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Update kallistobustools/ref module (#465)
* Bump version and format references to use raw params.test_data * Apply suggestions from code review Co-authored-by: Kevin Menden <kevin.menden@live.com> * Updated tags Missed on in last commit. Co-authored-by: Kevin Menden <kevin.menden@live.com>
This commit is contained in:
Florian Wuennemann
GitHub
parent
d7a3286a9a
commit
a5d0cf3686
3 changed files with 35 additions and 23 deletions
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@ -11,11 +11,11 @@ process KALLISTOBUSTOOLS_REF {
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mode: params.publish_dir_mode,
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saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:[:], publish_by_meta:[]) }
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conda (params.enable_conda ? "bioconda::kb-python=0.25.1" : null)
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conda (params.enable_conda ? "bioconda::kb-python=0.26.0" : null)
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if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
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container "https://depot.galaxyproject.org/singularity/kb-python:0.25.1--py_0"
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container "https://depot.galaxyproject.org/singularity/kb-python:0.26.0--pyhdfd78af_0"
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} else {
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container "quay.io/biocontainers/kb-python:0.25.1--py_0"
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container "quay.io/biocontainers/kb-python:0.26.0--pyhdfd78af_0"
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}
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input:
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@ -6,8 +6,8 @@ include { KALLISTOBUSTOOLS_REF } from '../../../../software/kallistobustools/ref
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workflow test_kallistobustools_ref_standard {
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fasta = file("https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/delete_me/kallistobustools/GRCm39.chr19_100k.fa.gz", checkIfExists: true)
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gtf = file("https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/delete_me/kallistobustools/gencode.VM26.chr19_10k.gtf.gz", checkIfExists: true)
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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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workflow = "standard"
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KALLISTOBUSTOOLS_REF(fasta, gtf, workflow)
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@ -15,18 +15,18 @@ workflow test_kallistobustools_ref_standard {
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workflow test_kallistobustools_ref_lamanno {
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fasta = file("https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/delete_me/kallistobustools/GRCm39.chr19_100k.fa.gz", checkIfExists: true)
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gtf = file("https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/delete_me/kallistobustools/gencode.VM26.chr19_10k.gtf.gz", checkIfExists: true)
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workflow = "standard"
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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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workflow = "lamanno"
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KALLISTOBUSTOOLS_REF( fasta, gtf, workflow)
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}
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workflow test_kallistobustools_ref_nucleus {
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fasta = file("https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/delete_me/kallistobustools/GRCm39.chr19_100k.fa.gz", checkIfExists: true)
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gtf = file("https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/delete_me/kallistobustools/gencode.VM26.chr19_10k.gtf.gz", checkIfExists: true)
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workflow = "standard"
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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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workflow = "nucleus"
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KALLISTOBUSTOOLS_REF( fasta, gtf, workflow)
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}
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@ -1,38 +1,50 @@
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- name: kallistobustools ref test_kallistobustools_ref_standard
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command: nextflow run tests/software/kallistobustools/ref -entry test_kallistobustools_ref_standard -c tests/config/nextflow.config
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tags:
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- kallistobustools
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- kallistobustools/ref
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- kallistobustools
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files:
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- path: output/kallistobustools/cdna.fa
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md5sum: da194221c883656c68e2f90d8f77a56b
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md5sum: 0de7fdac9e7418576987ed93640927c7
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- path: output/kallistobustools/kb_ref_out.idx
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md5sum: c0ffe9554cb6fdcc7cbb4a1285ca8f29
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md5sum: 7d5cd0731e7c467e5521d761f7d79895
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- path: output/kallistobustools/t2g.txt
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md5sum: 3089d303d9cd1a39a27969eca2dcaba7
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md5sum: d5bcfd61ff078aa92e576abf8cc4fc08
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- name: kallistobustools ref test_kallistobustools_ref_lamanno
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command: nextflow run tests/software/kallistobustools/ref -entry test_kallistobustools_ref_lamanno -c tests/config/nextflow.config
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tags:
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- kallistobustools
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- kallistobustools/ref
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- kallistobustools
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files:
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- path: output/kallistobustools/cdna.fa
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md5sum: da194221c883656c68e2f90d8f77a56b
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md5sum: 0de7fdac9e7418576987ed93640927c7
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- path: output/kallistobustools/cdna_t2c.txt
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md5sum: 6d583083eaf6ca81e409332a40d2e74c
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- path: output/kallistobustools/intron.fa
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md5sum: ca5ca147afa0a25f6a730edfb39a6098
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- path: output/kallistobustools/intron_t2c.txt
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md5sum: 728480007abfdbdb248f7ba9de6026ef
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- path: output/kallistobustools/kb_ref_out.idx
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md5sum: c0ffe9554cb6fdcc7cbb4a1285ca8f29
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md5sum: 48ca8323aadd30b1762d4e8f5a7d7aee
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- path: output/kallistobustools/t2g.txt
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md5sum: 3089d303d9cd1a39a27969eca2dcaba7
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md5sum: 7cae93dfb9a26f70adf4a57fe2a83027
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- name: kallistobustools ref test_kallistobustools_ref_nucleus
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command: nextflow run tests/software/kallistobustools/ref -entry test_kallistobustools_ref_nucleus -c tests/config/nextflow.config
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tags:
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- kallistobustools
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- kallistobustools/ref
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- kallistobustools
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files:
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- path: output/kallistobustools/cdna.fa
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md5sum: da194221c883656c68e2f90d8f77a56b
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md5sum: 0de7fdac9e7418576987ed93640927c7
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- path: output/kallistobustools/cdna_t2c.txt
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md5sum: 6d583083eaf6ca81e409332a40d2e74c
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- path: output/kallistobustools/intron.fa
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md5sum: ca5ca147afa0a25f6a730edfb39a6098
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- path: output/kallistobustools/intron_t2c.txt
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md5sum: 728480007abfdbdb248f7ba9de6026ef
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- path: output/kallistobustools/kb_ref_out.idx
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md5sum: c0ffe9554cb6fdcc7cbb4a1285ca8f29
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md5sum: 48ca8323aadd30b1762d4e8f5a7d7aee
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- path: output/kallistobustools/t2g.txt
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md5sum: 3089d303d9cd1a39a27969eca2dcaba7
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md5sum: 7cae93dfb9a26f70adf4a57fe2a83027
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