From d65d6cc4f32c51e9ed9310950ee1b01288978094 Mon Sep 17 00:00:00 2001 From: Felipe Marques de Almeida Date: Mon, 10 Jun 2024 07:28:22 +0000 Subject: [PATCH 1/8] add force / removal --- modules/local/QualityAssessment/quast.nf | 2 ++ 1 file changed, 2 insertions(+) diff --git a/modules/local/QualityAssessment/quast.nf b/modules/local/QualityAssessment/quast.nf index 4e920042..c17f581e 100644 --- a/modules/local/QualityAssessment/quast.nf +++ b/modules/local/QualityAssessment/quast.nf @@ -54,6 +54,7 @@ process quast { // any case """ # run quast + rm -rf ${assembler}/ quast.py \\ -o ${assembler} \\ -t $task.cpus \\ @@ -68,6 +69,7 @@ process quast { # run busco cp -r /opt/busco_db . busco \\ + -f \\ --tar \\ --download_path ./ \\ -i ${contigs} \\ From 597b2353f997196ca4d0d62de9ca5185755e62b8 Mon Sep 17 00:00:00 2001 From: Felipe Marques de Almeida Date: Sun, 21 Jul 2024 11:51:43 +0000 Subject: [PATCH 2/8] update changelog --- markdown/CHANGELOG.md | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/markdown/CHANGELOG.md b/markdown/CHANGELOG.md index 52d7476f..7d867ec6 100644 --- a/markdown/CHANGELOG.md +++ b/markdown/CHANGELOG.md @@ -2,6 +2,10 @@ The tracking for changes started in v2. +## dev + +* [#77](https://github.com/fmalmeida/MpGAP/issues/77) - Add cleanup to avoid `overwrite existing files` error in BUSCO when resuming a run. + ## v3.2 -- [2024-Mar-06] * Update unicyler to v0.5.0 From 8149ced07f54a47a8d73887e2b4d52e04cc5ddcd Mon Sep 17 00:00:00 2001 From: Felipe Marques de Almeida Date: Tue, 23 Jul 2024 16:51:32 +0000 Subject: [PATCH 3/8] update version and changelog --- .zenodo.json | 2 +- markdown/CHANGELOG.md | 7 ++++++- nextflow.config | 2 +- 3 files changed, 8 insertions(+), 3 deletions(-) diff --git a/.zenodo.json b/.zenodo.json index f30a0f78..c3b8143a 100644 --- a/.zenodo.json +++ b/.zenodo.json @@ -2,7 +2,7 @@ "description": "

MpGAP is built using Nextflow, a workflow tool to run tasks across multiple compute infrastructures in a very portable manner. It uses Docker/Singularity containers making installation trivial and results highly reproducible. It is an easy to use pipeline that adopts well known software for _de novo_ genome assembly of Illumina, Pacbio and Oxford Nanopore sequencing data through illumina only, long reads only or hybrid modes.

