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Update salmon/quant to provide '--libType A' option (#536)
* Update salmon/quant to provide '--libType A' option * Modify lib_type description to be a string * Update tests * lyb_type can be explicitly overwrite * Update main.nf * Update main.nf * Update main.nf Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
This commit is contained in:
Jose Espinosa-Carrasco
GitHub
parent
c8168bc351
commit
e621f78757
4 changed files with 93 additions and 8 deletions
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@ -24,6 +24,7 @@ process SALMON_QUANT {
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path gtf
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path transcript_fasta
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val alignment_mode
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val lib_type
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output:
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tuple val(meta), path("${prefix}"), emit: results
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@ -40,11 +41,26 @@ process SALMON_QUANT {
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input_reads = "-a $reads"
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}
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def strandedness = meta.single_end ? 'U' : 'IU'
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if (meta.strandedness == 'forward') {
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strandedness = meta.single_end ? 'SF' : 'ISF'
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} else if (meta.strandedness == 'reverse') {
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strandedness = meta.single_end ? 'SR' : 'ISR'
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def strandedness_opts = [
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'A', 'U', 'SF', 'SR',
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'IS', 'IU' , 'ISF', 'ISR',
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'OS', 'OU' , 'OSF', 'OSR',
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'MS', 'MU' , 'MSF', 'MSR'
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]
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def strandedness = 'A'
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if (lib_type) {
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if (strandedness_opts.contains(lib_type)) {
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strandedness = lib_type
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} else {
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log.info "[Salmon Quant] Invalid library type specified '--libType=${lib_type}', defaulting to auto-detection with '--libType=A'."
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}
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} else {
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strandedness = meta.single_end ? 'U' : 'IU'
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if (meta.strandedness == 'forward') {
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strandedness = meta.single_end ? 'SF' : 'ISF'
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} else if (meta.strandedness == 'reverse') {
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strandedness = meta.single_end ? 'SR' : 'ISR'
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}
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}
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"""
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salmon quant \\
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@ -35,6 +35,10 @@ input:
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- alignment_mode:
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type: boolean
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description: whether to run salmon in alignment mode
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- lib_type:
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type: string
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description: |
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Override library type inferred based on strandedness defined in meta object
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output:
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- sample_output:
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@ -8,14 +8,14 @@ include { SALMON_QUANT } from '../../../../software/salmon/quant/main.nf' addPar
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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(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true)
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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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SALMON_QUANT ( input, SALMON_INDEX.out.index, gtf, transcript_fasta, false, '' )
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}
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@ -30,6 +30,21 @@ workflow test_salmon_quant_paired_end {
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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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SALMON_QUANT ( input, SALMON_INDEX.out.index, gtf, transcript_fasta, false, '' )
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}
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workflow test_salmon_quant_single_end_lib_type_A {
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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, 'A' )
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}
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@ -95,7 +95,57 @@
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md5sum: 8d1970505b2b08ca0eb5ff7722b48cde
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- path: ./output/index/salmon/ctg_offsets.bin
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md5sum: 27a76542337df436436e66017f66dd25
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- path: ./output/index/salmon/rank.bin
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md5sum: 3f34dca1ec26cdf89a6d19b1d1c07e71
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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 test_salmon_quant_single_end_lib_type_A
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command: nextflow run tests/software/salmon/quant -entry test_salmon_quant_single_end_lib_type_A -c tests/config/nextflow.config
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tags:
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- salmon/quant
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- salmon
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files:
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- path: ./output/salmon/test/cmd_info.json
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- path: output/salmon/test/quant.sf
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md5sum: 687368b9963874c1797d210310b38516
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- path: ./output/salmon/test/lib_format_counts.json
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- path: ./output/salmon/test/quant.genes.sf
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md5sum: ad4d31437f06db49b2436abeec29c78e
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- path: ./output/salmon/test/logs/salmon_quant.log
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- path: output/salmon/test/aux_info/expected_bias.gz
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md5sum: 24ee10af39b41ecf4f4e08faaaf537ee
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- path: output/salmon/test/aux_info/observed_bias_3p.gz
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md5sum: ef13c06a538e9c34ca9f84212c82f44e
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- path: ./output/salmon/test/aux_info/meta_info.json
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- path: ./output/salmon/test/aux_info/fld.gz
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- path: output/salmon/test/aux_info/ambig_info.tsv
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md5sum: 2ee3dc3080ad7222e0687481e7a1ee03
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- path: ./output/salmon/test/aux_info/observed_bias.gz
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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/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/index/salmon/versionInfo.json
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md5sum: 204865f645102587c4953fccb256797c
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- path: output/index/salmon/complete_ref_lens.bin
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md5sum: f57562f1fca3ae7b133f895ae13c3d08
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- path: output/index/salmon/mphf.bin
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md5sum: 53669a47610e33e031faafd32703b714
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- path: output/index/salmon/duplicate_clusters.tsv
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md5sum: 51b5292e3a874119c0e1aa566e95d70c
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- path: output/index/salmon/reflengths.bin
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md5sum: f57562f1fca3ae7b133f895ae13c3d08
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- path: output/index/salmon/info.json
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md5sum: 61ff4d3471134c280668355ddd39e99f
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- path: output/index/salmon/refAccumLengths.bin
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md5sum: 8d1970505b2b08ca0eb5ff7722b48cde
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- path: output/index/salmon/ctg_offsets.bin
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md5sum: 27a76542337df436436e66017f66dd25
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- path: output/index/salmon/rank.bin
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md5sum: 3f34dca1ec26cdf89a6d19b1d1c07e71
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- path: ./output/index/salmon/pos.bin
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- path: ./output/index/salmon/seq.bin
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