From ca79d543b3f4dac20b9480a67be31b727848d8b3 Mon Sep 17 00:00:00 2001 From: "renovate[bot]" <29139614+renovate[bot]@users.noreply.github.com> Date: Thu, 2 May 2024 00:22:59 +0000 Subject: [PATCH 1/6] chore(deps): update codecov/codecov-action digest to 5ecb98a --- .github/workflows/pytest.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/pytest.yml b/.github/workflows/pytest.yml index 03576fa310..70b9cfd0a8 100644 --- a/.github/workflows/pytest.yml +++ b/.github/workflows/pytest.yml @@ -184,7 +184,7 @@ jobs: coverage report coverage xml - - uses: codecov/codecov-action@84508663e988701840491b86de86b666e8a86bed # v4 + - uses: codecov/codecov-action@5ecb98a3c6b747ed38dc09f787459979aebb39be # v4 with: files: coverage.xml env: From c5d55b8f4a5b4c2107ef6c4be0f660cd24e4796a Mon Sep 17 00:00:00 2001 From: nf-core-bot Date: Fri, 3 May 2024 03:48:04 +0000 Subject: [PATCH 2/6] [automated] Update CHANGELOG.md --- CHANGELOG.md | 1 + 1 file changed, 1 insertion(+) diff --git a/CHANGELOG.md b/CHANGELOG.md index b618f947ba..439c38769d 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -61,6 +61,7 @@ - Update gitpod/workspace-base Docker digest to 5aeb24f ([#2929](https://github.com/nf-core/tools/pull/2929)) - Update pre-commit hook pre-commit/mirrors-mypy to v1.10.0 ([#2933](https://github.com/nf-core/tools/pull/2933)) - Update GitHub Actions ([#2939](https://github.com/nf-core/tools/pull/2939)) +- Update codecov/codecov-action digest to 5ecb98a ([#2948](https://github.com/nf-core/tools/pull/2948)) ## [v2.13.1 - Tin Puppy Patch](https://github.com/nf-core/tools/releases/tag/2.13) - [2024-02-29] From 80fcd09575dc2b4972c792622543d2f1e9f39d30 Mon Sep 17 00:00:00 2001 From: mashehu Date: Fri, 3 May 2024 08:03:13 +0200 Subject: [PATCH 3/6] update components to fix CI testing --- nf_core/pipeline-template/modules.json | 4 ++-- nf_core/pipeline-template/modules/nf-core/fastqc/main.nf | 6 ++++++ .../subworkflows/nf-core/utils_nfcore_pipeline/main.nf | 8 +++++++- 3 files changed, 15 insertions(+), 3 deletions(-) diff --git a/nf_core/pipeline-template/modules.json b/nf_core/pipeline-template/modules.json index 38aa622063..9137c59675 100644 --- a/nf_core/pipeline-template/modules.json +++ b/nf_core/pipeline-template/modules.json @@ -7,7 +7,7 @@ "nf-core": { "fastqc": { "branch": "master", - "git_sha": "f4ae1d942bd50c5c0b9bd2de1393ce38315ba57c", + "git_sha": "285a50500f9e02578d90b3ce6382ea3c30216acd", "installed_by": ["modules"] }, "multiqc": { @@ -26,7 +26,7 @@ }, "utils_nfcore_pipeline": { "branch": "master", - "git_sha": "5caf7640a9ef1d18d765d55339be751bb0969dfa", + "git_sha": "92de218a329bfc9a9033116eb5f65fd270e72ba3", "installed_by": ["subworkflows"] }, "utils_nfvalidation_plugin": { diff --git a/nf_core/pipeline-template/modules/nf-core/fastqc/main.nf b/nf_core/pipeline-template/modules/nf-core/fastqc/main.nf index 9e19a74c56..d79f1c862d 100644 --- a/nf_core/pipeline-template/modules/nf-core/fastqc/main.nf +++ b/nf_core/pipeline-template/modules/nf-core/fastqc/main.nf @@ -25,6 +25,11 @@ process FASTQC { def old_new_pairs = reads instanceof Path || reads.size() == 1 ? [[ reads, "${prefix}.${reads.extension}" ]] : reads.withIndex().collect { entry, index -> [ entry, "${prefix}_${index + 1}.${entry.extension}" ] } def rename_to = old_new_pairs*.join(' ').join(' ') def renamed_files = old_new_pairs.collect{ old_name, new_name -> new_name }.join(' ') + + def memory_in_mb = MemoryUnit.of("${task.memory}").toUnit('MB') + // FastQC memory value allowed range (100 - 10000) + def fastqc_memory = memory_in_mb > 10000 ? 10000 : (memory_in_mb < 100 ? 100 : memory_in_mb) + """ printf "%s %s\\n" $rename_to | while read old_name new_name; do [ -f "\${new_name}" ] || ln -s \$old_name \$new_name @@ -33,6 +38,7 @@ process FASTQC { fastqc \\ $args \\ --threads $task.cpus \\ + --memory $fastqc_memory \\ $renamed_files cat <<-END_VERSIONS > versions.yml diff --git a/nf_core/pipeline-template/subworkflows/nf-core/utils_nfcore_pipeline/main.nf b/nf_core/pipeline-template/subworkflows/nf-core/utils_nfcore_pipeline/main.nf index a8b55d6fe1..14558c3927 100644 --- a/nf_core/pipeline-template/subworkflows/nf-core/utils_nfcore_pipeline/main.nf +++ b/nf_core/pipeline-template/subworkflows/nf-core/utils_nfcore_pipeline/main.nf @@ -65,9 +65,15 @@ def checkProfileProvided(nextflow_cli_args) { // Citation string for pipeline // def workflowCitation() { + def temp_doi_ref = "" + String[] manifest_doi = workflow.manifest.doi.tokenize(",") + // Using a loop to handle multiple DOIs + // Removing `https://doi.org/` to handle pipelines using DOIs vs DOI resolvers + // Removing ` ` since the manifest.doi is a string and not a proper list + for (String doi_ref: manifest_doi) temp_doi_ref += " https://doi.org/${doi_ref.replace('https://doi.org/', '').replace(' ', '')}\n" return "If you use ${workflow.manifest.name} for your analysis please cite:\n\n" + "* The pipeline\n" + - " ${workflow.manifest.doi}\n\n" + + temp_doi_ref + "\n" + "* The nf-core framework\n" + " https://doi.org/10.1038/s41587-020-0439-x\n\n" + "* Software dependencies\n" + From 13b1f10f796729acd8c680ca7d16516ac56827a1 Mon Sep 17 00:00:00 2001 From: nf-core-bot Date: Fri, 3 May 2024 06:04:58 +0000 Subject: [PATCH 4/6] [automated] Update CHANGELOG.md --- CHANGELOG.md | 1 + 1 file changed, 1 insertion(+) diff --git a/CHANGELOG.md b/CHANGELOG.md index d7ba6a7a46..015a1d0825 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -57,6 +57,7 @@ - chore(deps): update pre-commit hook astral-sh/ruff-pre-commit to v0.3.6 ([#2915](https://github.com/nf-core/tools/pull/2915)) - chore(deps): update pre-commit hook astral-sh/ruff-pre-commit to v0.3.7 ([#2917](https://github.com/nf-core/tools/pull/2917)) - Update gitpod/workspace-base Docker digest to 0af257e ([#2919](https://github.com/nf-core/tools/pull/2919)) +- update components to fix CI testing ([#2949](https://github.com/nf-core/tools/pull/2949)) ## [v2.13.1 - Tin Puppy Patch](https://github.com/nf-core/tools/releases/tag/2.13) - [2024-02-29] From 32ac3837e94d52f1ce0331cead78f86ef5761dbf Mon Sep 17 00:00:00 2001 From: nf-core-bot Date: Fri, 3 May 2024 06:14:02 +0000 Subject: [PATCH 5/6] [automated] Update CHANGELOG.md --- CHANGELOG.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index 3e38d8bb39..5e10a63824 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -58,13 +58,13 @@ - chore(deps): update pre-commit hook astral-sh/ruff-pre-commit to v0.3.6 ([#2915](https://github.com/nf-core/tools/pull/2915)) - chore(deps): update pre-commit hook astral-sh/ruff-pre-commit to v0.3.7 ([#2917](https://github.com/nf-core/tools/pull/2917)) - Update gitpod/workspace-base Docker digest to 0af257e ([#2919](https://github.com/nf-core/tools/pull/2919)) -- update components to fix CI testing ([#2949](https://github.com/nf-core/tools/pull/2949)) - Update GitHub Actions ([#2927](https://github.com/nf-core/tools/pull/2927)) - Update gitpod/workspace-base Docker digest to 5aeb24f ([#2929](https://github.com/nf-core/tools/pull/2929)) - Update pre-commit hook pre-commit/mirrors-mypy to v1.10.0 ([#2933](https://github.com/nf-core/tools/pull/2933)) - Update GitHub Actions ([#2939](https://github.com/nf-core/tools/pull/2939)) - Update codecov/codecov-action digest to 5ecb98a ([#2948](https://github.com/nf-core/tools/pull/2948)) - Update gitpod/workspace-base Docker digest to 124f2b8 ([#2943](https://github.com/nf-core/tools/pull/2943)) +- Template: Update included components ([#2949](https://github.com/nf-core/tools/pull/2949)) ## [v2.13.1 - Tin Puppy Patch](https://github.com/nf-core/tools/releases/tag/2.13) - [2024-02-29] From 0adbe37e19ae36e3488b0d592e08b08fbaf62d1f Mon Sep 17 00:00:00 2001 From: mashehu Date: Fri, 3 May 2024 08:16:48 +0200 Subject: [PATCH 6/6] fix changelog --- CHANGELOG.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index 5e10a63824..40450bc51d 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -14,6 +14,7 @@ - Remove `pyproject.toml` from template root - Shorten lines in pipeline template ([#2908](https://github.com/nf-core/tools/pull/2908)) - Permanently activated pipeline-specific institutional configs support for all pipelines without need for manual intervention ([#2936](https://github.com/nf-core/tools/pull/2936)) +- Update included components ([#2949](https://github.com/nf-core/tools/pull/2949)) ### Linting @@ -64,7 +65,6 @@ - Update GitHub Actions ([#2939](https://github.com/nf-core/tools/pull/2939)) - Update codecov/codecov-action digest to 5ecb98a ([#2948](https://github.com/nf-core/tools/pull/2948)) - Update gitpod/workspace-base Docker digest to 124f2b8 ([#2943](https://github.com/nf-core/tools/pull/2943)) -- Template: Update included components ([#2949](https://github.com/nf-core/tools/pull/2949)) ## [v2.13.1 - Tin Puppy Patch](https://github.com/nf-core/tools/releases/tag/2.13) - [2024-02-29]