From 602595b629b2c287ff635ca763c5aa77d25674af Mon Sep 17 00:00:00 2001 From: prototaxites Date: Thu, 10 Aug 2023 12:12:15 +0000 Subject: [PATCH 1/2] update concoct --- modules.json | 12 ++++++------ modules/nf-core/concoct/concoct/main.nf | 6 +++--- modules/nf-core/concoct/concoctcoveragetable/main.nf | 2 +- modules/nf-core/concoct/cutupfasta/main.nf | 2 +- modules/nf-core/concoct/extractfastabins/main.nf | 2 +- modules/nf-core/concoct/mergecutupclustering/main.nf | 2 +- subworkflows/nf-core/fasta_binning_concoct/meta.yml | 3 ++- 7 files changed, 15 insertions(+), 14 deletions(-) diff --git a/modules.json b/modules.json index 2ee1f7ed..77c1b751 100644 --- a/modules.json +++ b/modules.json @@ -53,27 +53,27 @@ }, "concoct/concoct": { "branch": "master", - "git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c", + "git_sha": "c684a6edba2c8516a0d2cfeafb12489b99d2fffb", "installed_by": ["fasta_binning_concoct"] }, "concoct/concoctcoveragetable": { "branch": "master", - "git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c", + "git_sha": "911696ea0b62df80e900ef244d7867d177971f73", "installed_by": ["fasta_binning_concoct"] }, "concoct/cutupfasta": { "branch": "master", - "git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c", + "git_sha": "911696ea0b62df80e900ef244d7867d177971f73", "installed_by": ["fasta_binning_concoct"] }, "concoct/extractfastabins": { "branch": "master", - "git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c", + "git_sha": "911696ea0b62df80e900ef244d7867d177971f73", "installed_by": ["fasta_binning_concoct"] }, "concoct/mergecutupclustering": { "branch": "master", - "git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c", + "git_sha": "911696ea0b62df80e900ef244d7867d177971f73", "installed_by": ["fasta_binning_concoct"] }, "custom/dumpsoftwareversions": { @@ -214,7 +214,7 @@ "nf-core": { "fasta_binning_concoct": { "branch": "master", - "git_sha": "038be4287743ec3afd8fdf7eb06039d7407bb631", + "git_sha": "dedc0e31087f3306101c38835d051bf49789445a", "installed_by": ["subworkflows"] } } diff --git a/modules/nf-core/concoct/concoct/main.nf b/modules/nf-core/concoct/concoct/main.nf index 563f28fb..536d195d 100644 --- a/modules/nf-core/concoct/concoct/main.nf +++ b/modules/nf-core/concoct/concoct/main.nf @@ -1,12 +1,12 @@ process CONCOCT_CONCOCT { tag "$meta.id" - label 'process_low' + label 'process_high' conda "bioconda::concoct=1.1.0" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/concoct:1.1.0--py38h7be5676_2': - 'quay.io/biocontainers/concoct:1.1.0--py38h7be5676_2' }" + 'https://depot.galaxyproject.org/singularity/concoct:1.1.0--py311h245ed52_4': + 'biocontainers/concoct:1.1.0--py311h245ed52_4' }" input: tuple val(meta), path(coverage_file), path(fasta) diff --git a/modules/nf-core/concoct/concoctcoveragetable/main.nf b/modules/nf-core/concoct/concoctcoveragetable/main.nf index 5be484ae..1833fb67 100644 --- a/modules/nf-core/concoct/concoctcoveragetable/main.nf +++ b/modules/nf-core/concoct/concoctcoveragetable/main.nf @@ -6,7 +6,7 @@ process CONCOCT_CONCOCTCOVERAGETABLE { conda "bioconda::concoct=1.1.0" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/concoct:1.1.0--py38h7be5676_2': - 'quay.io/biocontainers/concoct:1.1.0--py38h7be5676_2' }" + 'biocontainers/concoct:1.1.0--py38h7be5676_2' }" input: