From 47a9cf8ecbe4de4dcb8b9cc6731fece82b934ab7 Mon Sep 17 00:00:00 2001 From: Harshil Patel Date: Mon, 13 Dec 2021 14:10:29 +0000 Subject: [PATCH] Fix transcriptome staging issues on DNAnexus for rsem/prepareference (#1163) --- modules/rsem/preparereference/main.nf | 10 +++++++--- 1 file changed, 7 insertions(+), 3 deletions(-) diff --git a/modules/rsem/preparereference/main.nf b/modules/rsem/preparereference/main.nf index 95597b74..a5b8922a 100644 --- a/modules/rsem/preparereference/main.nf +++ b/modules/rsem/preparereference/main.nf @@ -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 ?: '' @@ -40,6 +40,8 @@ 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") @@ -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")