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69 lines
2.3 KiB
Text
69 lines
2.3 KiB
Text
process RSEM_PREPAREREFERENCE {
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tag "$fasta"
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label 'process_high'
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conda (params.enable_conda ? "bioconda::rsem=1.3.3 bioconda::star=2.7.6a" : null)
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container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
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'https://depot.galaxyproject.org/singularity/mulled-v2-cf0123ef83b3c38c13e3b0696a3f285d3f20f15b:606b713ec440e799d53a2b51a6e79dbfd28ecf3e-0' :
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'quay.io/biocontainers/mulled-v2-cf0123ef83b3c38c13e3b0696a3f285d3f20f15b:606b713ec440e799d53a2b51a6e79dbfd28ecf3e-0' }"
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input:
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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 "*transcripts.fa", emit: transcript_fasta
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path "versions.yml" , emit: versions
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script:
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def args = task.ext.args ?: ''
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def args2 = task.ext.args2 ?: ''
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def args_list = args.tokenize()
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if (args_list.contains('--star')) {
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args_list.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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STAR \\
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--runMode genomeGenerate \\
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--genomeDir rsem/ \\
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--genomeFastaFiles $fasta \\
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--sjdbGTFfile $gtf \\
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--runThreadN $task.cpus \\
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$memory \\
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$args2
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rsem-prepare-reference \\
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--gtf $gtf \\
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--num-threads $task.cpus \\
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${args_list.join(' ')} \\
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$fasta \\
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rsem/genome
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cp rsem/genome.transcripts.fa .
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cat <<-END_VERSIONS > versions.yml
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"${task.process}":
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rsem: \$(rsem-calculate-expression --version | sed -e "s/Current version: RSEM v//g")
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star: \$(STAR --version | sed -e "s/STAR_//g")
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END_VERSIONS
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"""
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} else {
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"""
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rsem-prepare-reference \\
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--gtf $gtf \\
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--num-threads $task.cpus \\
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$args \\
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$fasta \\
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rsem/genome
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cp rsem/genome.transcripts.fa .
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cat <<-END_VERSIONS > versions.yml
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"${task.process}":
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rsem: \$(rsem-calculate-expression --version | sed -e "s/Current version: RSEM v//g")
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star: \$(STAR --version | sed -e "s/STAR_//g")
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END_VERSIONS
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"""
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}
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}
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