fix rseqc/junctionsaturation (#553)

* bump bcftools filter

* junctionsaturation meta.yml and test

* pytest config entry

* bump bcftools version down again

* fix test

* fix bcftools
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Kevin Menden 2021-07-02 13:31:09 +02:00 committed by GitHub
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commit b59e8054e4
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name: rseqc_junctionsaturation
description: compare detected splice junctions to reference gene model
keywords:
- junctions
- splicing
- rnaseq
tools:
- rseqc:
description: |
RSeQC package provides a number of useful modules that can comprehensively evaluate
high throughput sequence data especially RNA-seq data.
homepage: http://rseqc.sourceforge.net/
documentation: http://rseqc.sourceforge.net/
doi: 10.1093/bioinformatics/bts356
input:
- meta:
type: map
description: |
Groovy Map containing sample information
e.g. [ id:'test', single_end:false ]
- bam:
type: file
description: the alignment in bam format
pattern: "*.{bam}"
- bed:
type: file
description: a bed file for the reference gene model
pattern: "*.{bed}"
output:
- pdf:
type: file
description: Junction saturation report
pattern: "*.pdf"
- rscript:
type: file
description: Junction saturation R-script
pattern: "*.r"
- version:
type: file
description: File containing software version
pattern: "*.{version.txt}"
authors:
- "@drpatelh"
- "@kevinmenden"

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@ -603,6 +603,10 @@ rseqc/junctionannotation:
- software/rseqc/junctionannotation/**
- tests/software/rseqc/junctionannotation/**
rseqc/junctionsaturation:
- software/rseqc/junctionsaturation/**
- tests/software/rseqc/junctionsaturation/**
rseqc/readdistribution:
- software/rseqc/readdistribution/**
- tests/software/rseqc/readdistribution/**

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#!/usr/bin/env nextflow
nextflow.enable.dsl = 2
include { RSEQC_JUNCTIONSATURATION } from '../../../../software/rseqc/junctionsaturation/main.nf' addParams(options: [:])
workflow test_rseqc_junctionsaturation {
input = [
[ id:'test', single_end: false ], // meta map
file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true)
]
bed = file(params.test_data['sarscov2']['genome']['test_bed'], checkIfExists: true)
RSEQC_JUNCTIONSATURATION ( input, bed )
}

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- name: rseqc junctionsaturation test_rseqc_junctionsaturation
command: nextflow run tests/software/rseqc/junctionsaturation -entry test_rseqc_junctionsaturation -c tests/config/nextflow.config
tags:
- rseqc/junctionsaturation
- rseqc
files:
- path: output/rseqc/test.junctionSaturation_plot.pdf
- path: output/rseqc/test.junctionSaturation_plot.r
md5sum: caa6e63dcb477aabb169882b2f30dadd