nf-core_modules/tests/modules/star/align/main.nf

57 lines
4 KiB
Text
Raw Normal View History

#!/usr/bin/env nextflow
nextflow.enable.dsl = 2
include { STAR_GENOMEGENERATE } from '../../../../modules/star/genomegenerate/main.nf' addParams( options: [args: '--genomeSAindexNbases 9'] )
include { STAR_ALIGN } from '../../../../modules/star/align/main.nf' addParams( options: [args: '--readFilesCommand zcat'] )
include { STAR_ALIGN as STAR_FOR_ARRIBA } from '../../../../modules/star/align/main.nf' addParams( options: [args: '--readFilesCommand zcat --outSAMtype BAM Unsorted --outSAMunmapped Within --outBAMcompression 0 --outFilterMultimapNmax 50 --peOverlapNbasesMin 10 --alignSplicedMateMapLminOverLmate 0.5 --alignSJstitchMismatchNmax 5 -1 5 5 --chimSegmentMin 10 --chimOutType WithinBAM HardClip --chimJunctionOverhangMin 10 --chimScoreDropMax 30 --chimScoreJunctionNonGTAG 0 --chimScoreSeparation 1 --chimSegmentReadGapMax 3 --chimMultimapNmax 50'] )
include { STAR_ALIGN as STAR_FOR_STARFUSION } from '../../../../modules/star/align/main.nf' addParams( options: [args: '--readFilesCommand zcat --outSAMtype BAM Unsorted --outReadsUnmapped None --twopassMode Basic --outSAMstrandField intronMotif --outSAMunmapped Within --chimSegmentMin 12 --chimJunctionOverhangMin 8 --chimOutJunctionFormat 1 --alignSJDBoverhangMin 10 --alignMatesGapMax 100000 --alignIntronMax 100000 --alignSJstitchMismatchNmax 5 -1 5 5 --chimMultimapScoreRange 3 --chimScoreJunctionNonGTAG -4 --chimMultimapNmax 20 --chimNonchimScoreDropMin 10 --peOverlapNbasesMin 12 --peOverlapMMp 0.1 --alignInsertionFlush Right --alignSplicedMateMapLminOverLmate 0 --alignSplicedMateMapLmin 30'] )
workflow test_star_alignment_single_end {
input = [ [ id:'test', single_end:true ], // meta map
[ file(params.test_data['homo_sapiens']['illumina']['test_rnaseq_1_fastq_gz'], checkIfExists: true) ]
]
fasta = file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true)
gtf = file(params.test_data['homo_sapiens']['genome']['genome_gtf'], checkIfExists: true)
STAR_GENOMEGENERATE ( fasta, gtf )
STAR_ALIGN ( input, STAR_GENOMEGENERATE.out.index, gtf )
}
workflow test_star_alignment_paired_end {
input = [ [ id:'test', single_end:false ], // meta map
[ file(params.test_data['homo_sapiens']['illumina']['test_rnaseq_1_fastq_gz'], checkIfExists: true),
file(params.test_data['homo_sapiens']['illumina']['test_rnaseq_2_fastq_gz'], checkIfExists: true) ]
]
fasta = file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true)
gtf = file(params.test_data['homo_sapiens']['genome']['genome_gtf'], checkIfExists: true)
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
STAR_GENOMEGENERATE ( fasta, gtf )
STAR_ALIGN ( input, STAR_GENOMEGENERATE.out.index, gtf )
}
workflow test_star_alignment_paired_end_for_fusion {
input = [ [ id:'test', single_end:false ], // meta map
[ file(params.test_data['homo_sapiens']['illumina']['test_rnaseq_1_fastq_gz'], checkIfExists: true),
file(params.test_data['homo_sapiens']['illumina']['test_rnaseq_2_fastq_gz'], checkIfExists: true) ]
]
fasta = file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true)
gtf = file(params.test_data['homo_sapiens']['genome']['genome_gtf'], checkIfExists: true)
STAR_GENOMEGENERATE ( fasta, gtf )
STAR_FOR_ARRIBA ( input, STAR_GENOMEGENERATE.out.index, gtf )
}
workflow test_star_alignment_paired_end_for_starfusion {
input = [ [ id:'test', single_end:false ], // meta map
[ file(params.test_data['homo_sapiens']['illumina']['test_rnaseq_1_fastq_gz'], checkIfExists: true),
file(params.test_data['homo_sapiens']['illumina']['test_rnaseq_2_fastq_gz'], checkIfExists: true) ]
]
fasta = file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true)
gtf = file(params.test_data['homo_sapiens']['genome']['genome_gtf'], checkIfExists: true)
STAR_GENOMEGENERATE ( fasta, gtf )
STAR_FOR_STARFUSION ( input, STAR_GENOMEGENERATE.out.index, gtf )
}