diff --git a/modules/nf-core/phantompeakqualtools/environment.yml b/modules/nf-core/phantompeakqualtools/environment.yml index 095b7b4b..8967e158 100644 --- a/modules/nf-core/phantompeakqualtools/environment.yml +++ b/modules/nf-core/phantompeakqualtools/environment.yml @@ -1,9 +1,7 @@ --- # yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json -name: "phantompeakqualtools" channels: - conda-forge - bioconda - - defaults dependencies: - "bioconda::phantompeakqualtools=1.2.2" diff --git a/modules/nf-core/phantompeakqualtools/main.nf b/modules/nf-core/phantompeakqualtools/main.nf index f0f7dc63..e1f22699 100644 --- a/modules/nf-core/phantompeakqualtools/main.nf +++ b/modules/nf-core/phantompeakqualtools/main.nf @@ -5,7 +5,7 @@ process PHANTOMPEAKQUALTOOLS { // WARN: Version information not provided by tool on CLI. Please update version string below when bumping container versions. conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'oras://community.wave.seqera.io/library/phantompeakqualtools:1.2.2--50be7727b2a72700' : + 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/4a/4a1cddfad5b503ee347cc5de17d172e1876c547fca00aa844559c9e764fb400f/data' : 'community.wave.seqera.io/library/phantompeakqualtools:1.2.2--f8026fe2526a5e18' }" input: diff --git a/modules/nf-core/phantompeakqualtools/meta.yml b/modules/nf-core/phantompeakqualtools/meta.yml index 276f6fdd..d9c7cdac 100644 --- a/modules/nf-core/phantompeakqualtools/meta.yml +++ b/modules/nf-core/phantompeakqualtools/meta.yml @@ -19,40 +19,55 @@ tools: tool_dev_url: "https://github.com/kundajelab/phantompeakqualtools" doi: "10.1101/gr.136184.111" licence: ["BSD-3-clause"] + identifier: biotools:phantompeakqualtools input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - bam: - type: file - description: BAM/CRAM/SAM file - pattern: "*.{bam,cram,sam}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - bam: + type: file + description: BAM/CRAM/SAM file + pattern: "*.{bam,cram,sam}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - spp: - type: file - description: | - A ChIP-Seq Processing Pipeline file containing - peakshift/phantomPeak results - pattern: "*.{out}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.out": + type: file + description: | + A ChIP-Seq Processing Pipeline file containing + peakshift/phantomPeak results + pattern: "*.{out}" - pdf: - type: file - description: A pdf containing save cross-correlation plots - pattern: "*.{pdf}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.pdf": + type: file + description: A pdf containing save cross-correlation plots + pattern: "*.{pdf}" - rdata: - type: file - description: Rdata file containing the R session - pattern: "*.{Rdata}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.Rdata": + type: file + description: Rdata file containing the R session + pattern: "*.{Rdata}" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@drpatelh" - "@edmundmiller"