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Fix salmon quant tests

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This commit is contained in:
drpatelh 2021-02-03 17:36:06 +00:00
parent 550494cbd1
commit 0683efc679
2 changed files with 3 additions and 3 deletions
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4
tests/software/salmon/quant/main.nf
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@ -14,7 +14,7 @@ workflow test_salmon_quant_single_end {
file("${launchDir}/tests/data/fastq/rna/sarscov2/EPI_ISL_486436_1.fastq.gz", checkIfExists: true) ] file("${launchDir}/tests/data/fastq/rna/sarscov2/EPI_ISL_486436_1.fastq.gz", checkIfExists: true) ]
SALMON_INDEX ( genome_fasta, transcript_fasta ) SALMON_INDEX ( genome_fasta, transcript_fasta )
SALMON_QUANT( input, SALMON_INDEX.out.index, gtf, transcript_fasta, false) SALMON_QUANT ( input, SALMON_INDEX.out.index, gtf, transcript_fasta, false )
} }
@ -28,6 +28,6 @@ workflow test_salmon_quant_paired_end {
file("${launchDir}/tests/data/fastq/rna/sarscov2/EPI_ISL_486436_2.fastq.gz", checkIfExists: true) ] ] file("${launchDir}/tests/data/fastq/rna/sarscov2/EPI_ISL_486436_2.fastq.gz", checkIfExists: true) ] ]
SALMON_INDEX ( genome_fasta, transcript_fasta ) SALMON_INDEX ( genome_fasta, transcript_fasta )
SALMON_QUANT( input, SALMON_INDEX.out.index, gtf, transcript_fasta, false) SALMON_QUANT ( input, SALMON_INDEX.out.index, gtf, transcript_fasta, false )
} }

2
tests/software/salmon/quant/test.yml
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@ -53,7 +53,7 @@
md5sum: b08095ac70f89efc3146cdf488d0eb73 md5sum: b08095ac70f89efc3146cdf488d0eb73
- name: salmon quant paired end - name: salmon quant paired end
command: nextflow run ./tests/software/salmon -entry test_salmon_quant_paired_end -c tests/config/nextflow.config command: nextflow run ./tests/software/salmon/quant -entry test_salmon_quant_paired_end -c tests/config/nextflow.config
tags: tags:
- salmon - salmon
- salmon_quant - salmon_quant