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Merge pull request #68 from drpatelh/versions

Browse source 
Update tool versions
This commit is contained in:
Harshil Patel 2020-10-12 16:22:31 +01:00 committed by GitHub
commit d8f202c563
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15 changed files with 48 additions and 47 deletions
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6
software/gffread/main.nf
View file

@ -7,10 +7,10 @@ process GFFREAD {
mode: params.publish_dir_mode, mode: params.publish_dir_mode,
saveAs: { filename -> saveFiles(filename:filename, options:options, publish_dir:getSoftwareName(task.process), publish_id:'') } saveAs: { filename -> saveFiles(filename:filename, options:options, publish_dir:getSoftwareName(task.process), publish_id:'') }
container "quay.io/biocontainers/gffread:0.11.7--h8b12597_0" container "quay.io/biocontainers/gffread:0.12.1--h8b12597_0"
//container https://depot.galaxyproject.org/singularity/gffread:0.11.7--h8b12597_0 //container https://depot.galaxyproject.org/singularity/gffread:0.12.1--h8b12597_0
conda (params.conda ? "bioconda::gffread=0.11.7" : null) conda (params.conda ? "bioconda::gffread=0.12.1" : null)
input: input:
path gff path gff

6
software/picard/collectmultiplemetrics/main.nf
View file

@ -8,10 +8,10 @@ process PICARD_COLLECTMULTIPLEMETRICS {
mode: params.publish_dir_mode, mode: params.publish_dir_mode,
saveAs: { filename -> saveFiles(filename:filename, options:options, publish_dir:getSoftwareName(task.process), publish_id:meta.id) } saveAs: { filename -> saveFiles(filename:filename, options:options, publish_dir:getSoftwareName(task.process), publish_id:meta.id) }
container "quay.io/biocontainers/picard:2.23.2--0" container "quay.io/biocontainers/picard:2.23.6--0"
//container "https://depot.galaxyproject.org/singularity/picard:2.23.2--0" //container "https://depot.galaxyproject.org/singularity/picard:2.23.6--0"
conda (params.conda ? "bioconda::picard=2.23.2" : null) conda (params.conda ? "bioconda::picard=2.23.6" : null)
input: input:
tuple val(meta), path(bam) tuple val(meta), path(bam)

6
software/picard/markduplicates/main.nf
View file

@ -8,10 +8,10 @@ process PICARD_MARKDUPLICATES {
mode: params.publish_dir_mode, mode: params.publish_dir_mode,
saveAs: { filename -> saveFiles(filename:filename, options:options, publish_dir:getSoftwareName(task.process), publish_id:meta.id) } saveAs: { filename -> saveFiles(filename:filename, options:options, publish_dir:getSoftwareName(task.process), publish_id:meta.id) }
container "quay.io/biocontainers/picard:2.23.2--0" container "quay.io/biocontainers/picard:2.23.6--0"
//container "https://depot.galaxyproject.org/singularity/picard:2.23.2--0" //container "https://depot.galaxyproject.org/singularity/picard:2.23.6--0"
conda (params.conda ? "bioconda::picard=2.23.2" : null) conda (params.conda ? "bioconda::picard=2.23.6" : null)
input: input:
tuple val(meta), path(bam) tuple val(meta), path(bam)

6
software/picard/mergesamfiles/main.nf
View file

@ -8,10 +8,10 @@ process PICARD_MERGESAMFILES {
mode: params.publish_dir_mode, mode: params.publish_dir_mode,
saveAs: { filename -> saveFiles(filename:filename, options:options, publish_dir:getSoftwareName(task.process), publish_id:meta.id) } saveAs: { filename -> saveFiles(filename:filename, options:options, publish_dir:getSoftwareName(task.process), publish_id:meta.id) }
container "quay.io/biocontainers/picard:2.23.2--0" container "quay.io/biocontainers/picard:2.23.6--0"
//container "https://depot.galaxyproject.org/singularity/picard:2.23.2--0" //container "https://depot.galaxyproject.org/singularity/picard:2.23.6--0"
conda (params.conda ? "bioconda::picard=2.23.2" : null) conda (params.conda ? "bioconda::picard=2.23.6" : null)
input: input:
tuple val(meta), path(bams) tuple val(meta), path(bams)

