diff --git a/modules.json b/modules.json index 113f5139f..67970abf1 100644 --- a/modules.json +++ b/modules.json @@ -90,9 +90,8 @@ }, "qualimap/rnaseq": { "branch": "master", - "git_sha": "4657d98bc9f565e067c4d924126ce107056f5e2f", - "installed_by": ["modules"], - "patch": "modules/nf-core/qualimap/rnaseq/qualimap-rnaseq.diff" + "git_sha": "3902a0cfeb7a4bc12872371d1bea93aba692243b", + "installed_by": ["modules"] }, "rsem/calculateexpression": { "branch": "master", diff --git a/modules/nf-core/qualimap/rnaseq/environment.yml b/modules/nf-core/qualimap/rnaseq/environment.yml new file mode 100644 index 000000000..590ae85f7 --- /dev/null +++ b/modules/nf-core/qualimap/rnaseq/environment.yml @@ -0,0 +1,7 @@ +name: qualimap_rnaseq +channels: + - conda-forge + - bioconda + - defaults +dependencies: + - bioconda::qualimap=2.3 diff --git a/modules/nf-core/qualimap/rnaseq/main.nf b/modules/nf-core/qualimap/rnaseq/main.nf index b8a370973..4411d8689 100644 --- a/modules/nf-core/qualimap/rnaseq/main.nf +++ b/modules/nf-core/qualimap/rnaseq/main.nf @@ -2,7 +2,7 @@ process QUALIMAP_RNASEQ { tag "$meta.id" label 'process_medium' - conda "bioconda::qualimap=2.3" + conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/qualimap:2.3--hdfd78af_0' : 'biocontainers/qualimap:2.3--hdfd78af_0' }" diff --git a/modules/nf-core/qualimap/rnaseq/meta.yml b/modules/nf-core/qualimap/rnaseq/meta.yml index 7738f08d8..6f766e4f5 100644 --- a/modules/nf-core/qualimap/rnaseq/meta.yml +++ b/modules/nf-core/qualimap/rnaseq/meta.yml @@ -50,3 +50,5 @@ output: pattern: "versions.yml" authors: - "@FriederikeHanssen" +maintainers: + - "@FriederikeHanssen" diff --git a/modules/nf-core/qualimap/rnaseq/qualimap-rnaseq.diff b/modules/nf-core/qualimap/rnaseq/qualimap-rnaseq.diff deleted file mode 100644 index 48f498081..000000000 --- a/modules/nf-core/qualimap/rnaseq/qualimap-rnaseq.diff +++ /dev/null @@ -1,19 +0,0 @@ -Changes in module 'nf-core/qualimap/rnaseq' ---- modules/nf-core/qualimap/rnaseq/main.nf -+++ modules/nf-core/qualimap/rnaseq/main.nf -@@ -2,10 +2,10 @@ - tag "$meta.id" - label 'process_medium' - -- conda "bioconda::qualimap=2.2.2d" -+ conda "bioconda::qualimap=2.3" - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? -- 'https://depot.galaxyproject.org/singularity/qualimap:2.2.2d--1' : -- 'biocontainers/qualimap:2.2.2d--1' }" -+ 'https://depot.galaxyproject.org/singularity/qualimap:2.3--hdfd78af_0' : -+ 'biocontainers/qualimap:2.3--hdfd78af_0' }" - - input: - tuple val(meta), path(bam) - -************************************************************