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Bump STAR version to 2.7.10a for RSEM modules (#1573)

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* Bump STAR version to 2.7.10a for RSEM modules

* Fix tests
This commit is contained in:
Harshil Patel 2022-04-27 19:21:26 +01:00 committed by GitHub
parent 2134031879
commit 1b5d3f5ac2
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4 changed files with 10 additions and 10 deletions
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6
modules/rsem/calculateexpression/main.nf
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@ -2,10 +2,10 @@ process RSEM_CALCULATEEXPRESSION {
tag "$meta.id" tag "$meta.id"
label 'process_high' label 'process_high'
conda (params.enable_conda ? "bioconda::rsem=1.3.3 bioconda::star=2.7.6a" : null) conda (params.enable_conda ? "bioconda::rsem=1.3.3 bioconda::star=2.7.10a" : null)
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/mulled-v2-cf0123ef83b3c38c13e3b0696a3f285d3f20f15b:606b713ec440e799d53a2b51a6e79dbfd28ecf3e-0' : 'https://depot.galaxyproject.org/singularity/mulled-v2-cf0123ef83b3c38c13e3b0696a3f285d3f20f15b:64aad4a4e144878400649e71f42105311be7ed87-0' :
'quay.io/biocontainers/mulled-v2-cf0123ef83b3c38c13e3b0696a3f285d3f20f15b:606b713ec440e799d53a2b51a6e79dbfd28ecf3e-0' }" 'quay.io/biocontainers/mulled-v2-cf0123ef83b3c38c13e3b0696a3f285d3f20f15b:64aad4a4e144878400649e71f42105311be7ed87-0' }"
input: input:
tuple val(meta), path(reads) tuple val(meta), path(reads)

6
modules/rsem/preparereference/main.nf
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@ -2,10 +2,10 @@ process RSEM_PREPAREREFERENCE {
tag "$fasta" tag "$fasta"
label 'process_high' label 'process_high'
conda (params.enable_conda ? "bioconda::rsem=1.3.3 bioconda::star=2.7.6a" : null) conda (params.enable_conda ? "bioconda::rsem=1.3.3 bioconda::star=2.7.10a" : null)
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/mulled-v2-cf0123ef83b3c38c13e3b0696a3f285d3f20f15b:606b713ec440e799d53a2b51a6e79dbfd28ecf3e-0' : 'https://depot.galaxyproject.org/singularity/mulled-v2-cf0123ef83b3c38c13e3b0696a3f285d3f20f15b:64aad4a4e144878400649e71f42105311be7ed87-0' :
'quay.io/biocontainers/mulled-v2-cf0123ef83b3c38c13e3b0696a3f285d3f20f15b:606b713ec440e799d53a2b51a6e79dbfd28ecf3e-0' }" 'quay.io/biocontainers/mulled-v2-cf0123ef83b3c38c13e3b0696a3f285d3f20f15b:64aad4a4e144878400649e71f42105311be7ed87-0' }"
input: input:
path fasta, stageAs: "rsem/*" path fasta, stageAs: "rsem/*"

4
tests/config/test_data.config
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@ -245,8 +245,8 @@ params {
test2_2_fastq_gz = "${test_data_dir}/genomics/homo_sapiens/illumina/fastq/test2_2.fastq.gz" test2_2_fastq_gz = "${test_data_dir}/genomics/homo_sapiens/illumina/fastq/test2_2.fastq.gz"
test2_umi_1_fastq_gz = "${test_data_dir}/genomics/homo_sapiens/illumina/fastq/test2.umi_1.fastq.gz" test2_umi_1_fastq_gz = "${test_data_dir}/genomics/homo_sapiens/illumina/fastq/test2.umi_1.fastq.gz"
test2_umi_2_fastq_gz = "${test_data_dir}/genomics/homo_sapiens/illumina/fastq/test2.umi_2.fastq.gz" test2_umi_2_fastq_gz = "${test_data_dir}/genomics/homo_sapiens/illumina/fastq/test2.umi_2.fastq.gz"
test_rnaseq_1_fastq_gz = "${test_data_dir}/genomics/homo_sapiens/illumina/fastq/test.rnaseq_1.fastq.gz" test_rnaseq_1_fastq_gz = "${test_data_dir}/genomics/homo_sapiens/illumina/fastq/test_rnaseq_1.fastq.gz"
test_rnaseq_2_fastq_gz = "${test_data_dir}/genomics/homo_sapiens/illumina/fastq/test.rnaseq_2.fastq.gz" test_rnaseq_2_fastq_gz = "${test_data_dir}/genomics/homo_sapiens/illumina/fastq/test_rnaseq_2.fastq.gz"
test_baserecalibrator_table = "${test_data_dir}/genomics/homo_sapiens/illumina/gatk/test.baserecalibrator.table" test_baserecalibrator_table = "${test_data_dir}/genomics/homo_sapiens/illumina/gatk/test.baserecalibrator.table"
test2_baserecalibrator_table = "${test_data_dir}/genomics/homo_sapiens/illumina/gatk/test2.baserecalibrator.table" test2_baserecalibrator_table = "${test_data_dir}/genomics/homo_sapiens/illumina/gatk/test2.baserecalibrator.table"

4
tests/modules/rsem/calculateexpression/test.yml
View file

@ -42,7 +42,7 @@
- path: output/rsem/rsem/genome.transcripts.fa - path: output/rsem/rsem/genome.transcripts.fa
md5sum: 050c521a2719c2ae48267c1e65218f29 md5sum: 050c521a2719c2ae48267c1e65218f29
- path: output/rsem/rsem/genomeParameters.txt - path: output/rsem/rsem/genomeParameters.txt
md5sum: 2fe3a030e1706c3e8cd4df3818e6dd2f md5sum: df5a456e3242520cc36e0083a6a7d9dd
- path: output/rsem/rsem/sjdbInfo.txt - path: output/rsem/rsem/sjdbInfo.txt
md5sum: 5690ea9d9f09f7ff85b7fd47bd234903 md5sum: 5690ea9d9f09f7ff85b7fd47bd234903
- path: output/rsem/rsem/sjdbList.fromGTF.out.tab - path: output/rsem/rsem/sjdbList.fromGTF.out.tab
@ -63,4 +63,4 @@
- path: output/rsem/test.stat/test.theta - path: output/rsem/test.stat/test.theta
md5sum: de2e4490c98cc5383a86ae8225fd0a28 md5sum: de2e4490c98cc5383a86ae8225fd0a28
- path: output/rsem/test.transcript.bam - path: output/rsem/test.transcript.bam
md5sum: 7846491086c478858419667d60f18edd md5sum: ed681d39f5700ffc74d6321525330d93