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Fix the test path salmon/index and quant after switching to config data (#385)
* fix the test path in main.nf for salmon/index and quant * fix typo * Apply suggestions from code review * Apply suggestions from code review * Apply suggestions from code review Mannnn, hopefully I finally got it right :) * replaced /salmon/salmon/ with /index/salmon/ Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
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Batool
GitHub
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3 changed files with 55 additions and 51 deletions
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@ -5,8 +5,8 @@ nextflow.enable.dsl = 2
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include { SALMON_INDEX } from '../../../../software/salmon/index/main.nf' addParams( options: [:] )
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workflow test_salmon_index {
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genome = file("${launchDir}/tests/data/genomics/sarscov2/genome/genome.fasta", checkIfExists: true)
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transcriptome = file("${launchDir}/tests/data/genomics/sarscov2/genome/transcriptome.fasta", checkIfExists: true)
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genome_fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
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transcript_fasta = file(params.test_data['sarscov2']['genome']['transcriptome_fasta'], checkIfExists: true)
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SALMON_INDEX ( genome, transcriptome )
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SALMON_INDEX ( genome_fasta, transcript_fasta )
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}
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@ -6,26 +6,30 @@ include { SALMON_INDEX } from '../../../../software/salmon/index/main.nf' addPar
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include { SALMON_QUANT } from '../../../../software/salmon/quant/main.nf' addParams( options: [args: '--minAssignedFrags 1'] )
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workflow test_salmon_quant_single_end {
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input = [ [ id:'test', single_end:true ], // meta map
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file("${launchDir}/tests/data/genomics/sarscov2/illumina/fastq/test_1.fastq.gz", checkIfExists: true)
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]
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genome = file("${launchDir}/tests/data/genomics/sarscov2/genome/genome.fasta", checkIfExists: true)
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transcriptome = file("${launchDir}/tests/data/genomics/sarscov2/genome/transcriptome.fasta", checkIfExists: true)
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gtf = file("${launchDir}/tests/data/genomics/sarscov2/genome/genome.gtf", checkIfExists: true)
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SALMON_INDEX ( genome, transcriptome )
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SALMON_QUANT ( input, SALMON_INDEX.out.index, gtf, transcriptome, false )
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input = [ [ id:'test', single_end:true ], // meta map
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file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true)
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]
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genome_fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
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transcript_fasta = file(params.test_data['sarscov2']['genome']['transcriptome_fasta'], checkIfExists: true)
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gtf = file(params.test_data['sarscov2']['genome']['genome_gtf'], checkIfExists: true)
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SALMON_INDEX ( genome_fasta, transcript_fasta )
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SALMON_QUANT ( input, SALMON_INDEX.out.index, gtf, transcript_fasta, false )
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}
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workflow test_salmon_quant_paired_end {
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input = [ [ id:'test', single_end:false ], // meta map
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[ file("${launchDir}/tests/data/genomics/sarscov2/illumina/fastq/test_1.fastq.gz", checkIfExists: true),
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file("${launchDir}/tests/data/genomics/sarscov2/illumina/fastq/test_2.fastq.gz", checkIfExists: true) ]
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]
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genome = file("${launchDir}/tests/data/genomics/sarscov2/genome/genome.fasta", checkIfExists: true)
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transcriptome = file("${launchDir}/tests/data/genomics/sarscov2/genome/transcriptome.fasta", checkIfExists: true)
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gtf = file("${launchDir}/tests/data/genomics/sarscov2/genome/genome.gtf", checkIfExists: true)
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SALMON_INDEX ( genome, transcriptome )
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SALMON_QUANT ( input, SALMON_INDEX.out.index, gtf, transcriptome, false )
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input = [ [ id:'test', single_end:false ], // meta map
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[ file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true),
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file(params.test_data['sarscov2']['illumina']['test_2_fastq_gz'], checkIfExists: true) ]
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]
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genome_fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
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transcript_fasta = file(params.test_data['sarscov2']['genome']['transcriptome_fasta'], checkIfExists: true)
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gtf = file(params.test_data['sarscov2']['genome']['genome_gtf'], checkIfExists: true)
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SALMON_INDEX ( genome_fasta, transcript_fasta )
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SALMON_QUANT ( input, SALMON_INDEX.out.index, gtf, transcript_fasta, false )
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}
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@ -24,31 +24,31 @@
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md5sum: ef13c06a538e9c34ca9f84212c82f44e
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- path: ./output/salmon/test/libParams/flenDist.txt
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md5sum: 2de170bdc9f6fd237d286429b292bb28
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- path: ./output/salmon/salmon/ref_indexing.log
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- path: ./output/salmon/salmon/refseq.bin
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- path: ./output/index/salmon/ref_indexing.log
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- path: ./output/index/salmon/refseq.bin
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md5sum: 79c4ddf34be3a98d5a7b9d153629a6f7
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- path: ./output/salmon/salmon/versionInfo.json
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- path: ./output/index/salmon/versionInfo.json
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md5sum: 204865f645102587c4953fccb256797c
