From 9f61438ff74150d3b6ecb1b06c5b7c27a353d277 Mon Sep 17 00:00:00 2001 From: Emilio Garcia Date: Tue, 1 Aug 2023 14:51:38 +0200 Subject: [PATCH 1/3] Update MEGAHIT container URLs --- modules/nf-core/megahit/main.nf | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/modules/nf-core/megahit/main.nf b/modules/nf-core/megahit/main.nf index d9dbf350717..ac250a860f0 100644 --- a/modules/nf-core/megahit/main.nf +++ b/modules/nf-core/megahit/main.nf @@ -4,8 +4,8 @@ process MEGAHIT { conda "bioconda::megahit=1.2.9 conda-forge::pigz=2.6" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/mulled-v2-0f92c152b180c7cd39d9b0e6822f8c89ccb59c99:8ec213d21e5d03f9db54898a2baeaf8ec729b447-0' : - 'biocontainers/mulled-v2-0f92c152b180c7cd39d9b0e6822f8c89ccb59c99:8ec213d21e5d03f9db54898a2baeaf8ec729b447-0' }" + 'https://depot.galaxyproject.org/singularity/megahit:1.2.9--h5b5514e_2' : + 'quay.io/biocontainers/megahit:1.2.9--h5b5514e_3' }" input: tuple val(meta), path(reads) From 0b80d1eb6e9c3eb9366a80edde50b61822d39bdc Mon Sep 17 00:00:00 2001 From: Emilio Garcia Date: Tue, 1 Aug 2023 16:28:14 +0200 Subject: [PATCH 2/3] 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 \\ - $args2 \\ + gzip \\ megahit_out/*.fa \\ megahit_out/intermediate_contigs/*.fa From ec365b0cda0a775f1e2ac5eca29067007dc8d693 Mon Sep 17 00:00:00 2001 From: Emilio Garcia Date: Wed, 2 Aug 2023 22:37:07 +0200 Subject: [PATCH 3/3] Update modules/nf-core/megahit/main.nf Co-authored-by: Adam Talbot <12817534+adamrtalbot@users.noreply.github.com> --- modules/nf-core/megahit/main.nf | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/modules/nf-core/megahit/main.nf b/modules/nf-core/megahit/main.nf index 42aece36ff2..3a55d7ff76c 100644 --- a/modules/nf-core/megahit/main.nf +++ b/modules/nf-core/megahit/main.nf @@ -5,7 +5,7 @@ process MEGAHIT { conda "bioconda::megahit=1.2.9 conda-forge::pigz=2.6" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/megahit:1.2.9--h5b5514e_2' : - 'quay.io/biocontainers/megahit:1.2.9--h5b5514e_3' }" + 'biocontainers/megahit:1.2.9--h5b5514e_3' }" input: tuple val(meta), path(reads)