From 88b7f037019155cc88064627052aafb9b34e55f4 Mon Sep 17 00:00:00 2001 From: asp8200 Date: Tue, 12 Sep 2023 08:55:18 +0000 Subject: [PATCH 1/3] New version of BCFTOOLS_SORT-module with '--temp-dir .' added as option for 'bcftools sort' --- modules.json | 2 +- modules/nf-core/bcftools/sort/main.nf | 1 + 2 files changed, 2 insertions(+), 1 deletion(-) diff --git a/modules.json b/modules.json index 6f13ad15dd..290bb1c2a0 100644 --- a/modules.json +++ b/modules.json @@ -22,7 +22,7 @@ }, "bcftools/sort": { "branch": "master", - "git_sha": "911696ea0b62df80e900ef244d7867d177971f73", + "git_sha": "d6d112a1af2ee8c97fc1932df008183341e7d8fe", "installed_by": ["modules"] }, "bcftools/stats": { diff --git a/modules/nf-core/bcftools/sort/main.nf b/modules/nf-core/bcftools/sort/main.nf index ef41fd25da..702d510f37 100644 --- a/modules/nf-core/bcftools/sort/main.nf +++ b/modules/nf-core/bcftools/sort/main.nf @@ -30,6 +30,7 @@ process BCFTOOLS_SORT { bcftools \\ sort \\ --output ${prefix}.${extension} \\ + --temp-dir . \\ $args \\ $vcf From ee9e5616230067d88d3c3264b28017f7fb2bbea4 Mon Sep 17 00:00:00 2001 From: asp8200 Date: Tue, 12 Sep 2023 09:13:51 +0000 Subject: [PATCH 2/3] Update changelog --- CHANGELOG.md | 1 + 1 file changed, 1 insertion(+) diff --git a/CHANGELOG.md b/CHANGELOG.md index 986b0c9441..4c006d6cc9 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -64,6 +64,7 @@ Rapaselet is a delta formed by the Rapaätno river between the Bielloriehppe mas - [#1216](https://github.com/nf-core/sarek/pull/1216) - Better test coverage for variant calling `*_all` subworkflows - [#1217](https://github.com/nf-core/sarek/pull/1217) - Fix `groupTuple` statement for mutect2 tumor_only subworkflows - [#1220](https://github.com/nf-core/sarek/pull/1220) - Fix channel and meta logic for `joint_mutect2` feature +- [#1224](https://github.com/nf-core/sarek/pull/1224) - New version of BCFTOOLS_SORT-module with `--temp-dir .` added as option for `bcftools sort`. The tool itself was not updated. The addition of the option was required in order to run the module with Singularity. ### Dependencies From 87d74e8681a92dd441ad92f275164f6a580f215d Mon Sep 17 00:00:00 2001 From: Anders Sune Pedersen <37172585+asp8200@users.noreply.github.com> Date: Tue, 12 Sep 2023 11:28:01 +0200 Subject: [PATCH 3/3] Update CHANGELOG.md Co-authored-by: Maxime U Garcia --- CHANGELOG.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index c0f5cafc5b..aae9f7c6b6 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -64,7 +64,7 @@ Rapaselet is a delta formed by the Rapaätno river between the Bielloriehppe mas - [#1216](https://github.com/nf-core/sarek/pull/1216) - Better test coverage for variant calling `*_all` subworkflows - [#1217](https://github.com/nf-core/sarek/pull/1217) - Fix `groupTuple` statement for mutect2 tumor_only subworkflows - [#1220](https://github.com/nf-core/sarek/pull/1220) - Fix channel and meta logic for `joint_mutect2` feature -- [#1224](https://github.com/nf-core/sarek/pull/1224) - New version of BCFTOOLS_SORT-module with `--temp-dir .` added as option for `bcftools sort`. The tool itself was not updated. The addition of the option was required in order to run the module with Singularity. +- [#1224](https://github.com/nf-core/sarek/pull/1224) - Update BCFTOOLS_SORT module with `--temp-dir .` added as option, which was required for Singularity - [#1225](https://github.com/nf-core/sarek/pull/1225) - Better test coverage for all tests ### Dependencies