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Bump version of kallistobustools/count (#1834)
* Bump version of kallistobustools/count * Trying to update the entire call of kbtools for scrnaseq * Improved tests for kallistobustools/count * Add memory, remove workflow as this is passed as args now * Update modules/kallistobustools/count/main.nf Co-authored-by: Gregor Sturm <mail@gregor-sturm.de> * adding missing value * workflow properly chained together * changing --workflow to ext.args * fix intron channel * fixed checking whether filename is empty or not * bump indentation * fixed if else * Fix linting Co-authored-by: Gregor Sturm <mail@gregor-sturm.de> Co-authored-by: Felipe Marques de Almeida <almeidafmarques@gmail.com>
This commit is contained in:
Alexander Peltzer
GitHub
parent
aed45dd766
commit
ed5594bee3
4 changed files with 40 additions and 37 deletions
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@ -2,10 +2,10 @@ process KALLISTOBUSTOOLS_COUNT {
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tag "$meta.id"
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label 'process_medium'
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conda (params.enable_conda ? 'bioconda::kb-python=0.26.3' : null)
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conda (params.enable_conda ? 'bioconda::kb-python=0.27.2' : null)
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container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
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'https://depot.galaxyproject.org/singularity/kb-python:0.26.3--pyhdfd78af_0' :
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'quay.io/biocontainers/kb-python:0.26.3--pyhdfd78af_0' }"
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'https://depot.galaxyproject.org/singularity/kb-python:0.27.2--pyhdfd78af_0' :
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'quay.io/biocontainers/kb-python:0.27.2--pyhdfd78af_0' }"
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input:
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tuple val(meta), path(reads)
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@ -13,7 +13,6 @@ process KALLISTOBUSTOOLS_COUNT {
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path t2g
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path t1c
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path t2c
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val workflow_mode
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val technology
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output:
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@ -24,10 +23,10 @@ process KALLISTOBUSTOOLS_COUNT {
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task.ext.when == null || task.ext.when
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script:
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def args = task.ext.args ?: ''
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def prefix = task.ext.prefix ?: "${meta.id}"
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def cdna = t1c ? "-c1 $t1c" : ''
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def introns = t2c ? "-c2 $t2c" : ''
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def args = task.ext.args ?: ''
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def prefix = task.ext.prefix ?: "${meta.id}"
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def cdna = t1c ? "-c1 $t1c" : ''
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def introns = t2c ? "-c2 $t2c" : ''
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"""
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kb \\
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count \\
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@ -36,12 +35,11 @@ process KALLISTOBUSTOOLS_COUNT {
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-g $t2g \\
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$cdna \\
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$introns \\
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--workflow $workflow_mode \\
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-x $technology \\
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$args \\
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-o ${prefix}.count \\
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${reads[0]} \\
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${reads[1]}
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${reads.join( " " )} \\
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-m ${task.memory.toGiga()}G
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cat <<-END_VERSIONS > versions.yml
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"${task.process}":
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@ -2,23 +2,31 @@
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nextflow.enable.dsl = 2
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include { KALLISTOBUSTOOLS_REF } from '../../../../modules/kallistobustools/ref/main.nf'
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include { KALLISTOBUSTOOLS_COUNT } from '../../../../modules/kallistobustools/count/main.nf'
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workflow test_kallistobustools_count {
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input = [
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[id:'test'], // meta map
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[ file(params.test_data['homo_sapiens']['illumina']['test_10x_1_fastq_gz'], checkIfExists: true),
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[
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file(params.test_data['homo_sapiens']['illumina']['test_10x_1_fastq_gz'], checkIfExists: true),
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file(params.test_data['homo_sapiens']['illumina']['test_10x_2_fastq_gz'], checkIfExists: true)
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]
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]
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index = file("https://github.com/FloWuenne/test-datasets/blob/scrnaseq/reference/kallistobustools/kb_ref.idx?raw=true", checkIfExists: true)
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t2g = file("https://raw.githubusercontent.com/FloWuenne/test-datasets/scrnaseq/reference/kallistobustools/t2g.txt", checkIfExists: true)
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t1c = []
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t2c = []
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workflow = "standard"
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technology = "10XV3"
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fasta = file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true)
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gtf = file(params.test_data['homo_sapiens']['genome']['genome_gtf'], checkIfExists: true)
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sc_workflow = "standard"
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technology = "10XV3"
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KALLISTOBUSTOOLS_COUNT ( input, index, t2g, t1c, t2c, workflow, technology )
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KALLISTOBUSTOOLS_REF(fasta, gtf, sc_workflow)
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KALLISTOBUSTOOLS_COUNT (
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input,
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KALLISTOBUSTOOLS_REF.out.index,
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KALLISTOBUSTOOLS_REF.out.t2g,
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KALLISTOBUSTOOLS_REF.out.cdna_t2c.ifEmpty{ [] }, // when empty the module doesn't run unless something is passed.
