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..d8be2487 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. + +## 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/modules/local/QualityAssessment/multiqc.nf b/modules/local/QualityAssessment/multiqc.nf index 8869b88f..ea957aea 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 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 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