", "license": "other-open", "title": "fmalmeida/MpGAP: A generic multi-platform genome assembly pipeline", - "version": "v3.2", + "version": "v3.2.1", "upload_type": "software", "creators": [ { diff --git a/markdown/CHANGELOG.md b/markdown/CHANGELOG.md index 52d7476f..9b12ad71 100644 --- a/markdown/CHANGELOG.md +++ b/markdown/CHANGELOG.md @@ -2,7 +2,12 @@ The tracking for changes started in v2. -## v3.2 -- [2024-Mar-06] +## v3.2.1 + +* [#79](https://github.com/fmalmeida/MpGAP/issues/79) + * Add if-else in MultiQC module so that if Quast report has different set of columns, we print it all to avoid breaking. + +## v3.2.0 -- [2024-Mar-06] * Update unicyler to v0.5.0 * Adjust Pilon polishing module to select how many rounds of polishing to run. Default is 4. diff --git a/nextflow.config b/nextflow.config index 9f9c9c89..57ceb2d0 100644 --- a/nextflow.config +++ b/nextflow.config @@ -109,5 +109,5 @@ manifest { homePage = "https://github.com/fmalmeida/mpgap" mainScript = "main.nf" nextflowVersion = "!>=21.10.3" - version = "3.2" + version = "3.2.1" } \ No newline at end of file From da112c0ef497a2067aa651d58212a19a1c4ba3a1 Mon Sep 17 00:00:00 2001 From: Felipe Marques de Almeida Date: Tue, 23 Jul 2024 16:54:15 +0000 Subject: [PATCH 4/8] add 'else' snippet --- modules/local/QualityAssessment/multiqc.nf | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/modules/local/QualityAssessment/multiqc.nf b/modules/local/QualityAssessment/multiqc.nf index 8869b88f..b5ed7af0 100644 --- a/modules/local/QualityAssessment/multiqc.nf +++ b/modules/local/QualityAssessment/multiqc.nf @@ -31,7 +31,8 @@ process multiqc { echo \"\" >> ASSEMBLY_SUMMARY.txt echo \"## Main QUAST statistics\" >> ASSEMBLY_SUMMARY.txt echo \"\" >> ASSEMBLY_SUMMARY.txt - csvtk cut -t -f 1,14,15,16,17,18,22,27,28,31 multiqc_data/multiqc_quast.txt | csvtk -t pretty >> ASSEMBLY_SUMMARY.txt + csvtk cut -t -f 1,14,15,16,17,18,22,27,28,31 multiqc_data/multiqc_quast.txt | csvtk -t pretty >> ASSEMBLY_SUMMARY.txt || \ + csvtk -t pretty multiqc_data/multiqc_quast.txt >> ASSEMBLY_SUMMARY.txt echo \"\" >> ASSEMBLY_SUMMARY.txt echo \"## Main BUSCO statistics\" >> ASSEMBLY_SUMMARY.txt echo \"\" >> ASSEMBLY_SUMMARY.txt From a20dcc4ff43f54952d7d81ec72d876ae5cb44d26 Mon Sep 17 00:00:00 2001 From: Felipe Marques de Almeida Date: Tue, 23 Jul 2024 17:46:57 +0000 Subject: [PATCH 5/8] get all other columns but the mapping ones in case they are not available --- modules/local/QualityAssessment/multiqc.nf | 8 ++++++-- 1 file changed, 6 insertions(+), 2 deletions(-) diff --git a/modules/local/QualityAssessment/multiqc.nf b/modules/local/QualityAssessment/multiqc.nf index b5ed7af0..0eec5127 100644 --- a/modules/local/QualityAssessment/multiqc.nf +++ b/modules/local/QualityAssessment/multiqc.nf @@ -31,8 +31,12 @@ process multiqc { echo \"\" >> ASSEMBLY_SUMMARY.txt echo \"## Main QUAST statistics\" >> ASSEMBLY_SUMMARY.txt echo \"\" >> ASSEMBLY_SUMMARY.txt - csvtk cut -t -f 1,14,15,16,17,18,22,27,28,31 multiqc_data/multiqc_quast.txt | csvtk -t pretty >> ASSEMBLY_SUMMARY.txt || \ - csvtk -t pretty multiqc_data/multiqc_quast.txt >> ASSEMBLY_SUMMARY.txt + csvtk cut -t \\ + -f 1,14,15,16,17,18,22,27,28,31 \\ + multiqc_data/multiqc_quast.txt | csvtk -t pretty >> ASSEMBLY_SUMMARY.txt || \ + cat multiqc_data/multiqc_quast.txt | \\ + csvtk cut -t \\ + -f Sample,#\ contigs,Largest\ contig,Total\ length,GC\ (%),N50,L90,#\ predicted\ rRNA\ genes | csvtk -t pretty >> ASSEMBLY_SUMMARY.txt echo \"\" >> ASSEMBLY_SUMMARY.txt echo \"## Main BUSCO statistics\" >> ASSEMBLY_SUMMARY.txt echo \"\" >> ASSEMBLY_SUMMARY.txt From c3214141f544c0d48d350e031bfec32aa7fc7048 Mon Sep 17 00:00:00 2001 From: Felipe Marques de Almeida Date: Tue, 23 Jul 2024 17:48:46 +0000 Subject: [PATCH 6/8] fix col selector --- modules/local/QualityAssessment/multiqc.nf | 8 ++------ 1 file changed, 2 insertions(+), 6 deletions(-) diff --git a/modules/local/QualityAssessment/multiqc.nf b/modules/local/QualityAssessment/multiqc.nf index 0eec5127..ea957aea 100644 --- a/modules/local/QualityAssessment/multiqc.nf +++ b/modules/local/QualityAssessment/multiqc.nf @@ -31,12 +31,8 @@ process multiqc { echo \"\" >> ASSEMBLY_SUMMARY.txt echo \"## Main QUAST statistics\" >> ASSEMBLY_SUMMARY.txt echo \"\" >> ASSEMBLY_SUMMARY.txt - csvtk cut -t \\ - -f 1,14,15,16,17,18,22,27,28,31 \\ - multiqc_data/multiqc_quast.txt | csvtk -t pretty >> ASSEMBLY_SUMMARY.txt || \ - cat multiqc_data/multiqc_quast.txt | \\ - csvtk cut -t \\ - -f Sample,#\ contigs,Largest\ contig,Total\ length,GC\ (%),N50,L90,#\ predicted\ rRNA\ genes | csvtk -t pretty >> ASSEMBLY_SUMMARY.txt + csvtk cut -t -f 1,14,15,16,17,18,22,27,28,31 multiqc_data/multiqc_quast.txt | csvtk -t pretty >> ASSEMBLY_SUMMARY.txt || \ + csvtk cut -t -f "Sample,# contigs,Largest contig,Total length,GC (%),N50,L90,# predicted rRNA genes" multiqc_data/multiqc_quast.txt | csvtk -t pretty >> ASSEMBLY_SUMMARY.txt echo \"\" >> ASSEMBLY_SUMMARY.txt echo \"## Main BUSCO statistics\" >> ASSEMBLY_SUMMARY.txt echo \"\" >> ASSEMBLY_SUMMARY.txt From 5ba04f89c38733dd92a6b8a37bd5a7e3a064562b Mon Sep 17 00:00:00 2001 From: Felipe Marques de Almeida Date: Tue, 23 Jul 2024 17:50:43 +0000 Subject: [PATCH 7/8] update changelog --- markdown/CHANGELOG.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/markdown/CHANGELOG.md b/markdown/CHANGELOG.md index 9b12ad71..d8be2487 100644 --- a/markdown/CHANGELOG.md +++ b/markdown/CHANGELOG.md @@ -5,7 +5,7 @@ The tracking for changes started in v2. ## v3.2.1 * [#79](https://github.com/fmalmeida/MpGAP/issues/79) - * Add if-else in MultiQC module so that if Quast report has different set of columns, we print it all to avoid breaking. + * Add if-else in MultiQC module so that if Quast report has different set of columns. ## v3.2.0 -- [2024-Mar-06] From 8cbde6c65290110d403bf51a0d073e7eaa11ef27 Mon Sep 17 00:00:00 2001 From: Felipe Marques de Almeida Date: Tue, 23 Jul 2024 16:13:42 -0400 Subject: [PATCH 8/8] Update CHANGELOG.md --- markdown/CHANGELOG.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/markdown/CHANGELOG.md b/markdown/CHANGELOG.md index 03aa2d4a..365051dd 100644 --- a/markdown/CHANGELOG.md +++ b/markdown/CHANGELOG.md @@ -2,7 +2,7 @@ The tracking for changes started in v2. -## v3.2.1 +## v3.2.1 -- [2024-Jul-24] * [#77](https://github.com/fmalmeida/MpGAP/issues/77) * Add cleanup to avoid `overwrite existing files` error in BUSCO when resuming a run.