template update for nf-core/tools v3.0.2 +- [#283](https://github.com/nf-core/demultiplex/pull/283) nf-core modules and subworkflows update. nf-test version update. ### `Fixed` From 27aff966727a36907c56820f2cdf8e9e69b1f7f7 Mon Sep 17 00:00:00 2001 From: atrigila <18577080+atrigila@users.noreply.github.com> Date: Mon, 4 Nov 2024 19:05:08 +0000 Subject: [PATCH 5/6] update snapshot --- tests/bases2fastq.nf.test.snap | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/tests/bases2fastq.nf.test.snap b/tests/bases2fastq.nf.test.snap index 89f094eb..d967e77e 100644 --- a/tests/bases2fastq.nf.test.snap +++ b/tests/bases2fastq.nf.test.snap @@ -206,10 +206,10 @@ ] ], "meta": { - "nf-test": "0.9.0", - "nextflow": "24.04.4" + "nf-test": "0.9.2", + "nextflow": "24.10.0" }, - "timestamp": "2024-10-30T15:25:52.803280321" + "timestamp": "2024-11-04T18:21:06.004398729" }, "rnaseq_samplesheet": { "content": [ From 4da452b7ec69e6f9ed40fdd9e1e6ab902435ee9f Mon Sep 17 00:00:00 2001 From: atrigila <18577080+atrigila@users.noreply.github.com> Date: Mon, 4 Nov 2024 21:44:59 +0000 Subject: [PATCH 6/6] fix pull number --- CHANGELOG.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index 294839d9..45473e26 100755 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -11,7 +11,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 - [#275](https://github.com/nf-core/demultiplex/pull/275) Update samshee module from nf-core. - [#276](https://github.com/nf-core/demultiplex/pull/276) Template update for nf-core/tools v3.0.2 -- [#283](https://github.com/nf-core/demultiplex/pull/283) nf-core modules and subworkflows update. nf-test version update. +- [#284](https://github.com/nf-core/demultiplex/pull/284) nf-core modules and subworkflows update. nf-test version update. ### `Fixed`