From decc69db5e943b0e9c5bfd9fa764bc18b3ca1e0e Mon Sep 17 00:00:00 2001 From: MaxUlysse Date: Mon, 10 Feb 2020 10:43:30 +0100 Subject: [PATCH 1/2] fix issue with downloading arriba references --- download-references.nf | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/download-references.nf b/download-references.nf index 355d7bb4..52c9fc63 100644 --- a/download-references.nf +++ b/download-references.nf @@ -117,7 +117,7 @@ process download_arriba { script: """ wget -N https://github.com/suhrig/arriba/releases/download/v1.1.0/arriba_v1.1.0.tar.gz -O arriba_v1.1.0.tar.gz - tar -xvzf arriba_v1.1.0.tar.gz && mv arriba_v1.1.0/database/* . && gunzip * && rm -rf arriba_* + tar -xvzf arriba_v1.1.0.tar.gz && mv arriba_v1.1.0/database/* . && gunzip *.gz && rm -rf arriba_* """ } From e8320fa7fb64d229da75f3cbe2a6dba19de6f99d Mon Sep 17 00:00:00 2001 From: MaxUlysse Date: Mon, 10 Feb 2020 10:48:04 +0100 Subject: [PATCH 2/2] fix params --- download-singularity-img.nf | 14 +++++++------- 1 file changed, 7 insertions(+), 7 deletions(-) diff --git a/download-singularity-img.nf b/download-singularity-img.nf index 2b1b5303..37de4428 100644 --- a/download-singularity-img.nf +++ b/download-singularity-img.nf @@ -57,13 +57,13 @@ if (params.help) exit 0, helpMessage() params.running_tools = ["nf-core/rnafusion/${workflow.manifest.version}"] if (!params.outdir) exit 1, "Output directory not specified!" -if (params.arriba || download_all) params.running_tools.add("Arriba") -if (params.star_fusion || download_all) params.running_tools.add("STAR-Fusion") -if (params.fusioncatcher || download_all) params.running_tools.add("Fusioncatcher") -if (params.ericscript || download_all) params.running_tools.add("Ericscript") -if (params.pizzly || download_all) params.running_tools.add("Pizzly") -if (params.squid || download_all) params.running_tools.add("Squid") -if (params.fusion_inspector || download_all) params.running_tools.add("Fusion-Inspector") +if (params.arriba || params.download_all) params.running_tools.add("Arriba") +if (params.star_fusion || params.download_all) params.running_tools.add("STAR-Fusion") +if (params.fusioncatcher || params.download_all) params.running_tools.add("Fusioncatcher") +if (params.ericscript || params.download_all) params.running_tools.add("Ericscript") +if (params.pizzly || params.download_all) params.running_tools.add("Pizzly") +if (params.squid || params.download_all) params.running_tools.add("Squid") +if (params.fusion_inspector || params.download_all) params.running_tools.add("Fusion-Inspector") // Header log info log.info nfcoreHeader()