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bowtie bam output

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kevinmenden 2020-12-16 11:02:58 +01:00
parent 0d7c8276b7
commit f35850bf14
3 changed files with 20 additions and 18 deletions
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18
software/bowtie/align/main.nf
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@ -11,15 +11,15 @@ process BOWTIE_ALIGN {
mode: params.publish_dir_mode, mode: params.publish_dir_mode,
saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), publish_id:meta.id) } saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), publish_id:meta.id) }
conda (params.enable_conda ? "bioconda::bowtie=1.3.0" : null) conda (params.enable_conda ? "bioconda::bowtie=1.3.0 bioconda::samtools=1.10" : null)
container "quay.io/biocontainers/bowtie:1.3.0--py38hed8969a_1" container "quay.io/biocontainers/mulled-v2-ffbf83a6b0ab6ec567a336cf349b80637135bca3:9e14e16c284d6860574cf5b624bbc44c793cb024-0"
input: input:
tuple val(meta), path(reads) tuple val(meta), path(reads)
path index path index
output: output:
tuple val(meta), path("*.sam"), emit: sam tuple val(meta), path("*.bam"), emit: bam
tuple val(meta), path("*.out"), emit: log tuple val(meta), path("*.out"), emit: log
path "bowtie.version.txt", emit: version path "bowtie.version.txt", emit: version
@ -27,15 +27,19 @@ process BOWTIE_ALIGN {
def software = getSoftwareName(task.process) def software = getSoftwareName(task.process)
def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}" def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
def unaligned = params.save_unaligned ? "--un ${prefix}.unmapped" : '' def unaligned = params.save_unaligned ? "--un ${prefix}.unmapped" : ''
def endedness = meta.single_end ? "$reads" : "-1 ${reads[0]} -2 ${reads[1]}"
""" """
INDEX=`find -L ./ -name "*.3.ebwt" | sed 's/.3.ebwt//'` INDEX=`find -L ./ -name "*.3.ebwt" | sed 's/.3.ebwt//'`
bowtie \\ bowtie \\
--threads $task.cpus \\ --threads $task.cpus \\
$options.args \\ --sam \\
\$INDEX \\ -x \$INDEX \\
-q ${reads} \\ -q \\
$unaligned \\ $unaligned \\
> ${prefix}.sam 2> ${prefix}.out $options.args \\
$endedness \\
2> ${prefix}.out \\
| samtools view $options.args2 -@ $task.cpus -bS -o ${prefix}.bam -
bowtie --version | head -n 1 | cut -d" " -f3 > ${software}.version.txt bowtie --version | head -n 1 | cut -d" " -f3 > ${software}.version.txt
""" """

8
tests/software/bowtie/main.nf
View file

@ -5,8 +5,6 @@ nextflow.enable.dsl = 2
include { BOWTIE_INDEX } from '../../../software/bowtie/index/main.nf' addParams( options: [:] ) include { BOWTIE_INDEX } from '../../../software/bowtie/index/main.nf' addParams( options: [:] )
include { BOWTIE_ALIGN } from '../../../software/bowtie/align/main.nf' addParams( options: [:] ) include { BOWTIE_ALIGN } from '../../../software/bowtie/align/main.nf' addParams( options: [:] )
workflow test_bowtie_index { workflow test_bowtie_index {
fasta = file("${launchDir}/tests/data/fasta/E_coli/NC_010473.fa", checkIfExists: true) fasta = file("${launchDir}/tests/data/fasta/E_coli/NC_010473.fa", checkIfExists: true)
BOWTIE_INDEX ( fasta ) BOWTIE_INDEX ( fasta )
@ -19,7 +17,7 @@ workflow test_bowtie_alignment_single_end {
def input = [] def input = []
input = [ [ id:'test', single_end:true ], // meta map input = [ [ id:'test', single_end:true ], // meta map
[ file("${launchDir}/tests/data/fastq/dna/Ecoli_DNA_R1.fastq.gz", checkIfExists: true) ] ] [ file("${launchDir}/tests/data/fastq/rna/test_R1.fastq.gz", checkIfExists: true) ] ]
BOWTIE_ALIGN ( input, BOWTIE_INDEX.out.index ) BOWTIE_ALIGN ( input, BOWTIE_INDEX.out.index )
} }
@ -29,8 +27,8 @@ workflow test_bowtie_alignment_paired_end {
def input = [] def input = []
input = [ [ id:'test', single_end:false ], // meta map input = [ [ id:'test', single_end:false ], // meta map
[ file("${launchDir}/tests/data/fastq/dna/Ecoli_DNA_R1.fastq.gz", checkIfExists: true), [ file("${launchDir}/tests/data/fastq/rna/test_R1.fastq.gz", checkIfExists: true),
file("${launchDir}/tests/data/fastq/dna/Ecoli_DNA_R2.fastq.gz", checkIfExists: true) ] ] file("${launchDir}/tests/data/fastq/rna/test_R2.fastq.gz", checkIfExists: true) ] ]
BOWTIE_ALIGN ( input, BOWTIE_INDEX.out.index ) BOWTIE_ALIGN ( input, BOWTIE_INDEX.out.index )
} }

12
tests/software/bowtie/test.yml
View file

@ -36,9 +36,9 @@
- path: output/bowtie/bowtie/NC_010473.index.rev.2.ebwt - path: output/bowtie/bowtie/NC_010473.index.rev.2.ebwt
md5sum: f3c398bba5158f4039334a932d79c051 md5sum: f3c398bba5158f4039334a932d79c051
- path: output/bowtie/test.out - path: output/bowtie/test.out
md5sum: 6edce9d0d8ad7f5ce837a5be7e0d7fbe md5sum: a81cb18024616415a6cec3108a36fccd
- path: output/bowtie/test.sam - path: output/bowtie/test.bam
md5sum: acdb36ea915ac2ac71b69a0b704d9d8a md5sum: 8179c68a819accbc9137dc881736106f
- name: Run bowtie index and align paired_end - name: Run bowtie index and align paired_end
@ -60,7 +60,7 @@
- path: output/bowtie/bowtie/NC_010473.index.rev.2.ebwt - path: output/bowtie/bowtie/NC_010473.index.rev.2.ebwt
md5sum: f3c398bba5158f4039334a932d79c051 md5sum: f3c398bba5158f4039334a932d79c051
- path: output/bowtie/test.out - path: output/bowtie/test.out
md5sum: 6edce9d0d8ad7f5ce837a5be7e0d7fbe md5sum: a23e9a2a76e949aeb3693bcfae41a615
- path: output/bowtie/test.sam - path: output/bowtie/test.bam
md5sum: d41d8cd98f00b204e9800998ecf8427e md5sum: 9ce5aebf37128f4bb1d24e9548e22009