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

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merged 1 commit into from
Dec 13, 2021
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Fix transcriptome staging issues on DNAnexus for rsem/prepareference #1163

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10 changes: 7 additions & 3 deletions modules/rsem/preparereference/main.nf
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Original file line number Diff line number Diff line change
Expand Up @@ -12,9 +12,9 @@ process RSEM_PREPAREREFERENCE {
path gtf

output:
path "rsem" , emit: index
path "rsem/*transcripts.fa", emit: transcript_fasta
path "versions.yml" , emit: versions
path "rsem" , emit: index
path "*transcripts.fa", emit: transcript_fasta
path "versions.yml" , emit: versions

script:
def args = task.ext.args ?: ''
Expand All @@ -40,6 +40,8 @@ process RSEM_PREPAREREFERENCE {
$fasta \\
rsem/genome

cp rsem/genome.transcripts.fa .
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cat <<-END_VERSIONS > versions.yml
"${task.process}":
rsem: \$(rsem-calculate-expression --version | sed -e "s/Current version: RSEM v//g")
Expand All @@ -55,6 +57,8 @@ process RSEM_PREPAREREFERENCE {
$fasta \\
rsem/genome

cp rsem/genome.transcripts.fa .

cat <<-END_VERSIONS > versions.yml
"${task.process}":
rsem: \$(rsem-calculate-expression --version | sed -e "s/Current version: RSEM v//g")
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