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 diff --git a/CHANGELOG.md b/CHANGELOG.md index d69efc39..b8558dac 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 +- [#284](https://github.com/nf-core/demultiplex/pull/284) nf-core modules and subworkflows update. nf-test version update. ### `Fixed` diff --git a/modules.json b/modules.json index 3be139fe..326a8259 100644 --- a/modules.json +++ b/modules.json @@ -67,7 +67,7 @@ }, "samshee": { "branch": "master", - "git_sha": "3c464e75051db485c1b37ab9f1ea2182fb3d3533", + "git_sha": "467c202a876d26af544fa8c4b22a050a535462a7", "installed_by": ["modules"] }, "seqtk/sample": { @@ -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/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: 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 { 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": [