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Fix transcriptome staging issues on DNAnexus for rsem/prepareference (#1163)

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Harshil Patel 2021-12-13 14:10:29 +00:00 committed by GitHub
parent edbbbbf420
commit 47a9cf8ecb
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1 changed files with 7 additions and 3 deletions
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10
modules/rsem/preparereference/main.nf
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@ -12,9 +12,9 @@ process RSEM_PREPAREREFERENCE {
path gtf path gtf
output: output:
path "rsem" , emit: index path "rsem" , emit: index
path "rsem/*transcripts.fa", emit: transcript_fasta path "*transcripts.fa", emit: transcript_fasta
path "versions.yml" , emit: versions path "versions.yml" , emit: versions
script: script:
def args = task.ext.args ?: '' def args = task.ext.args ?: ''
@ -40,6 +40,8 @@ process RSEM_PREPAREREFERENCE {
$fasta \\ $fasta \\
rsem/genome rsem/genome
cp rsem/genome.transcripts.fa .
cat <<-END_VERSIONS > versions.yml cat <<-END_VERSIONS > versions.yml
"${task.process}": "${task.process}":
rsem: \$(rsem-calculate-expression --version | sed -e "s/Current version: RSEM v//g") rsem: \$(rsem-calculate-expression --version | sed -e "s/Current version: RSEM v//g")
@ -55,6 +57,8 @@ process RSEM_PREPAREREFERENCE {
$fasta \\ $fasta \\
rsem/genome rsem/genome
cp rsem/genome.transcripts.fa .
cat <<-END_VERSIONS > versions.yml cat <<-END_VERSIONS > versions.yml
"${task.process}": "${task.process}":
rsem: \$(rsem-calculate-expression --version | sed -e "s/Current version: RSEM v//g") rsem: \$(rsem-calculate-expression --version | sed -e "s/Current version: RSEM v//g")