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https://github.com/MillironX/nf-core_modules.git
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Version bumps and minor module updates (#406)
* Version bumps and minor module updates * Fix Pangolin tests * Fix SPAdes tests * stageAs @phue
This commit is contained in:
Harshil Patel
GitHub
parent
3b1dcc9cc0
commit
242fdb2f73
7 changed files with 16 additions and 76 deletions
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@ -11,11 +11,11 @@ process PANGOLIN {
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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), publish_id:meta.id) }
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conda (params.enable_conda ? 'bioconda::pangolin=2.3.2' : null)
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conda (params.enable_conda ? 'bioconda::pangolin=2.3.8' : null)
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if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
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container 'https://depot.galaxyproject.org/singularity/pangolin:2.3.2--py_0'
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container 'https://depot.galaxyproject.org/singularity/pangolin:2.3.8--py_0'
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} else {
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container 'quay.io/biocontainers/pangolin:2.3.2--py_0'
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container 'quay.io/biocontainers/pangolin:2.3.8--py_0'
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}
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input:
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@ -19,12 +19,13 @@ process RSEM_PREPAREREFERENCE {
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}
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input:
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path fasta
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path fasta, stageAs: "rsem/*"
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path gtf
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output:
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path "rsem" , emit: index
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path "*.version.txt", emit: version
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path "rsem/*transcripts.fa", emit: transcript_fasta
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path "*.version.txt" , emit: version
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script:
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def software = getSoftwareName(task.process)
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@ -33,7 +34,6 @@ process RSEM_PREPAREREFERENCE {
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args.removeIf { it.contains('--star') }
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def memory = task.memory ? "--limitGenomeGenerateRAM ${task.memory.toBytes() - 100000000}" : ''
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"""
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mkdir rsem
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STAR \\
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--runMode genomeGenerate \\
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--genomeDir rsem/ \\
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@ -54,7 +54,6 @@ process RSEM_PREPAREREFERENCE {
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"""
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} else {
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"""
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mkdir rsem
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rsem-prepare-reference \\
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--gtf $gtf \\
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--num-threads $task.cpus \\
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@ -11,17 +11,16 @@ process SPADES {
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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), publish_id:meta.id) }
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conda (params.enable_conda ? "bioconda::spades=3.15.0" : null)
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conda (params.enable_conda ? "bioconda::spades=3.15.2" : null)
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if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
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container "https://depot.galaxyproject.org/singularity/spades:3.15.0--h633aebb_0"
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container "https://depot.galaxyproject.org/singularity/spades:3.15.2--h95f258a_1"
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} else {
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container "quay.io/biocontainers/spades:3.15.0--h633aebb_0"
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container "quay.io/biocontainers/spades:3.15.2--h95f258a_1"
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}
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input:
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tuple val(meta), path(reads)
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path hmm
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val coronaspades
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output:
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tuple val(meta), path('*.scaffolds.fa') , optional:true, emit: scaffolds
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@ -37,9 +36,8 @@ process SPADES {
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def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
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def input_reads = meta.single_end ? "-s $reads" : "-1 ${reads[0]} -2 ${reads[1]}"
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def custom_hmms = params.spades_hmm ? "--custom-hmms $hmm" : ""
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def command = coronaspades ? "coronaspades.py" : "spades.py"
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"""
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$command \\
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spades.py \\
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$options.args \\
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--threads $task.cpus \\
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$custom_hmms \\
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@ -29,11 +29,6 @@ input:
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type: file
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description:
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File or directory with amino acid HMMs for Spades HMM-guided mode.
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- coronaspades:
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type: boolean
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description: |
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Run coronaspades instead of default spades mode. coronaSPAdes is a special
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mode of rnaviralSPAdes specifically aimed for SARS-CoV-2 de novo assembly.
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output:
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- meta:
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type: map
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@ -4,4 +4,4 @@
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- pangolin
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files:
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- path: ./output/pangolin/test.pangolin.csv
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md5sum: 1d513775cec0901ebee1359c91035d3a
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md5sum: c8b1720f98c9e032908f61bbc05a0fe2
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@ -8,9 +8,7 @@ workflow test_spades_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_2_fastq_gz'], checkIfExists: true) ]
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]
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coronaspades = false
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SPADES ( input, [], coronaspades )
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SPADES ( input, [] )
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}
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workflow test_spades_paired_end {
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@ -18,27 +16,6 @@ workflow test_spades_paired_end {
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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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coronaspades = false
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SPADES ( input, [], coronaspades )
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SPADES ( input, [] )
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}
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workflow test_coronospades_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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]
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coronaspades = true
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SPADES ( input, [], coronaspades )
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}
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workflow test_coronospades_paired_end {
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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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coronaspades = true
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SPADES ( input, [], coronaspades )
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}
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@ -19,36 +19,7 @@
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- spades_paired_end
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files:
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- path: output/spades/test.assembly.gfa
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md5sum: d546f9042f5ff911757e895e7b21f620
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md5sum: faf76135ee390606b899c0197dc38e04
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- path: output/spades/test.contigs.fa
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md5sum: f3e87d68521aa485d70aecd82de519b4
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md5sum: 6148e25b33890c80f176f90f2dd88989
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- path: output/spades/test.spades.log
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- name: coronaspades single end
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command: nextflow run ./tests/software/spades -entry test_coronospades_single_end -c tests/config/nextflow.config
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tags:
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- spades
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- coronaspades_single_end
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files:
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- path: output/spades/test.assembly.gfa
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md5sum: 46531ec9b845c1a1cb469627688fecb7
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- path: output/spades/test.contigs.fa
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md5sum: f2c4a48ebba560aa5c8fde04dbe905fc
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- path: output/spades/test.scaffolds.fa
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md5sum: f2c4a48ebba560aa5c8fde04dbe905fc
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- path: output/spades/test.gene_clusters.fa
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- path: output/spades/test.spades.log
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- name: coronaspades paired end
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command: nextflow run ./tests/software/spades -entry test_coronospades_paired_end -c tests/config/nextflow.config
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tags:
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- spades
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- coronaspades_paired_end
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files:
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- path: output/spades/test.assembly.gfa
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md5sum: d546f9042f5ff911757e895e7b21f620
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- path: output/spades/test.contigs.fa
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md5sum: f3e87d68521aa485d70aecd82de519b4
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- path: output/spades/test.gene_clusters.fa
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- path: output/spades/test.spades.log
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