nf-core_modules/tests/software/star/align/main.nf
Kevin Menden 4566525da2
Converge test data usage (#249)
* initial data restructuing

* fixed bedtools_complement

* fixed bedtools_genomecov

* fixed bedtools_getfasta

* fixed bedtools_intersect

* fixed bedtools maskfasta

* fixed bedtools_merge

* fixed bedtools_slop

* fixed bedtools_sort

* fixed bismark_genome_preparation

* fixed blast

* fixed bowtie data

* fixed bowtie2 data

* fixed bwa data

* fixed bwamem2 data usage

* fixed cat_fastq data

* fixed cutadapt data

* fixed dsh data

* fixed fastp data

* fixed fastqc; fixed bug with wrong fastq format

* fixed gatk

* fixed data for gffread, gunzip

* fixed ivar paths

* fixed data paths for minimap2

* fixed mosdepth

* fixed multiqc, pangolin

* fixed picard data paths

* fixed data paths for qualimap, quast

* fixed salmon data paths

* fixed samtools paths

* fixed seqwish, stringtie paths

* fixed tabix, trimgalore paths

* cleaned up data

* added first description to README

* changed test data naming again; everything up to bwa fixed

* everything up to gatk4

* fixed everything up to ivar

* fixed everything up to picard

* everything up to quast

* everything fixed up to stringtie

* switched everyting to 'test' naming scheme

* fixed samtools and ivar tests

* cleaned up README a bit

* add (simulated) methylation test data

based on SARS-CoV-2 genome; simulated with Sherman --non_dir --genome sarscov2/fasta/ --paired -n 10000 -l 100 --CG 20 --CH 90

* bwameth/align: update data paths and checksums

also, build index on the go

* bwameth/index: update data paths and checksums

* methyldackel/extract: update data paths and checksums

* methyldackel/mbias: update data paths and checksums

* bismark/deduplicate: update data paths and checksums

* remove obsolete testdata

* remove empty 'dummy_file.txt'

* update data/README.md

* methyldackel: fix test

* Revert "methyldackel: fix test"

This reverts commit f175a32d144b1b0bfa0c6885da80c51e3cfe038a.

* methyldackel: fix test

for real

* move test.genome.sizes

* changed test names

* switched genomic to genome and transcriptome

* fix bedtools, blast

* fix gtf, tabix, .paf

* fix bowtie,bwa,bwameth

* fixed: bwa, bwamem, gatk, gffread, quast

* fixed bismark and blast

* fixed remaining tests

* delete bam file

Co-authored-by: phue <patrick.huether@gmail.com>
2021-03-04 10:10:57 +00:00

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#!/usr/bin/env nextflow
nextflow.enable.dsl = 2
include { STAR_GENOMEGENERATE } from '../../../../software/star/genomegenerate/main.nf' addParams( options: [args: '--genomeSAindexNbases 9'] )
include { STAR_ALIGN } from '../../../../software/star/align/main.nf' addParams( options: [args: '--readFilesCommand zcat'] )
workflow test_star_alignment_single_end {
def fasta = file("${launchDir}/tests/data/generic/fasta/GCF_000019425.1_ASM1942v1_genomic.fna", checkIfExists: true)
def gtf = file("${launchDir}/tests/data/generic/gtf/GCF_000019425.1_ASM1942v1_genomic.gtf", checkIfExists: true)
STAR_GENOMEGENERATE ( fasta, gtf )
input = [ [ id:'test', single_end:true ], // meta map
[ file("${launchDir}/tests/data/generic/fastq/test_single_end.fastq.gz", checkIfExists: true) ] ]
STAR_ALIGN ( input, STAR_GENOMEGENERATE.out.index, gtf )
}
workflow test_star_alignment_paired_end {
def fasta = file("${launchDir}/tests/data/generic/fasta/GCF_000019425.1_ASM1942v1_genomic.fna", checkIfExists: true)
def gtf = file("${launchDir}/tests/data/generic/gtf/GCF_000019425.1_ASM1942v1_genomic.gtf", checkIfExists: true)
STAR_GENOMEGENERATE ( fasta, gtf )
input = [ [ id:'test', single_end:false ], // meta map
[ file("${launchDir}/tests/data/generic/fastq/test_R1.fastq.gz", checkIfExists: true),
file("${launchDir}/tests/data/generic/fastq/test_R2.fastq.gz", checkIfExists: true) ] ]
STAR_ALIGN ( input, STAR_GENOMEGENERATE.out.index, gtf )
}