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added tests for bowtie module

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This commit is contained in:
kevinmenden 2020-12-08 13:59:14 +01:00
parent 9d67da2b2c
commit 6660a597a3
2 changed files with 36 additions and 27 deletions
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3
tests/software/bowtie/main.nf
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@ -16,11 +16,10 @@ workflow test_bowtie_alignment_single_end {
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 )
}
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/dna/Ecoli_DNA_R1.fastq.gz", checkIfExists: true) ] ]
BOWTIE_ALIGN ( input, BOWTIE_INDEX.index ) BOWTIE_ALIGN ( input, BOWTIE_INDEX.out.index )
} }

60
tests/software/bowtie/test.yml
View file

@ -1,32 +1,42 @@
- name: Run bowtie index - name: Run bowtie index
command: nextflow run ./tests/software/bwa -profile docker -entry test_bwa_index -c tests/config/nextflow.config command: nextflow run ./tests/software/bowtie -profile docker -entry test_bowtie_index -c tests/config/nextflow.config
tags: tags:
- bwa - bowtie
- bwa_index - bowtie_index
files: files:
- path: output/bwa/NC_010473.fa.amb - path: output/bowtie/NC_010473.index.1.ebwt
md5sum: 942a990ae872f1c0b8d72dda2db405d5 md5sum: 90f0b7aa5bbaeaaa999839ac13ad203c
- path: output/bwa/NC_010473.fa.bwt - path: output/bowtie/NC_010473.index.2.ebwt
md5sum: 7301b52e2ecb893d429a49fa692447ae md5sum: bfd10c5319c6a0dbc540fd789254a5dd
- path: output/bwa/NC_010473.fa.pac - path: output/bowtie/NC_010473.index.3.ebwt
md5sum: 4d5e6fc45bbc968f7f859e9ca2cc89ad md5sum: cd201e81724f3099131aec16ef2cc53b
- path: output/bwa/NC_010473.fa.sa - path: output/bowtie/NC_010473.index.4.ebwt
md5sum: a47dcc92e750e2f16fbd979b8ff9538e md5sum: bbb9d6d21ad765d135f95290204e8433
- path: output/bowtie/NC_010473.index.rev.1.ebwt
md5sum: 44f719c2fe42e1f35d54e798775846d1
- path: output/bowtie/NC_010473.index.rev.2.ebwt
md5sum: f3c398bba5158f4039334a932d79c051
- name: Run bwa mem single-end - name: Run bowtie index and align signle-end
command: nextflow run ./tests/software/bwa -profile docker -entry test_bwa_mem_single_end -c tests/config/nextflow.config command: nextflow run ./tests/software/bowtie -profile docker -entry test_bowtie_alignment_single_end -c tests/config/nextflow.config
tags: tags:
- bwa - bowtie
- bwa_mem - bwa_align
files: files:
- path: output/test_single_end/test.bam - path: output/bowtie/NC_010473.index.1.ebwt
md5sum: 3ee21210bac387e0335008146e4728bc md5sum: 90f0b7aa5bbaeaaa999839ac13ad203c
- path: output/bowtie/NC_010473.index.2.ebwt
md5sum: bfd10c5319c6a0dbc540fd789254a5dd
- path: output/bowtie/NC_010473.index.3.ebwt
md5sum: cd201e81724f3099131aec16ef2cc53b
- path: output/bowtie/NC_010473.index.4.ebwt
md5sum: bbb9d6d21ad765d135f95290204e8433
- path: output/bowtie/NC_010473.index.rev.1.ebwt
md5sum: 44f719c2fe42e1f35d54e798775846d1
- path: output/bowtie/NC_010473.index.rev.2.ebwt
md5sum: f3c398bba5158f4039334a932d79c051
- path: output/bowtie/test.out
md5sum: 6edce9d0d8ad7f5ce837a5be7e0d7fbe
- path: output/bowtie/test.sam
md5sum: acdb36ea915ac2ac71b69a0b704d9d8a
- name: Run bwa mem paired-end
command: nextflow run ./tests/software/bwa -profile docker -entry test_bwa_mem_paired_end -c tests/config/nextflow.config
tags:
- bwa
- bwa_mem
files:
- path: output/test_paired_end/test.bam
md5sum: 510d8acc6448c07cdacce8e64ec0904c