diff --git a/modules.json b/modules.json index 968eaf0..64ed110 100644 --- a/modules.json +++ b/modules.json @@ -22,7 +22,7 @@ }, "spaceranger/count": { "branch": "master", - "git_sha": "e89a3110141cdf77abd4fbc85cd0d7cb8f01b49b", + "git_sha": "3bd057bfdfb64578636ff3ae7f7cb8eeab3c0cb6", "installed_by": ["modules"] }, "untar": { diff --git a/modules/nf-core/spaceranger/count/main.nf b/modules/nf-core/spaceranger/count/main.nf index c0f10e5..cac83e0 100644 --- a/modules/nf-core/spaceranger/count/main.nf +++ b/modules/nf-core/spaceranger/count/main.nf @@ -10,7 +10,7 @@ process SPACERANGER_COUNT { path(probeset) output: - tuple val(meta), path("**/outs/**"), emit: outs + tuple val(meta), path("outs/**"), emit: outs path "versions.yml", emit: versions when: @@ -46,6 +46,7 @@ process SPACERANGER_COUNT { $alignment \\ $slidefile \\ $args + mv ${prefix}/outs outs cat <<-END_VERSIONS > versions.yml "${task.process}": @@ -58,10 +59,9 @@ process SPACERANGER_COUNT { if (workflow.profile.tokenize(',').intersect(['conda', 'mamba']).size() >= 1) { error "SPACERANGER_COUNT module does not support Conda. Please use Docker / Singularity / Podman instead." } - def prefix = task.ext.prefix ?: "${meta.id}" """ - mkdir -p "${prefix}/outs/" - touch ${prefix}/outs/fake_file.txt + mkdir -p outs/ + touch outs/fake_file.txt cat <<-END_VERSIONS > versions.yml "${task.process}": diff --git a/modules/nf-core/spaceranger/count/meta.yml b/modules/nf-core/spaceranger/count/meta.yml index 123c96c..167ac8c 100644 --- a/modules/nf-core/spaceranger/count/meta.yml +++ b/modules/nf-core/spaceranger/count/meta.yml @@ -1,7 +1,7 @@ --- # yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/yaml-schema.json name: "spaceranger_count" -description: Module to use the 10x Spaceranger pipeline to proces 10x spatial transcriptomics data +description: Module to use the 10x Space Ranger pipeline to process 10x spatial transcriptomics data keywords: - align - count @@ -70,7 +70,7 @@ input: pattern: "*.json" - reference: type: directory - description: Folder containing all the reference indices needed by Spaceranger + description: Folder containing all the reference indices needed by Space Ranger - probeset: type: file description: OPTIONAL - Probe set specification. @@ -83,8 +83,8 @@ output: e.g. [ id:'test', single_end:false ] - outs: type: file - description: Files containing the outputs of Cell Ranger, see official 10X Genomics documentation for a complete list - pattern: "${meta.id}/outs/*" + description: Files containing the outputs of Space Ranger, see official 10X Genomics documentation for a complete list + pattern: "outs/*" - versions: type: file description: File containing software versions