From 0b80d1eb6e9c3eb9366a80edde50b61822d39bdc Mon Sep 17 00:00:00 2001 From: Emilio Garcia Date: Tue, 1 Aug 2023 16:28:14 +0200 Subject: [PATCH] Using gzip until Docker image gets updated As per https://github.com/voutcn/megahit/pull/360 pigz is not currently installed in the MEGAHIT biocontainer images (singularity: https://depot.galaxyproject.org/singularity/megahit:1.2.9--h5b5514e_2 - docker: quay.io/biocontainers/megahit:1.2.9--h5b5514e_3). Therefore, the NF-Core module will fail to compress the contigs using pigz. This commit resolves the described fix. --- modules/nf-core/megahit/main.nf | 10 ++-------- 1 file changed, 2 insertions(+), 8 deletions(-) diff --git a/modules/nf-core/megahit/main.nf b/modules/nf-core/megahit/main.nf index ac250a860f0..42aece36ff2 100644 --- a/modules/nf-core/megahit/main.nf +++ b/modules/nf-core/megahit/main.nf @@ -33,10 +33,7 @@ process MEGAHIT { $args \\ --out-prefix $prefix - pigz \\ - --no-name \\ - -p $task.cpus \\ - $args2 \\ + gzip \\ megahit_out/*.fa \\ megahit_out/intermediate_contigs/*.fa @@ -54,10 +51,7 @@ process MEGAHIT { $args \\ --out-prefix $prefix - pigz \\ - --no-name \\ - -p $task.cpus \\ - $args2 \\ + gzip \\ megahit_out/*.fa \\ megahit_out/intermediate_contigs/*.fa