From 1ef93a0b4f20cadb09a361975090b39d313ff9e9 Mon Sep 17 00:00:00 2001 From: "James A. Fellows Yates" Date: Tue, 10 Dec 2024 12:59:09 +0100 Subject: [PATCH 1/2] Fix input to single-end MEGAHIT runs --- CHANGELOG.md | 1 + modules.json | 2 +- modules/nf-core/megahit/main.nf | 2 +- 3 files changed, 3 insertions(+), 2 deletions(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index 24ab3868..be12ee70 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -17,6 +17,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 - [#716](https://github.com/nf-core/mag/pull/692) - Make short read processing a subworkflow (added by @muabnezor) - [#708](https://github.com/nf-core/mag/pull/708) - Fixed channel passed as GUNC input (added by @dialvarezs) +- [#727](https://github.com/nf-core/mag/pull/727) - Fixed misspecified multi-FASTQ input for single-end data in MEGAHIT (reported by John Richards, fix by @jfy133) ### `Dependencies` diff --git a/modules.json b/modules.json index d56420d0..3204d5bf 100644 --- a/modules.json +++ b/modules.json @@ -179,7 +179,7 @@ }, "megahit": { "branch": "master", - "git_sha": "7755db15e36b30da564cd67fffdfe18a255092aa", + "git_sha": "9142b390538283705c084e4d612170972ff60326", "installed_by": ["modules"] }, "metabat2/jgisummarizebamcontigdepths": { diff --git a/modules/nf-core/megahit/main.nf b/modules/nf-core/megahit/main.nf index f6e50f94..db061242 100644 --- a/modules/nf-core/megahit/main.nf +++ b/modules/nf-core/megahit/main.nf @@ -25,7 +25,7 @@ process MEGAHIT { def args = task.ext.args ?: '' def args2 = task.ext.args2 ?: '' def prefix = task.ext.prefix ?: "${meta.id}" - def reads_command = meta.single_end || !reads2 ? "-r ${reads1}" : "-1 ${reads1.join(',')} -2 ${reads2.join(',')}" + def reads_command = meta.single_end || !reads2 ? "-r ${reads1.join(',')}" : "-1 ${reads1.join(',')} -2 ${reads2.join(',')}" """ megahit \\ ${reads_command} \\ From 3020a1c0968e17af956650904ad986a51e999b21 Mon Sep 17 00:00:00 2001 From: "James A. Fellows Yates" Date: Tue, 10 Dec 2024 13:00:02 +0100 Subject: [PATCH 2/2] Update CHANGELOG.md --- CHANGELOG.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index be12ee70..ad4510bb 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -17,7 +17,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 - [#716](https://github.com/nf-core/mag/pull/692) - Make short read processing a subworkflow (added by @muabnezor) - [#708](https://github.com/nf-core/mag/pull/708) - Fixed channel passed as GUNC input (added by @dialvarezs) -- [#727](https://github.com/nf-core/mag/pull/727) - Fixed misspecified multi-FASTQ input for single-end data in MEGAHIT (reported by John Richards, fix by @jfy133) +- [#729](https://github.com/nf-core/mag/pull/729) - Fixed misspecified multi-FASTQ input for single-end data in MEGAHIT (reported by John Richards, fix by @jfy133) ### `Dependencies`