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KALLISTOBUSTOOLS_REF.out.intron_t2c.ifEmpty{ [] }, // when empty the module doesn't run unless something is passed.
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technology
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)
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}
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@ -3,7 +3,7 @@ process {
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publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
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withName: KALLISTOBUSTOOLS_COUNT {
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ext.args = '--cellranger -m 1'
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ext.args = '--cellranger -m 1 --workflow standard'
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}
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}
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@ -1,36 +1,33 @@
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- name: kallistobustools count test_kallistobustools_count
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command: nextflow run ./tests/modules/kallistobustools/count -entry test_kallistobustools_count -c ./tests/config/nextflow.config -c ./tests/modules/kallistobustools/count/nextflow.config
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command: nextflow run ./tests/modules/kallistobustools/count -entry test_kallistobustools_count -c ./tests/config/nextflow.config -c ./tests/modules/kallistobustools/count/nextflow.config
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tags:
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- kallistobustools/count
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- kallistobustools
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- kallistobustools/count
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files:
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- path: output/kallistobustools/cdna.fa
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- path: output/kallistobustools/kb_ref_out.idx
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- path: output/kallistobustools/t2g.txt
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- path: output/kallistobustools/test.count/10x_version3_whitelist.txt
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md5sum: 3d36d0a4021fd292b265e2b5e72aaaf3
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- path: output/kallistobustools/test.count/counts_unfiltered/cellranger/barcodes.tsv
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md5sum: 8f734732c46f52c4d1c025bfe4134bd2
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md5sum: 8a41142de30df61fbb9551b29dd05a83
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- path: output/kallistobustools/test.count/counts_unfiltered/cellranger/genes.tsv
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md5sum: fbebf995a3de568db8ac028cd0c5d993
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md5sum: 1b31f05f9b20a4c0ac3e07b9e3ff3a14
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- path: output/kallistobustools/test.count/counts_unfiltered/cellranger/matrix.mtx
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md5sum: 4847bae27c41961496d504bcfe9890ba
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md5sum: 5b7bff2d19fc90168733f4ac812c7d7b
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- path: output/kallistobustools/test.count/counts_unfiltered/cells_x_genes.barcodes.txt
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md5sum: cafdf96423987e3d9e807cdc16139541
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md5sum: 8d7ef602416818a598f5680a707756a7
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- path: output/kallistobustools/test.count/counts_unfiltered/cells_x_genes.genes.txt
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md5sum: 52d0627aaf0418bebe3ef75ad77da53f
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md5sum: fe6d5501923867b514a0447aa4b4995f
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- path: output/kallistobustools/test.count/counts_unfiltered/cells_x_genes.mtx
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md5sum: d05e1582385ba5f215fa73c470343c06
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md5sum: 0a84dc5a7570b5821da4eef6b5769a0c
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- path: output/kallistobustools/test.count/inspect.json
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md5sum: d3d23063f3fc07f7fbd24748aa4271a9
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md5sum: b853330f160e06fc8af170a837384ef5
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- path: output/kallistobustools/test.count/kb_info.json
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contains:
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- "kallisto"
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- path: output/kallistobustools/test.count/matrix.ec
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md5sum: cd8340e3fb78d74ad85fabdbe0a778f0
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- path: output/kallistobustools/test.count/output.bus
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md5sum: f4702922bd0c142e34b3680c2251426a
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md5sum: f5d8efa83f107826824292cbbdb4e37b
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- path: output/kallistobustools/test.count/output.unfiltered.bus
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md5sum: e38f99748e598e33fe035b89e7c89fb5
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md5sum: dcbc651dc64eb38ae14e0b90795b30d2
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- path: output/kallistobustools/test.count/run_info.json
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contains:
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- "n_targets"
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- path: output/kallistobustools/test.count/transcripts.txt
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md5sum: 6d583083eaf6ca81e409332a40d2e74c
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