From 19b55fc67cd61ddbffb2211636366a0bf8012213 Mon Sep 17 00:00:00 2001 From: sruthipsuresh <sruthiprabhasuresh@gmail.com> Date: Wed, 27 Jan 2021 08:09:49 -0600 Subject: [PATCH] Fixed intersect, complement indentation issues --- software/bedtools/complement/main.nf | 18 +++++++++----- software/bedtools/complement/meta.yml | 1 - software/bedtools/intersect/main.nf | 34 +++++++++++++-------------- software/bedtools/intersect/meta.yml | 11 +++++---- 4 files changed, 36 insertions(+), 28 deletions(-) diff --git a/software/bedtools/complement/main.nf b/software/bedtools/complement/main.nf index 7dce461d..850be828 100644 --- a/software/bedtools/complement/main.nf +++ b/software/bedtools/complement/main.nf @@ -26,10 +26,16 @@ process BEDTOOLS_COMPLEMENT { path "*.version.txt" , emit: version script: - def software = getSoftwareName(task.process) - def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}" - """ - bedtools complement -i $beds -g $sizes ${options.args} > ${prefix}.complement.bed - bedtools --version | sed -e "s/bedtools v//g" > ${software}.version.txt - """ + def software = getSoftwareName(task.process) + def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}" + """ + bedtools \\ + complement \\ + -i $beds \\ + -g $sizes \\ + $options.args \\ + > ${prefix}.complement.bed + + bedtools --version | sed -e "s/bedtools v//g" > ${software}.version.txt + """ } diff --git a/software/bedtools/complement/meta.yml b/software/bedtools/complement/meta.yml index a4cd9eee..1ab533ac 100644 --- a/software/bedtools/complement/meta.yml +++ b/software/bedtools/complement/meta.yml @@ -8,7 +8,6 @@ tools: description: | A set of tools for genomic analysis tasks, specifically enabling genome arithmetic (merge, count, complement) on various file types. documentation: https://bedtools.readthedocs.io/en/latest/content/tools/complement.html - params: - outdir: type: string diff --git a/software/bedtools/intersect/main.nf b/software/bedtools/intersect/main.nf index 2dd6f2d8..16c11da1 100644 --- a/software/bedtools/intersect/main.nf +++ b/software/bedtools/intersect/main.nf @@ -20,22 +20,22 @@ process BEDTOOLS_INTERSECT { input: tuple val(meta), path(bed1), path(bed2) - - output: - tuple val(meta), path("*.intersect.bed"), emit: bed - path "*.version.txt", emit: version - script: // TODO change script to account for multiple possible intersections - def software = getSoftwareName(task.process) - def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}" - """ - bedtools \\ - intersect \\ - -a ${bed1} \\ - -b ${bed2} \\ - $options.args \\ - > ${prefix}.intersect.bed - - bedtools --version | sed -e "s/bedtools v//g" > ${software}.version.txt - """ + output: + tuple val(meta), path("*.intersect.bed"), emit: bed + path "*.version.txt", emit: version + + script: + def software = getSoftwareName(task.process) + def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}" + """ + bedtools \\ + intersect \\ + -a ${bed1} \\ + -b ${bed2} \\ + $options.args \\ + > ${prefix}.intersect.bed + + bedtools --version | sed -e "s/bedtools v//g" > ${software}.version.txt + """ } diff --git a/software/bedtools/intersect/meta.yml b/software/bedtools/intersect/meta.yml index b6e5e91c..03b00c80 100644 --- a/software/bedtools/intersect/meta.yml +++ b/software/bedtools/intersect/meta.yml @@ -9,7 +9,6 @@ tools: description: | A set of tools for genomic analysis tasks, specifically enabling genome arithmetic (merge, count, complement) on various file types. documentation: https://bedtools.readthedocs.io/en/latest/content/tools/intersect.html - params: - outdir: type: string @@ -33,10 +32,15 @@ input: description: | Groovy Map containing sample information e.g. [ id:'test', single_end:false ] - - bed: + - bed1: type: file - description: List of bed files + description: Bed file, each feature in 1 is compared to 2 in search of overlaps pattern: "*.{bed}" + - bed2: + type: file + description: Second bed file, used to compare to 1. + pattern: "*.{bed}" + output: - meta: type: map @@ -52,7 +56,6 @@ output: type: file description: File containing software version pattern: "*.{version.txt}" - authors: -"@Emiller88" -"@sruthipsuresh"