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Bug fixes

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This commit is contained in:
drpatelh 2020-10-12 16:20:22 +01:00
parent a1b705d412
commit 64377d4035
1 changed files with 6 additions and 5 deletions
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11
software/rsem/calculateexpression/main.nf
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@ -8,10 +8,10 @@ process RSEM_CALCULATEEXPRESSION {
mode: params.publish_dir_mode,
saveAs: { filename -> saveFiles(filename:filename, options:options, publish_dir:getSoftwareName(task.process), publish_id:meta.id) }
container "quay.io/biocontainers/rsem:1.3.3--pl526ha52163a_0"
//container "https://depot.galaxyproject.org/singularity/rsem:1.3.3--pl526ha52163a_0"
container "quay.io/biocontainers/mulled-v2-cf0123ef83b3c38c13e3b0696a3f285d3f20f15b:606b713ec440e799d53a2b51a6e79dbfd28ecf3e-0"
//container "https://depot.galaxyproject.org/singularity/mulled-v2-cf0123ef83b3c38c13e3b0696a3f285d3f20f15b:606b713ec440e799d53a2b51a6e79dbfd28ecf3e-0"
conda (params.conda ? "bioconda::rsem=1.3.3" : null)
conda (params.conda ? "bioconda::rsem=1.3.3 bioconda::star=2.7.6a" : null)
input:
tuple val(meta), path(reads)
@ -22,6 +22,7 @@ process RSEM_CALCULATEEXPRESSION {
tuple val(meta), path("*.genes.results") , emit: counts_gene
tuple val(meta), path("*.isoforms.results"), emit: counts_transcript
tuple val(meta), path("*.stat") , emit: stat
tuple val(meta), path("*.log") , emit: logs
path "*.version.txt" , emit: version
tuple val(meta), path("*.STAR.genome.bam") , optional:true, emit: bam_star
@ -32,7 +33,7 @@ process RSEM_CALCULATEEXPRESSION {
def software = getSoftwareName(task.process)
def ioptions = initOptions(options)
prefix = ioptions.suffix ? "${meta.id}${ioptions.suffix}" : "${meta.id}"
def strandedness = ''
if (meta.strandedness == 'forward') {
strandedness = '--strandedness forward'
@ -45,8 +46,8 @@ process RSEM_CALCULATEEXPRESSION {
rsem-calculate-expression \\
--num-threads $task.cpus \\
--temporary-folder ./tmp/ \\
$paired_end \\
$strandedness \\
$paired_end \\
$ioptions.args \\
$reads \\
\$INDEX \\