From 3c57d6ebd731cd71b90085a521c5a6d3407e0a36 Mon Sep 17 00:00:00 2001 From: Alexander Peltzer Date: Tue, 17 Sep 2024 14:30:31 +0000 Subject: [PATCH] Updated all modules --- modules.json | 22 +++++++++---------- modules/nf-core/checkqc/environment.yml | 2 -- modules/nf-core/falco/environment.yml | 2 -- modules/nf-core/fastp/environment.yml | 2 -- modules/nf-core/fastqc/environment.yml | 2 -- modules/nf-core/fqtk/environment.yml | 2 -- .../nf-core/kraken2/kraken2/environment.yml | 2 -- modules/nf-core/md5sum/environment.yml | 2 -- modules/nf-core/multiqc/environment.yml | 4 +--- modules/nf-core/multiqc/main.nf | 4 ++-- .../nf-core/multiqc/tests/main.nf.test.snap | 6 ++--- modules/nf-core/seqtk/sample/environment.yml | 2 -- modules/nf-core/sgdemux/environment.yml | 2 -- modules/nf-core/untar/environment.yml | 2 -- 14 files changed, 17 insertions(+), 39 deletions(-) diff --git a/modules.json b/modules.json index 9c303881..4202ad46 100644 --- a/modules.json +++ b/modules.json @@ -27,57 +27,57 @@ }, "checkqc": { "branch": "master", - "git_sha": "337bc962d03c2e08a728c9bf731a2148e323e731", + "git_sha": "06c8865e36741e05ad32ef70ab3fac127486af48", "installed_by": ["modules"] }, "falco": { "branch": "master", - "git_sha": "a236d2c2ec9e68db9b8501105d804acb359552b5", + "git_sha": "06c8865e36741e05ad32ef70ab3fac127486af48", "installed_by": ["modules"] }, "fastp": { "branch": "master", - "git_sha": "1ceaa8ba4d0fd886dbca0e545815d905b7407de7", + "git_sha": "06c8865e36741e05ad32ef70ab3fac127486af48", "installed_by": ["modules"] }, "fastqc": { "branch": "master", - "git_sha": "b49b8992e5271ce427f3a7cdb29628fc58400eb5", + "git_sha": "06c8865e36741e05ad32ef70ab3fac127486af48", "installed_by": ["modules"] }, "fqtk": { "branch": "master", - "git_sha": "c60c14b285b89bdd0607e371417dadb80385ad6e", + "git_sha": "06c8865e36741e05ad32ef70ab3fac127486af48", "installed_by": ["modules"] }, "kraken2/kraken2": { "branch": "master", - "git_sha": "a13d5d945742a60bbef6e5c177e81cda540f75dc", + "git_sha": "06c8865e36741e05ad32ef70ab3fac127486af48", "installed_by": ["fastq_contam_seqtk_kraken"] }, "md5sum": { "branch": "master", - "git_sha": "1164836d4d3922ab937865b17086485f0f472748", + "git_sha": "06c8865e36741e05ad32ef70ab3fac127486af48", "installed_by": ["modules"] }, "multiqc": { "branch": "master", - "git_sha": "19ca321db5d8bd48923262c2eca6422359633491", + "git_sha": "7c316cae26baf55e0add993bed2b0c9f7105c653", "installed_by": ["modules"] }, "seqtk/sample": { "branch": "master", - "git_sha": "730f3aee80d5f8d0b5fc532202ac59361414d006", + "git_sha": "06c8865e36741e05ad32ef70ab3fac127486af48", "installed_by": ["fastq_contam_seqtk_kraken"] }, "sgdemux": { "branch": "master", - "git_sha": "574074e6ea2497b53df1f226473a8c71524af0d0", + "git_sha": "06c8865e36741e05ad32ef70ab3fac127486af48", "installed_by": ["modules"] }, "untar": { "branch": "master", - "git_sha": "4e5f4687318f24ba944a13609d3ea6ebd890737d", + "git_sha": "06c8865e36741e05ad32ef70ab3fac127486af48", "installed_by": ["modules"] } } diff --git a/modules/nf-core/checkqc/environment.yml b/modules/nf-core/checkqc/environment.yml index e60237d5..1a054130 100644 --- a/modules/nf-core/checkqc/environment.yml +++ b/modules/nf-core/checkqc/environment.yml @@ -1,8 +1,6 @@ -name: checkqc channels: - conda-forge - bioconda - - defaults dependencies: - python=3.8 - numpy=1.26 diff --git a/modules/nf-core/falco/environment.yml b/modules/nf-core/falco/environment.yml index eeedb5b7..c48809cc 100644 --- a/modules/nf-core/falco/environment.yml +++ b/modules/nf-core/falco/environment.yml @@ -1,7 +1,5 @@ -name: falco channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::falco=1.2.1 diff --git a/modules/nf-core/fastp/environment.yml b/modules/nf-core/fastp/environment.yml index 70389e66..26d4aca5 100644 --- a/modules/nf-core/fastp/environment.yml +++ b/modules/nf-core/fastp/environment.yml @@ -1,7 +1,5 @@ -name: fastp channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::fastp=0.23.4 diff --git a/modules/nf-core/fastqc/environment.yml