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- path: ./output/salmon/salmon/complete_ref_lens.bin
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- path: ./output/index/salmon/complete_ref_lens.bin
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md5sum: f57562f1fca3ae7b133f895ae13c3d08
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- path: ./output/salmon/salmon/mphf.bin
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- path: ./output/index/salmon/mphf.bin
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md5sum: 53669a47610e33e031faafd32703b714
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- path: ./output/salmon/salmon/pre_indexing.log
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- path: ./output/salmon/salmon/ctable.bin
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- path: ./output/salmon/salmon/duplicate_clusters.tsv
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- path: ./output/index/salmon/pre_indexing.log
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- path: ./output/index/salmon/ctable.bin
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- path: ./output/index/salmon/duplicate_clusters.tsv
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md5sum: 51b5292e3a874119c0e1aa566e95d70c
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- path: ./output/salmon/salmon/reflengths.bin
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- path: ./output/index/salmon/reflengths.bin
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md5sum: f57562f1fca3ae7b133f895ae13c3d08
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- path: ./output/salmon/salmon/info.json
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- path: ./output/index/salmon/info.json
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md5sum: 61ff4d3471134c280668355ddd39e99f
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- path: ./output/salmon/salmon/refAccumLengths.bin
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- path: ./output/index/salmon/refAccumLengths.bin
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md5sum: 8d1970505b2b08ca0eb5ff7722b48cde
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- path: ./output/salmon/salmon/ctg_offsets.bin
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- path: ./output/index/salmon/ctg_offsets.bin
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md5sum: 27a76542337df436436e66017f66dd25
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- path: ./output/salmon/salmon/rank.bin
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- path: ./output/index/salmon/rank.bin
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md5sum: 3f34dca1ec26cdf89a6d19b1d1c07e71
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- path: ./output/salmon/salmon/pos.bin
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- path: ./output/salmon/salmon/seq.bin
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- path: ./output/index/salmon/pos.bin
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- path: ./output/index/salmon/seq.bin
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- name: salmon quant paired end
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command: nextflow run ./tests/software/salmon/quant -entry test_salmon_quant_paired_end -c tests/config/nextflow.config
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@ -76,28 +76,28 @@
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md5sum: ef13c06a538e9c34ca9f84212c82f44e
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- path: ./output/salmon/test/libParams/flenDist.txt
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md5sum: 221f754ed55dd1e34874f9b7b3f9d240
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- path: ./output/salmon/salmon/ref_indexing.log
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- path: ./output/salmon/salmon/refseq.bin
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- path: ./output/index/salmon/ref_indexing.log
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- path: ./output/index/salmon/refseq.bin
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md5sum: 79c4ddf34be3a98d5a7b9d153629a6f7
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- path: ./output/salmon/salmon/versionInfo.json
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- path: ./output/index/salmon/versionInfo.json
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md5sum: 204865f645102587c4953fccb256797c
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- path: ./output/salmon/salmon/complete_ref_lens.bin
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- path: ./output/index/salmon/complete_ref_lens.bin
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md5sum: f57562f1fca3ae7b133f895ae13c3d08
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- path: ./output/salmon/salmon/mphf.bin
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- path: ./output/index/salmon/mphf.bin
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md5sum: 53669a47610e33e031faafd32703b714
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- path: ./output/salmon/salmon/pre_indexing.log
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- path: ./output/salmon/salmon/ctable.bin
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- path: ./output/salmon/salmon/duplicate_clusters.tsv
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- path: ./output/index/salmon/pre_indexing.log
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- path: ./output/index/salmon/ctable.bin
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- path: ./output/index/salmon/duplicate_clusters.tsv
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md5sum: 51b5292e3a874119c0e1aa566e95d70c
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- path: ./output/salmon/salmon/reflengths.bin
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- path: ./output/index/salmon/reflengths.bin
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md5sum: f57562f1fca3ae7b133f895ae13c3d08
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- path: ./output/salmon/salmon/info.json
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- path: ./output/index/salmon/info.json
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md5sum: 61ff4d3471134c280668355ddd39e99f
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- path: ./output/salmon/salmon/refAccumLengths.bin
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- path: ./output/index/salmon/refAccumLengths.bin
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md5sum: 8d1970505b2b08ca0eb5ff7722b48cde
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- path: ./output/salmon/salmon/ctg_offsets.bin
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- path: ./output/index/salmon/ctg_offsets.bin
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md5sum: 27a76542337df436436e66017f66dd25
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- path: ./output/salmon/salmon/rank.bin
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- path: ./output/index/salmon/rank.bin
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md5sum: 3f34dca1ec26cdf89a6d19b1d1c07e71
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- path: ./output/salmon/salmon/pos.bin
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- path: ./output/salmon/salmon/seq.bin
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- path: ./output/index/salmon/pos.bin
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- path: ./output/index/salmon/seq.bin
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