From 1879ff5aa2a279dd5b29e541960dab5eb0e1e97f Mon Sep 17 00:00:00 2001 From: mashehu Date: Fri, 28 Apr 2023 09:59:28 +0200 Subject: [PATCH 1/2] update modules in template --- nf_core/pipeline-template/modules.json | 4 ++-- .../modules/nf-core/custom/dumpsoftwareversions/main.nf | 6 +++--- .../modules/nf-core/custom/dumpsoftwareversions/meta.yml | 5 ++--- .../dumpsoftwareversions/templates/dumpsoftwareversions.py | 0 nf_core/pipeline-template/modules/nf-core/multiqc/main.nf | 6 +++--- nf_core/pipeline-template/modules/nf-core/multiqc/meta.yml | 3 ++- 6 files changed, 12 insertions(+), 12 deletions(-) mode change 100755 => 100644 nf_core/pipeline-template/modules/nf-core/custom/dumpsoftwareversions/templates/dumpsoftwareversions.py diff --git a/nf_core/pipeline-template/modules.json b/nf_core/pipeline-template/modules.json index 08116ecbac..f3d45764e5 100644 --- a/nf_core/pipeline-template/modules.json +++ b/nf_core/pipeline-template/modules.json @@ -7,7 +7,7 @@ "nf-core": { "custom/dumpsoftwareversions": { "branch": "master", - "git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c", + "git_sha": "f2d63bd5b68925f98f572eed70993d205cc694b7", "installed_by": ["modules"] }, "fastqc": { @@ -17,7 +17,7 @@ }, "multiqc": { "branch": "master", - "git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c", + "git_sha": "f2d63bd5b68925f98f572eed70993d205cc694b7", "installed_by": ["modules"] } } diff --git a/nf_core/pipeline-template/modules/nf-core/custom/dumpsoftwareversions/main.nf b/nf_core/pipeline-template/modules/nf-core/custom/dumpsoftwareversions/main.nf index 3df21765b9..800a60991a 100644 --- a/nf_core/pipeline-template/modules/nf-core/custom/dumpsoftwareversions/main.nf +++ b/nf_core/pipeline-template/modules/nf-core/custom/dumpsoftwareversions/main.nf @@ -2,10 +2,10 @@ process CUSTOM_DUMPSOFTWAREVERSIONS { label 'process_single' // Requires `pyyaml` which does not have a dedicated container but is in the MultiQC container - conda "bioconda::multiqc=1.13" + conda "bioconda::multiqc=1.14" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/multiqc:1.13--pyhdfd78af_0' : - 'quay.io/biocontainers/multiqc:1.13--pyhdfd78af_0' }" + 'https://depot.galaxyproject.org/singularity/multiqc:1.14--pyhdfd78af_0' : + 'quay.io/biocontainers/multiqc:1.14--pyhdfd78af_0' }" input: path versions diff --git a/nf_core/pipeline-template/modules/nf-core/custom/dumpsoftwareversions/meta.yml b/nf_core/pipeline-template/modules/nf-core/custom/dumpsoftwareversions/meta.yml index c1bccd5f76..c32657de7a 100644 --- a/nf_core/pipeline-template/modules/nf-core/custom/dumpsoftwareversions/meta.yml +++ b/nf_core/pipeline-template/modules/nf-core/custom/dumpsoftwareversions/meta.yml @@ -3,9 +3,8 @@ name: custom_dumpsoftwareversions description: Custom module used to dump software versions within the nf-core pipeline template keywords: - custom - - software - - versions - + - dump + - version tools: - custom: description: Custom module used to dump software versions within the nf-core pipeline template diff --git a/nf_core/pipeline-template/modules/nf-core/custom/dumpsoftwareversions/templates/dumpsoftwareversions.py b/nf_core/pipeline-template/modules/nf-core/custom/dumpsoftwareversions/templates/dumpsoftwareversions.py old mode 100755 new mode 100644 diff --git a/nf_core/pipeline-template/modules/nf-core/multiqc/main.nf