From 967d21d072c4e38298640a31217c41a9982ee660 Mon Sep 17 00:00:00 2001 From: DLBPointon Date: Tue, 19 Sep 2023 12:54:10 +0100 Subject: [PATCH] Attempting to fix testing --- modules/local/bamtobed_sort.nf | 2 +- modules/local/cram_filter_align_bwamem2_fixmate_sort.nf | 2 +- modules/local/extract_repeat.nf | 2 +- modules/local/findhalfcoverage.nf | 2 +- modules/local/graphoverallcoverage.nf | 2 +- 5 files changed, 5 insertions(+), 5 deletions(-) diff --git a/modules/local/bamtobed_sort.nf b/modules/local/bamtobed_sort.nf index 3554159..7260ac4 100755 --- a/modules/local/bamtobed_sort.nf +++ b/modules/local/bamtobed_sort.nf @@ -4,7 +4,7 @@ process BAMTOBED_SORT { container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/mulled-v2-9d3a458f6420e5712103ae2af82c94d26d63f059:60b54b43045e8cf39ba307fd683c69d4c57240ce-0' : - 'quay.io/biocontainers/mulled-v2-9d3a458f6420e5712103ae2af82c94d26d63f059:60b54b43045e8cf39ba307fd683c69d4c57240ce-0' }" + 'biocontainers/mulled-v2-9d3a458f6420e5712103ae2af82c94d26d63f059:60b54b43045e8cf39ba307fd683c69d4c57240ce-0' }" input: tuple val(meta), path(bam) diff --git a/modules/local/cram_filter_align_bwamem2_fixmate_sort.nf b/modules/local/cram_filter_align_bwamem2_fixmate_sort.nf index d275dd4..3f15dfc 100755 --- a/modules/local/cram_filter_align_bwamem2_fixmate_sort.nf +++ b/modules/local/cram_filter_align_bwamem2_fixmate_sort.nf @@ -4,7 +4,7 @@ process CRAM_FILTER_ALIGN_BWAMEM2_FIXMATE_SORT { container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/mulled-v2-50d89b457e04ed90fa0cbf8ebc3ae1b9ffbc836b:caf993da1689e8d42f5e4c113ffc9ef81d26df96-0' : - 'quay.io/biocontainers/mulled-v2-50d89b457e04ed90fa0cbf8ebc3ae1b9ffbc836b:caf993da1689e8d42f5e4c113ffc9ef81d26df96-0' }" + 'biocontainers/mulled-v2-50d89b457e04ed90fa0cbf8ebc3ae1b9ffbc836b:caf993da1689e8d42f5e4c113ffc9ef81d26df96-0' }" input: tuple val(meta), path(cramfile), path(cramindex), val(from), val(to), val(base), val(chunkid), val(rglines), val(bwaprefix) diff --git a/modules/local/extract_repeat.nf b/modules/local/extract_repeat.nf index 13f2898..8258a30 100755 --- a/modules/local/extract_repeat.nf +++ b/modules/local/extract_repeat.nf @@ -5,7 +5,7 @@ process EXTRACT_REPEAT { conda "conda-forge::perl=5.26.2" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/perl:5.26.2' : - 'quay.io/biocontainers/perl:5.26.2' }" + 'biocontainers/perl:5.26.2' }" input: tuple val( meta ), path( file ) diff --git a/modules/local/findhalfcoverage.nf b/modules/local/findhalfcoverage.nf index 5659281..529f543 100755 --- a/modules/local/findhalfcoverage.nf +++ b/modules/local/findhalfcoverage.nf @@ -5,7 +5,7 @@ process FINDHALFCOVERAGE { conda "conda-forge::python=3.9" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/python:3.9' : - 'quay.io/biocontainers/python:3.9' }" + 'biocontainers/python:3.9' }" input: tuple val(meta), path(bedfile) diff --git a/modules/local/graphoverallcoverage.nf b/modules/local/graphoverallcoverage.nf index 3d9b054..217f1f5 100755 --- a/modules/local/graphoverallcoverage.nf +++ b/modules/local/graphoverallcoverage.nf @@ -5,7 +5,7 @@ process GRAPHOVERALLCOVERAGE { conda "conda-forge::perl=5.26.2" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/perl:5.26.2' : - 'quay.io/biocontainers/perl:5.26.2' }" + 'biocontainers/perl:5.26.2' }" input: tuple val(meta), path(bed)