b/modules/nf-core/fastqc/environment.yml index 1787b38a..691d4c76 100644 --- a/modules/nf-core/fastqc/environment.yml +++ b/modules/nf-core/fastqc/environment.yml @@ -1,7 +1,5 @@ -name: fastqc channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::fastqc=0.12.1 diff --git a/modules/nf-core/fqtk/environment.yml b/modules/nf-core/fqtk/environment.yml index 1ea15744..90897712 100644 --- a/modules/nf-core/fqtk/environment.yml +++ b/modules/nf-core/fqtk/environment.yml @@ -1,7 +1,5 @@ -name: fqtk channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::fqtk=0.2.1 diff --git a/modules/nf-core/kraken2/kraken2/environment.yml b/modules/nf-core/kraken2/kraken2/environment.yml index 0c067fee..ba776d31 100644 --- a/modules/nf-core/kraken2/kraken2/environment.yml +++ b/modules/nf-core/kraken2/kraken2/environment.yml @@ -1,8 +1,6 @@ -name: kraken2_kraken2 channels: - conda-forge - bioconda - - defaults dependencies: - "bioconda::kraken2=2.1.3" - "coreutils=9.4" diff --git a/modules/nf-core/md5sum/environment.yml b/modules/nf-core/md5sum/environment.yml index c196b013..c7eb9bd1 100644 --- a/modules/nf-core/md5sum/environment.yml +++ b/modules/nf-core/md5sum/environment.yml @@ -1,7 +1,5 @@ -name: md5sum channels: - conda-forge - bioconda - - defaults dependencies: - conda-forge::coreutils=8.30 diff --git a/modules/nf-core/multiqc/environment.yml b/modules/nf-core/multiqc/environment.yml index a31464c9..0fe12644 100644 --- a/modules/nf-core/multiqc/environment.yml +++ b/modules/nf-core/multiqc/environment.yml @@ -1,7 +1,5 @@ -name: multiqc channels: - conda-forge - bioconda - - defaults dependencies: - - bioconda::multiqc=1.24.1 + - bioconda::multiqc=1.25 diff --git a/modules/nf-core/multiqc/main.nf b/modules/nf-core/multiqc/main.nf index ceaec139..b9ccebdb 100644 --- a/modules/nf-core/multiqc/main.nf +++ b/modules/nf-core/multiqc/main.nf @@ -3,8 +3,8 @@ process MULTIQC { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/multiqc:1.24.1--pyhdfd78af_0' : - 'biocontainers/multiqc:1.24.1--pyhdfd78af_0' }" + 'https://depot.galaxyproject.org/singularity/multiqc:1.25--pyhdfd78af_0' : + 'biocontainers/multiqc:1.25--pyhdfd78af_0' }" input: path multiqc_files, stageAs: "?/*" diff --git a/modules/nf-core/multiqc/tests/main.nf.test.snap b/modules/nf-core/multiqc/tests/main.nf.test.snap index 83fa080c..b779e469 100644 --- a/modules/nf-core/multiqc/tests/main.nf.test.snap +++ b/modules/nf-core/multiqc/tests/main.nf.test.snap @@ -2,7 +2,7 @@ "multiqc_versions_single": { "content": [ [ - "versions.yml:md5,6eb13f3b11bbcbfc98ad3166420ff760" + "versions.yml:md5,8c8724363a5efe0c6f43ab34faa57efd" ] ], "meta": { @@ -17,7 +17,7 @@ "multiqc_report.html", "multiqc_data", "multiqc_plots", - "versions.yml:md5,6eb13f3b11bbcbfc98ad3166420ff760" + "versions.yml:md5,8c8724363a5efe0c6f43ab34faa57efd" ] ], "meta": { @@ -29,7 +29,7 @@ "multiqc_versions_config": { "content": [ [ - "versions.yml:md5,6eb13f3b11bbcbfc98ad3166420ff760" + "versions.yml:md5,8c8724363a5efe0c6f43ab34faa57efd" ] ], "meta": { diff --git a/modules/nf-core/seqtk/sample/environment.yml b/modules/nf-core/seqtk/sample/environment.yml index 3f856d31..693aa5c1 100644 --- a/modules/nf-core/seqtk/sample/environment.yml +++ b/modules/nf-core/seqtk/sample/environment.yml @@ -1,7 +1,5 @@ -name: seqtk_sample channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::seqtk=1.4 diff --git a/modules/nf-core/sgdemux/environment.yml b/modules/nf-core/sgdemux/environment.yml index 57eccdd2..ce09711a 100644 --- a/modules/nf-core/sgdemux/environment.yml +++ b/modules/nf-core/sgdemux/environment.yml @@ -1,7 +1,5 @@ -name: sgdemux channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::sgdemux=1.1.1 diff --git a/modules/nf-core/untar/environment.yml b/modules/nf-core/untar/environment.yml index 4f498244..c7794856 100644 --- a/modules/nf-core/untar/environment.yml +++ b/modules/nf-core/untar/environment.yml @@ -1,8 +1,6 @@ -name: untar channels: - conda-forge - bioconda - - defaults dependencies: - conda-forge::grep=3.11 - conda-forge::sed=4.8