b/nf_core/pipeline-template/modules/nf-core/multiqc/main.nf index 68f66bea74..4b604749f5 100644 --- a/nf_core/pipeline-template/modules/nf-core/multiqc/main.nf +++ b/nf_core/pipeline-template/modules/nf-core/multiqc/main.nf @@ -1,10 +1,10 @@ process MULTIQC { label 'process_single' - conda "bioconda::multiqc=1.13" + conda "bioconda::multiqc=1.14" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/multiqc:1.13--pyhdfd78af_0' : - 'quay.io/biocontainers/multiqc:1.13--pyhdfd78af_0' }" + 'https://depot.galaxyproject.org/singularity/multiqc:1.14--pyhdfd78af_0' : + 'quay.io/biocontainers/multiqc:1.14--pyhdfd78af_0' }" input: path multiqc_files, stageAs: "?/*" diff --git a/nf_core/pipeline-template/modules/nf-core/multiqc/meta.yml b/nf_core/pipeline-template/modules/nf-core/multiqc/meta.yml index ebc29b279d..f93b5ee519 100644 --- a/nf_core/pipeline-template/modules/nf-core/multiqc/meta.yml +++ b/nf_core/pipeline-template/modules/nf-core/multiqc/meta.yml @@ -1,3 +1,4 @@ +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/yaml-schema.json name: MultiQC description: Aggregate results from bioinformatics analyses across many samples into a single report keywords: @@ -37,7 +38,7 @@ output: description: MultiQC report file pattern: "multiqc_report.html" - data: - type: dir + type: directory description: MultiQC data dir pattern: "multiqc_data" - plots: From 95d7ef37b73b1541d5beec5fd8112fcb73a5bcf7 Mon Sep 17 00:00:00 2001 From: mirpedrol Date: Fri, 28 Apr 2023 10:24:20 +0200 Subject: [PATCH 2/2] allow labels between single quotes --- nf_core/modules/lint/main_nf.py | 2 +- tests/modules/lint.py | 18 +++++++++--------- 2 files changed, 10 insertions(+), 10 deletions(-) diff --git a/nf_core/modules/lint/main_nf.py b/nf_core/modules/lint/main_nf.py index e5aaa9e0c4..bacc7d7fbd 100644 --- a/nf_core/modules/lint/main_nf.py +++ b/nf_core/modules/lint/main_nf.py @@ -403,7 +403,7 @@ def check_process_labels(self, lines): if len(all_labels) > 0: for label in all_labels: try: - label = re.match("^label\s+([a-zA-Z0-9_-]+)$", label).group(1) + label = re.match(r"^label\s+'?([a-zA-Z0-9_-]+)'?$", label).group(1) except AttributeError: self.warned.append( ( diff --git a/tests/modules/lint.py b/tests/modules/lint.py index 90697fbf90..b7aaf610ca 100644 --- a/tests/modules/lint.py +++ b/tests/modules/lint.py @@ -122,7 +122,7 @@ def __init__(self): PROCESS_LABEL_GOOD = ( """ - label process_high + label 'process_high' cpus 12 """, 1, @@ -131,7 +131,7 @@ def __init__(self): ) PROCESS_LABEL_NON_ALPHANUMERIC = ( """ - label a:label:with:colons + label 'a:label:with:colons' cpus 12 """, 0, @@ -140,8 +140,8 @@ def __init__(self): ) PROCESS_LABEL_GOOD_CONFLICTING = ( """ - label process_high - label process_low + label 'process_high' + label 'process_low' cpus 12 """, 0, @@ -150,8 +150,8 @@ def __init__(self): ) PROCESS_LABEL_GOOD_DUPLICATES = ( """ - label process_high - label process_high + label 'process_high' + label 'process_high' cpus 12 """, 0, @@ -160,8 +160,8 @@ def __init__(self): ) PROCESS_LABEL_GOOD_AND_NONSTANDARD = ( """ - label process_high - label process_extra_label + label 'process_high' + label 'process_extra_label' cpus 12 """, 1, @@ -170,7 +170,7 @@ def __init__(self): ) PROCESS_LABEL_NONSTANDARD = ( """ - label process_extra_label + label 'process_extra_label' cpus 12 """, 0,