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Merge branch 'master' into add_compression_to_bam2fq

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Lauri Mesilaakso 2022-05-04 09:53:46 +03:00 committed by GitHub
commit 530b5ac661
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4 changed files with 59 additions and 2 deletions
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4
modules/bowtie2/align/main.nf
View file

@ -29,6 +29,8 @@ process BOWTIE2_ALIGN {
def unaligned = save_unaligned ? "--un-gz ${prefix}.unmapped.fastq.gz" : '' def unaligned = save_unaligned ? "--un-gz ${prefix}.unmapped.fastq.gz" : ''
""" """
INDEX=`find -L ./ -name "*.rev.1.bt2" | sed 's/.rev.1.bt2//'` INDEX=`find -L ./ -name "*.rev.1.bt2" | sed 's/.rev.1.bt2//'`
[ -z "\$INDEX" ] && INDEX=`find -L ./ -name "*.rev.1.bt2l" | sed 's/.rev.1.bt2l//'`
[ -z "\$INDEX" ] && echo "BT2 index files not found" 1>&2 && exit 1
bowtie2 \\ bowtie2 \\
-x \$INDEX \\ -x \$INDEX \\
-U $reads \\ -U $reads \\
@ -49,6 +51,8 @@ process BOWTIE2_ALIGN {
def unaligned = save_unaligned ? "--un-conc-gz ${prefix}.unmapped.fastq.gz" : '' def unaligned = save_unaligned ? "--un-conc-gz ${prefix}.unmapped.fastq.gz" : ''
""" """
INDEX=`find -L ./ -name "*.rev.1.bt2" | sed 's/.rev.1.bt2//'` INDEX=`find -L ./ -name "*.rev.1.bt2" | sed 's/.rev.1.bt2//'`
[ -z "\$INDEX" ] && INDEX=`find -L ./ -name "*.rev.1.bt2l" | sed 's/.rev.1.bt2l//'`
[ -z "\$INDEX" ] && echo "BT2 index files not found" 1>&2 && exit 1
bowtie2 \\ bowtie2 \\
-x \$INDEX \\ -x \$INDEX \\
-1 ${reads[0]} \\ -1 ${reads[0]} \\

2
tests/modules/bowtie2/align/main.nf
View file

@ -32,4 +32,4 @@ workflow test_bowtie2_align_paired_end {
BOWTIE2_BUILD ( fasta ) BOWTIE2_BUILD ( fasta )
BOWTIE2_ALIGN ( input, BOWTIE2_BUILD.out.index, save_unaligned ) BOWTIE2_ALIGN ( input, BOWTIE2_BUILD.out.index, save_unaligned )
} }

13
tests/modules/bowtie2/align/nextflow.config
View file

@ -1,5 +1,16 @@
params {
force_large_index = false
}
process { process {
publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" } publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
}
if (params.force_large_index) {
process {
withName: BOWTIE2_BUILD {
ext.args = '--large-index'
}
}
} }

42
tests/modules/bowtie2/align/test.yml
View file

@ -39,3 +39,45 @@
md5sum: 52be6950579598a990570fbcf5372184 md5sum: 52be6950579598a990570fbcf5372184
- path: ./output/bowtie2/bowtie2/genome.rev.2.bt2 - path: ./output/bowtie2/bowtie2/genome.rev.2.bt2
md5sum: e3b4ef343dea4dd571642010a7d09597 md5sum: e3b4ef343dea4dd571642010a7d09597
- name: bowtie2 align single-end large-index
command: nextflow run ./tests/modules/bowtie2/align -entry test_bowtie2_align_single_end -c ./tests/config/nextflow.config -c ./tests/modules/bowtie2/align/nextflow.config --force_large_index
tags:
- bowtie2
- bowtie2/align
files:
- path: ./output/bowtie2/test.bam
- path: ./output/bowtie2/test.bowtie2.log
- path: ./output/bowtie2/bowtie2/genome.3.bt2l
md5sum: 8952b3e0b1ce9a7a5916f2e147180853
- path: ./output/bowtie2/bowtie2/genome.2.bt2l
md5sum: 22c284084784a0720989595e0c9461fd
- path: ./output/bowtie2/bowtie2/genome.1.bt2l
md5sum: 07d811cd4e350d56267183d2ac7023a5
- path: ./output/bowtie2/bowtie2/genome.4.bt2l
md5sum: c25be5f8b0378abf7a58c8a880b87626
- path: ./output/bowtie2/bowtie2/genome.rev.1.bt2l
md5sum: fda48e35925fb24d1c0785f021981e25
- path: ./output/bowtie2/bowtie2/genome.rev.2.bt2l
md5sum: 802c26d32b970e1b105032b7ce7348b4
- name: bowtie2 align paired-end large-index
command: nextflow run ./tests/modules/bowtie2/align -entry test_bowtie2_align_paired_end -c ./tests/config/nextflow.config -c ./tests/modules/bowtie2/align/nextflow.config --force_large_index
tags:
- bowtie2
- bowtie2/align
files:
- path: ./output/bowtie2/test.bam
- path: ./output/bowtie2/test.bowtie2.log
- path: ./output/bowtie2/bowtie2/genome.3.bt2l
md5sum: 8952b3e0b1ce9a7a5916f2e147180853
- path: ./output/bowtie2/bowtie2/genome.2.bt2l
md5sum: 22c284084784a0720989595e0c9461fd
- path: ./output/bowtie2/bowtie2/genome.1.bt2l
md5sum: 07d811cd4e350d56267183d2ac7023a5
- path: ./output/bowtie2/bowtie2/genome.4.bt2l
md5sum: c25be5f8b0378abf7a58c8a880b87626
- path: ./output/bowtie2/bowtie2/genome.rev.1.bt2l
md5sum: fda48e35925fb24d1c0785f021981e25
- path: ./output/bowtie2/bowtie2/genome.rev.2.bt2l
md5sum: 802c26d32b970e1b105032b7ce7348b4