From 9a8554de2c43b727bbe361ab4839514c3670de38 Mon Sep 17 00:00:00 2001 From: Florian De Temmerman Date: Mon, 18 Sep 2023 16:01:02 +0200 Subject: [PATCH] chore: update pixelator source to bioconda/biocontainers --- modules/local/pixelator/collect_metadata.nf | 5 ++--- modules/local/pixelator/list_options.nf | 6 +++--- modules/local/pixelator/single-cell/amplicon/main.nf | 6 +++--- modules/local/pixelator/single-cell/analysis/main.nf | 6 +++--- modules/local/pixelator/single-cell/annotate/main.nf | 6 +++--- modules/local/pixelator/single-cell/collapse/main.nf | 5 ++--- modules/local/pixelator/single-cell/demux/main.nf | 6 +++--- modules/local/pixelator/single-cell/graph/main.nf | 6 +++--- modules/local/pixelator/single-cell/qc/main.nf | 6 +++--- modules/local/pixelator/single-cell/report/main.nf | 6 +++--- 10 files changed, 28 insertions(+), 30 deletions(-) diff --git a/modules/local/pixelator/collect_metadata.nf b/modules/local/pixelator/collect_metadata.nf index 7de2b4d0..0fe8eb7d 100644 --- a/modules/local/pixelator/collect_metadata.nf +++ b/modules/local/pixelator/collect_metadata.nf @@ -8,9 +8,8 @@ process PIXELATOR_COLLECT_METADATA { label 'process_single' cache false - // TODO: Update once pixelator is public in bioconda - conda "local::pixelator=0.13.0" - container 'ghcr.io/pixelgentechnologies/pixelator:0.12.0' + conda "bioconda::pixelator=0.13.1" + container "biocontainers/pixelator:0.13.1" input: diff --git a/modules/local/pixelator/list_options.nf b/modules/local/pixelator/list_options.nf index 3eab7dd6..35582796 100644 --- a/modules/local/pixelator/list_options.nf +++ b/modules/local/pixelator/list_options.nf @@ -1,9 +1,9 @@ process PIXELATOR_LIST_OPTIONS { label 'process_single' - // TODO: Update once pixelator is public in bioconda - conda "local::pixelator=0.13.0" - container "ghcr.io/pixelgentechnologies/pixelator:0.13.0" + + conda "bioconda::pixelator=0.13.1" + container "biocontainers/pixelator:0.13.1" output: path "design_options.txt" , emit: designs diff --git a/modules/local/pixelator/single-cell/amplicon/main.nf b/modules/local/pixelator/single-cell/amplicon/main.nf index e63fd97a..712dd6d0 100644 --- a/modules/local/pixelator/single-cell/amplicon/main.nf +++ b/modules/local/pixelator/single-cell/amplicon/main.nf @@ -2,9 +2,9 @@ process PIXELATOR_AMPLICON { tag "$meta.id" label 'process_low' - // TODO: Update once pixelator is public in bioconda - conda "local::pixelator=0.13.0" - container "ghcr.io/pixelgentechnologies/pixelator:0.13.0" + + conda "bioconda::pixelator=0.13.1" + container "biocontainers/pixelator:0.13.1" input: tuple val(meta), path(reads) diff --git a/modules/local/pixelator/single-cell/analysis/main.nf b/modules/local/pixelator/single-cell/analysis/main.nf index 811a7a64..aa907662 100644 --- a/modules/local/pixelator/single-cell/analysis/main.nf +++ b/modules/local/pixelator/single-cell/analysis/main.nf @@ -2,9 +2,9 @@ process PIXELATOR_ANALYSIS { tag "$meta.id" label 'process_medium' - // TODO: Update once pixelator is public in bioconda - conda "local::pixelator=0.13.0" - container "ghcr.io/pixelgentechnologies/pixelator:0.13.0" + + conda "bioconda::pixelator=0.13.1" + container "biocontainers/pixelator:0.13.1" input: tuple val(meta), path(data) diff --git a/modules/local/pixelator/single-cell/annotate/main.nf b/modules/local/pixelator/single-cell/annotate/main.nf index da25a6ec..a211503f 100644 --- a/modules/local/pixelator/single-cell/annotate/main.nf +++ b/modules/local/pixelator/single-cell/annotate/main.nf @@ -2,9 +2,9 @@ process PIXELATOR_ANNOTATE { tag "$meta.id" label 'process_medium' - // TODO: Update once pixelator is public in bioconda - conda "local::pixelator=0.13.0" - container "ghcr.io/pixelgentechnologies/pixelator:0.13.0" + + conda "bioconda::pixelator=0.13.1" + container "biocontainers/pixelator:0.13.1" input: tuple val(meta), path(dataset), path(panel_file), val(panel) diff --git a/modules/local/pixelator/single-cell/collapse/main.nf b/modules/local/pixelator/single-cell/collapse/main.nf index d551b769..41aa7702 100644 --- a/modules/local/pixelator/single-cell/collapse/main.nf +++ b/modules/local/pixelator/single-cell/collapse/main.nf @@ -2,9 +2,8 @@ process PIXELATOR_COLLAPSE { tag "$meta.id" label 'process_medium' - // TODO: Update once pixelator is public in bioconda - conda "local::pixelator=0.13.0" - container "ghcr.io/pixelgentechnologies/pixelator:0.13.0" + conda "bioconda::pixelator=0.13.1" + container "biocontainers/pixelator:0.13.1" input: tuple val(meta), path(reads), path(panel_file), val(panel) diff --git a/modules/local/pixelator/single-cell/demux/main.nf b/modules/local/pixelator/single-cell/demux/main.nf index fb81f4c5..2da35be7 100644 --- a/modules/local/pixelator/single-cell/demux/main.nf +++ b/modules/local/pixelator/single-cell/demux/main.nf @@ -2,9 +2,9 @@ process PIXELATOR_DEMUX { tag "$meta.id" label 'process_medium' - // TODO: Update once pixelator is public in bioconda - conda "local::pixelator=0.13.0" - container "ghcr.io/pixelgentechnologies/pixelator:0.13.0" + + conda "bioconda::pixelator=0.13.1" + container "biocontainers/pixelator:0.13.1" input: tuple val(meta), path(reads), path(panel_file), val(panel) diff --git a/modules/local/pixelator/single-cell/graph/main.nf b/modules/local/pixelator/single-cell/graph/main.nf index ac9c8bf4..04d85e6e 100644 --- a/modules/local/pixelator/single-cell/graph/main.nf +++ b/modules/local/pixelator/single-cell/graph/main.nf @@ -2,9 +2,9 @@ process PIXELATOR_GRAPH { tag "$meta.id" label 'process_medium' - // TODO: Update once pixelator is public in bioconda - conda "local::pixelator=0.13.0" - container "ghcr.io/pixelgentechnologies/pixelator:0.13.0" + + conda "bioconda::pixelator=0.13.1" + container "biocontainers/pixelator:0.13.1" input: tuple val(meta), path(edge_list) diff --git a/modules/local/pixelator/single-cell/qc/main.nf b/modules/local/pixelator/single-cell/qc/main.nf index 52728577..b3888ef4 100644 --- a/modules/local/pixelator/single-cell/qc/main.nf +++ b/modules/local/pixelator/single-cell/qc/main.nf @@ -2,9 +2,9 @@ process PIXELATOR_QC { tag "$meta.id" label 'process_medium' - // TODO: Update once pixelator is public in bioconda - conda "local::pixelator=0.13.0" - container "ghcr.io/pixelgentechnologies/pixelator:0.13.0" + + conda "bioconda::pixelator=0.13.1" + container "biocontainers/pixelator:0.13.1" input: tuple val(meta), path(reads) diff --git a/modules/local/pixelator/single-cell/report/main.nf b/modules/local/pixelator/single-cell/report/main.nf index f7c081c3..eea3d8b8 100644 --- a/modules/local/pixelator/single-cell/report/main.nf +++ b/modules/local/pixelator/single-cell/report/main.nf @@ -2,9 +2,9 @@ process PIXELATOR_REPORT { tag "$meta.id" label 'process_low' - // TODO: Update once pixelator is public in bioconda - conda "local::pixelator=0.13.0" - container "ghcr.io/pixelgentechnologies/pixelator:0.13.0" + + conda "bioconda::pixelator=0.13.1" + container "biocontainers/pixelator:0.13.1" input: tuple val(meta), path(panel_file), val(panel)