tuple val(meta), path(bed), path(bamfiles), path(baifiles) diff --git a/modules/nf-core/concoct/cutupfasta/main.nf b/modules/nf-core/concoct/cutupfasta/main.nf index a765d91c..8610bd53 100644 --- a/modules/nf-core/concoct/cutupfasta/main.nf +++ b/modules/nf-core/concoct/cutupfasta/main.nf @@ -6,7 +6,7 @@ process CONCOCT_CUTUPFASTA { conda "bioconda::concoct=1.1.0" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/concoct:1.1.0--py38h7be5676_2': - 'quay.io/biocontainers/concoct:1.1.0--py38h7be5676_2' }" + 'biocontainers/concoct:1.1.0--py38h7be5676_2' }" input: tuple val(meta), path(fasta) diff --git a/modules/nf-core/concoct/extractfastabins/main.nf b/modules/nf-core/concoct/extractfastabins/main.nf index da6dd91b..0fe49b2f 100644 --- a/modules/nf-core/concoct/extractfastabins/main.nf +++ b/modules/nf-core/concoct/extractfastabins/main.nf @@ -5,7 +5,7 @@ process CONCOCT_EXTRACTFASTABINS { conda "bioconda::concoct=1.1.0" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/concoct:1.1.0--py38h7be5676_2': - 'quay.io/biocontainers/concoct:1.1.0--py38h7be5676_2' }" + 'biocontainers/concoct:1.1.0--py38h7be5676_2' }" input: tuple val(meta), path(original_fasta), path(csv) diff --git a/modules/nf-core/concoct/mergecutupclustering/main.nf b/modules/nf-core/concoct/mergecutupclustering/main.nf index dac6a006..74bbdafc 100644 --- a/modules/nf-core/concoct/mergecutupclustering/main.nf +++ b/modules/nf-core/concoct/mergecutupclustering/main.nf @@ -5,7 +5,7 @@ process CONCOCT_MERGECUTUPCLUSTERING { conda "bioconda::concoct=1.1.0" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/concoct:1.1.0--py38h7be5676_2': - 'quay.io/biocontainers/concoct:1.1.0--py38h7be5676_2' }" + 'biocontainers/concoct:1.1.0--py38h7be5676_2' }" input: tuple val(meta), path(clustering_csv) diff --git a/subworkflows/nf-core/fasta_binning_concoct/meta.yml b/subworkflows/nf-core/fasta_binning_concoct/meta.yml index 5450dc49..5c5b4cb4 100644 --- a/subworkflows/nf-core/fasta_binning_concoct/meta.yml +++ b/subworkflows/nf-core/fasta_binning_concoct/meta.yml @@ -1,3 +1,4 @@ +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/subworkflows/yaml-schema.json name: "fasta_binning_concoct" description: Runs the CONCOCT workflow of contig binning keywords: @@ -5,7 +6,7 @@ keywords: - binning - metagenomics - contigs -modules: +components: - concoct/cutupfasta - concoct/concoctcoveragetable - concoct/concoct From 65a6aa098e5e9bca56c4dd39ce509d659e584532 Mon Sep 17 00:00:00 2001 From: prototaxites Date: Thu, 10 Aug 2023 13:14:19 +0000 Subject: [PATCH 2/2] update all concoct modules --- modules.json | 8 ++++---- modules/nf-core/concoct/concoctcoveragetable/main.nf | 4 ++-- modules/nf-core/concoct/cutupfasta/main.nf | 4 ++-- modules/nf-core/concoct/extractfastabins/main.nf | 4 ++-- modules/nf-core/concoct/mergecutupclustering/main.nf | 4 ++-- 5 files changed, 12 insertions(+), 12 deletions(-) diff --git a/modules.json b/modules.json index 77c1b751..fe9bff05 100644 --- a/modules.json +++ b/modules.json @@ -58,22 +58,22 @@ }, "concoct/concoctcoveragetable": { "branch": "master", - "git_sha": "911696ea0b62df80e900ef244d7867d177971f73", + "git_sha": "36aa9d3ce6561d9bd5c240bcf82fe109af543c0d", "installed_by": ["fasta_binning_concoct"] }, "concoct/cutupfasta": { "branch": "master", - "git_sha": "911696ea0b62df80e900ef244d7867d177971f73", + "git_sha": "36aa9d3ce6561d9bd5c240bcf82fe109af543c0d", "installed_by": ["fasta_binning_concoct"] }, "concoct/extractfastabins": { "branch": "master", - "git_sha": "911696ea0b62df80e900ef244d7867d177971f73", + "git_sha": "36aa9d3ce6561d9bd5c240bcf82fe109af543c0d", "installed_by": ["fasta_binning_concoct"] }, "concoct/mergecutupclustering": { "branch": "master", - "git_sha": "911696ea0b62df80e900ef244d7867d177971f73", + "git_sha": "36aa9d3ce6561d9bd5c240bcf82fe109af543c0d", "installed_by": ["fasta_binning_concoct"] }, "custom/dumpsoftwareversions": { diff --git a/modules/nf-core/concoct/concoctcoveragetable/main.nf b/modules/nf-core/concoct/concoctcoveragetable/main.nf index 1833fb67..21f0f218 100644 --- a/modules/nf-core/concoct/concoctcoveragetable/main.nf +++ b/modules/nf-core/concoct/concoctcoveragetable/main.nf @@ -5,8 +5,8 @@ process CONCOCT_CONCOCTCOVERAGETABLE { conda "bioconda::concoct=1.1.0" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/concoct:1.1.0--py38h7be5676_2': - 'biocontainers/concoct:1.1.0--py38h7be5676_2' }" + 'https://depot.galaxyproject.org/singularity/concoct:1.1.0--py311h245ed52_4': + 'biocontainers/concoct:1.1.0--py311h245ed52_4' }" input: tuple val(meta), path(bed), path(bamfiles), path(baifiles) diff --git a/modules/nf-core/concoct/cutupfasta/main.nf b/modules/nf-core/concoct/cutupfasta/main.nf index 8610bd53..dba2fc58 100644 --- a/modules/nf-core/concoct/cutupfasta/main.nf +++ b/modules/nf-core/concoct/cutupfasta/main.nf @@ -5,8 +5,8 @@ process CONCOCT_CUTUPFASTA { conda "bioconda::concoct=1.1.0" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/concoct:1.1.0--py38h7be5676_2': - 'biocontainers/concoct:1.1.0--py38h7be5676_2' }" + 'https://depot.galaxyproject.org/singularity/concoct:1.1.0--py311h245ed52_4': + 'biocontainers/concoct:1.1.0--py311h245ed52_4' }" input: tuple val(meta), path(fasta) diff --git a/modules/nf-core/concoct/extractfastabins/main.nf b/modules/nf-core/concoct/extractfastabins/main.nf index 0fe49b2f..102ea934 100644 --- a/modules/nf-core/concoct/extractfastabins/main.nf +++ b/modules/nf-core/concoct/extractfastabins/main.nf @@ -4,8 +4,8 @@ process CONCOCT_EXTRACTFASTABINS { conda "bioconda::concoct=1.1.0" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/concoct:1.1.0--py38h7be5676_2': - 'biocontainers/concoct:1.1.0--py38h7be5676_2' }" + 'https://depot.galaxyproject.org/singularity/concoct:1.1.0--py311h245ed52_4': + 'biocontainers/concoct:1.1.0--py311h245ed52_4' }" input: tuple val(meta), path(original_fasta), path(csv) diff --git a/modules/nf-core/concoct/mergecutupclustering/main.nf b/modules/nf-core/concoct/mergecutupclustering/main.nf index 74bbdafc..d95efde3 100644 --- a/modules/nf-core/concoct/mergecutupclustering/main.nf +++ b/modules/nf-core/concoct/mergecutupclustering/main.nf @@ -4,8 +4,8 @@ process CONCOCT_MERGECUTUPCLUSTERING { conda "bioconda::concoct=1.1.0" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/concoct:1.1.0--py38h7be5676_2': - 'biocontainers/concoct:1.1.0--py38h7be5676_2' }" + 'https://depot.galaxyproject.org/singularity/concoct:1.1.0--py311h245ed52_4': + 'biocontainers/concoct:1.1.0--py311h245ed52_4' }" input: tuple val(meta), path(clustering_csv)