From 1ad4190d2aa939026e624283b93a267d4caadd8f Mon Sep 17 00:00:00 2001 From: Annick Renevey <47788523+rannick@users.noreply.github.com> Date: Fri, 29 Sep 2023 11:41:56 +0200 Subject: [PATCH] update modules and fix linting --- README.md | 2 +- modules.json | 8 ++++---- modules/nf-core/custom/dumpsoftwareversions/main.nf | 4 ++-- modules/nf-core/gatk4/bedtointervallist/main.nf | 3 ++- modules/nf-core/gatk4/bedtointervallist/meta.yml | 3 ++- modules/nf-core/gatk4/createsequencedictionary/main.nf | 3 ++- modules/nf-core/gatk4/createsequencedictionary/meta.yml | 3 ++- modules/nf-core/multiqc/main.nf | 4 ++-- 8 files changed, 17 insertions(+), 13 deletions(-) diff --git a/README.md b/README.md index c284a7b9..7a71db11 100644 --- a/README.md +++ b/README.md @@ -1,7 +1,7 @@ # ![nf-core/rnafusion](docs/images/nf-core-rnafusion_logo_light.png#gh-light-mode-only) ![nf-core/rnafusion](docs/images/nf-core-rnafusion_logo_dark.png#gh-dark-mode-only) [![GitHub Actions CI Status](https://github.com/nf-core/rnafusion/workflows/nf-core%20CI/badge.svg)](https://github.com/nf-core/rnafusion/actions?query=workflow%3A%22nf-core+CI%22) -[![GitHub Actions Linting Status](https://github.com/nf-core/rnafusion/workflows/nf-core%20linting/badge.svg)](https://github.com/nf-core/rnafusion/actions?query=workflow%3A%22nf-core+linting%22)[![AWS CI](https://img.shields.io/badge/CI%20tests-full%20size-FF9900?labelColor=000000&logo=Amazon%20AWS)](https://nf-co.re/rnafusion/results)[![Cite with Zenodo](http://img.shields.io/badge/DOI-10.5281/zenodo.XXXXXXX-1073c8?labelColor=000000)](https://doi.org/10.5281/zenodo.XXXXXXX) +[![GitHub Actions Linting Status](https://github.com/nf-core/rnafusion/workflows/nf-core%20linting/badge.svg)](https://github.com/nf-core/rnafusion/actions?query=workflow%3A%22nf-core+linting%22)[![AWS CI](https://img.shields.io/badge/CI%20tests-full%20size-FF9900?labelColor=000000&logo=Amazon%20AWS)](https://nf-co.re/rnafusion/results)[![Cite with Zenodo](http://img.shields.io/badge/DOI-10.5281/zenodo.3946477-1073c8?labelColor=000000)](https://doi.org/10.5281/zenodo.3946477) [![Nextflow](https://img.shields.io/badge/nextflow%20DSL2-%E2%89%A523.04.0-23aa62.svg)](https://www.nextflow.io/) [![run with conda](http://img.shields.io/badge/run%20with-conda-3EB049?labelColor=000000&logo=anaconda)](https://docs.conda.io/en/latest/) diff --git a/modules.json b/modules.json index b9a83a62..47aad520 100644 --- a/modules.json +++ b/modules.json @@ -22,7 +22,7 @@ }, "custom/dumpsoftwareversions": { "branch": "master", - "git_sha": "911696ea0b62df80e900ef244d7867d177971f73", + "git_sha": "05c280924b6c768d484c7c443dad5e605c4ff4b4", "installed_by": ["modules"] }, "fastp": { @@ -32,17 +32,17 @@ }, "fastqc": { "branch": "master", - "git_sha": "bd8092b67b5103bdd52e300f75889442275c3117", + "git_sha": "9a4517e720bc812e95b56d23d15a1653b6db4f53", "installed_by": ["modules"] }, "gatk4/bedtointervallist": { "branch": "master", - "git_sha": "2df2a11d5b12f2a73bca74f103691bc35d83c5fd", + "git_sha": "cf8f9ace77aac01caa5c7cb92af5bbda7adb77bd", "installed_by": ["modules"] }, "gatk4/createsequencedictionary": { "branch": "master", - "git_sha": "541811d779026c5d395925895fa5ed35e7216cc0", + "git_sha": "cf8f9ace77aac01caa5c7cb92af5bbda7adb77bd", "installed_by": ["modules"] }, "kallisto/index": { diff --git a/modules/nf-core/custom/dumpsoftwareversions/main.nf b/modules/nf-core/custom/dumpsoftwareversions/main.nf index 71df79f9..c9d014b1 100644 --- a/modules/nf-core/custom/dumpsoftwareversions/main.nf +++ b/modules/nf-core/custom/dumpsoftwareversions/main.nf @@ -4,8 +4,8 @@ process CUSTOM_DUMPSOFTWAREVERSIONS { // Requires `pyyaml` which does not have a dedicated container but is in the MultiQC container conda "bioconda::multiqc=1.15" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/multiqc:1.14--pyhdfd78af_0' : - 'biocontainers/multiqc:1.14--pyhdfd78af_0' }" + 'https://depot.galaxyproject.org/singularity/multiqc:1.15--pyhdfd78af_0' : + 'biocontainers/multiqc:1.15--pyhdfd78af_0' }" input: path versions diff --git a/modules/nf-core/gatk4/bedtointervallist/main.nf b/modules/nf-core/gatk4/bedtointervallist/main.nf index a23abd06..24968c38 100644 --- a/modules/nf-core/gatk4/bedtointervallist/main.nf +++ b/modules/nf-core/gatk4/bedtointervallist/main.nf @@ -29,7 +29,8 @@ process GATK4_BEDTOINTERVALLIST { avail_mem = (task.memory.mega*0.8).intValue() } """ - gatk --java-options "-Xmx${avail_mem}M" BedToIntervalList \\ + gatk --java-options "-Xmx${avail_mem}M -XX:-UsePerfData" \\ + BedToIntervalList \\ --INPUT $bed \\ --OUTPUT ${prefix}.interval_list \\ --SEQUENCE_DICTIONARY $dict \\ diff --git a/modules/nf-core/gatk4/bedtointervallist/meta.yml b/modules/nf-core/gatk4/bedtointervallist/meta.yml index 40daf752..83617a7c 100644 --- a/modules/nf-core/gatk4/bedtointervallist/meta.yml +++ b/modules/nf-core/gatk4/bedtointervallist/meta.yml @@ -2,8 +2,9 @@ name: gatk4_bedtointervallist description: Creates an interval list from a bed file and a reference dict keywords: - bed - - interval list - bedtointervallist + - gatk4 + - interval list tools: - gatk4: description: | diff --git a/modules/nf-core/gatk4/createsequencedictionary/main.nf b/modules/nf-core/gatk4/createsequencedictionary/main.nf index 15a86bea..3e4efdd9 100644 --- a/modules/nf-core/gatk4/createsequencedictionary/main.nf +++ b/modules/nf-core/gatk4/createsequencedictionary/main.nf @@ -27,7 +27,8 @@ process GATK4_CREATESEQUENCEDICTIONARY { avail_mem = (task.memory.mega*0.8).intValue() } """ - gatk --java-options "-Xmx${avail_mem}M" CreateSequenceDictionary \\ + gatk --java-options "-Xmx${avail_mem}M -XX:-UsePerfData" \\ + CreateSequenceDictionary \\ --REFERENCE $fasta \\ --URI $fasta \\ --TMP_DIR . \\ diff --git a/modules/nf-core/gatk4/createsequencedictionary/meta.yml b/modules/nf-core/gatk4/createsequencedictionary/meta.yml index a421e681..9b8b8c89 100644 --- a/modules/nf-core/gatk4/createsequencedictionary/meta.yml +++ b/modules/nf-core/gatk4/createsequencedictionary/meta.yml @@ -1,9 +1,10 @@ name: gatk4_createsequencedictionary description: Creates a sequence dictionary for a reference sequence keywords: + - createsequencedictionary - dictionary - fasta - - createsequencedictionary + - gatk4 tools: - gatk: description: | diff --git a/modules/nf-core/multiqc/main.nf b/modules/nf-core/multiqc/main.nf index 7568297f..65d7dd0d 100644 --- a/modules/nf-core/multiqc/main.nf +++ b/modules/nf-core/multiqc/main.nf @@ -3,8 +3,8 @@ process MULTIQC { conda "bioconda::multiqc=1.15" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/multiqc:1.14--pyhdfd78af_0' : - 'biocontainers/multiqc:1.14--pyhdfd78af_0' }" + 'https://depot.galaxyproject.org/singularity/multiqc:1.15--pyhdfd78af_0' : + 'biocontainers/multiqc:1.15--pyhdfd78af_0' }" input: path multiqc_files, stageAs: "?/*"