11
software/rsem/calculateexpression/main.nf
View file

@ -8,10 +8,10 @@ process RSEM_CALCULATEEXPRESSION {
mode: params.publish_dir_mode, mode: params.publish_dir_mode,
saveAs: { filename -> saveFiles(filename:filename, options:options, publish_dir:getSoftwareName(task.process), publish_id:meta.id) } 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 "quay.io/biocontainers/mulled-v2-cf0123ef83b3c38c13e3b0696a3f285d3f20f15b:606b713ec440e799d53a2b51a6e79dbfd28ecf3e-0"
//container "https://depot.galaxyproject.org/singularity/rsem:1.3.3--pl526ha52163a_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: input:
tuple val(meta), path(reads) 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("*.genes.results") , emit: counts_gene
tuple val(meta), path("*.isoforms.results"), emit: counts_transcript tuple val(meta), path("*.isoforms.results"), emit: counts_transcript
tuple val(meta), path("*.stat") , emit: stat tuple val(meta), path("*.stat") , emit: stat
tuple val(meta), path("*.log") , emit: logs
path "*.version.txt" , emit: version path "*.version.txt" , emit: version
tuple val(meta), path("*.STAR.genome.bam") , optional:true, emit: bam_star 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 software = getSoftwareName(task.process)
def ioptions = initOptions(options) def ioptions = initOptions(options)
prefix = ioptions.suffix ? "${meta.id}${ioptions.suffix}" : "${meta.id}" prefix = ioptions.suffix ? "${meta.id}${ioptions.suffix}" : "${meta.id}"
def strandedness = '' def strandedness = ''
if (meta.strandedness == 'forward') { if (meta.strandedness == 'forward') {
strandedness = '--strandedness forward' strandedness = '--strandedness forward'
@ -45,8 +46,8 @@ process RSEM_CALCULATEEXPRESSION {
rsem-calculate-expression \\ rsem-calculate-expression \\
--num-threads $task.cpus \\ --num-threads $task.cpus \\
--temporary-folder ./tmp/ \\ --temporary-folder ./tmp/ \\
$paired_end \\
$strandedness \\ $strandedness \\
$paired_end \\
$ioptions.args \\ $ioptions.args \\
$reads \\ $reads \\
\$INDEX \\ \$INDEX \\

6
software/rsem/preparereference/main.nf
View file

@ -8,10 +8,10 @@ process RSEM_PREPAREREFERENCE {
mode: params.publish_dir_mode, mode: params.publish_dir_mode,
saveAs: { filename -> saveFiles(filename:filename, options:options, publish_dir:getSoftwareName(task.process), publish_id:'') } saveAs: { filename -> saveFiles(filename:filename, options:options, publish_dir:getSoftwareName(task.process), publish_id:'') }
container "quay.io/biocontainers/rsem:1.3.3--pl526ha52163a_0" container "quay.io/biocontainers/mulled-v2-cf0123ef83b3c38c13e3b0696a3f285d3f20f15b:606b713ec440e799d53a2b51a6e79dbfd28ecf3e-0"
//container "https://depot.galaxyproject.org/singularity/rsem:1.3.3--pl526ha52163a_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: input:
path fasta path fasta

6
software/rseqc/bamstat/main.nf
View file

@ -8,10 +8,10 @@ process RSEQC_BAMSTAT {
mode: params.publish_dir_mode, mode: params.publish_dir_mode,
saveAs: { filename -> saveFiles(filename:filename, options:options, publish_dir:getSoftwareName(task.process), publish_id:meta.id) } saveAs: { filename -> saveFiles(filename:filename, options:options, publish_dir:getSoftwareName(task.process), publish_id:meta.id) }
container "quay.io/biocontainers/rseqc:3.0.1--py37h516909a_1" container "quay.io/biocontainers/rseqc:4.0.0--py38h0213d0e_0"
//container "https://depot.galaxyproject.org/singularity/rseqc:3.0.1--py37h516909a_1" //container "https://depot.galaxyproject.org/singularity/rseqc:4.0.0--py38h0213d0e_0"
conda (params.conda ? "bioconda::rseqc=3.0.1" : null) conda (params.conda ? "bioconda::rseqc=4.0.0" : null)
input: input:
tuple val(meta), path(bam) tuple val(meta), path(bam)

6
software/rseqc/inferexperiment/main.nf
View file

@ -8,10 +8,10 @@ process RSEQC_INFEREXPERIMENT {
mode: params.publish_dir_mode, mode: params.publish_dir_mode,
saveAs: { filename -> saveFiles(filename:filename, options:options, publish_dir:getSoftwareName(task.process), publish_id:meta.id) } saveAs: { filename -> saveFiles(filename:filename, options:options, publish_dir:getSoftwareName(task.process), publish_id:meta.id) }
container "quay.io/biocontainers/rseqc:3.0.1--py37h516909a_1" container "quay.io/biocontainers/rseqc:4.0.0--py38h0213d0e_0"
//container "https://depot.galaxyproject.org/singularity/rseqc:3.0.1--py37h516909a_1" //container "https://depot.galaxyproject.org/singularity/rseqc:4.0.0--py38h0213d0e_0"
conda (params.conda ? "bioconda::rseqc=3.0.1" : null) conda (params.conda ? "bioconda::rseqc=4.0.0" : null)
input: input:
tuple val(meta), path(bam) tuple val(meta), path(bam)

6
software/rseqc/innerdistance/main.nf
View file

@ -8,10 +8,10 @@ process RSEQC_INNERDISTANCE {
mode: params.publish_dir_mode, mode: params.publish_dir_mode,
saveAs: { filename -> saveFiles(filename:filename, options:options, publish_dir:getSoftwareName(task.process), publish_id:meta.id) } saveAs: { filename -> saveFiles(filename:filename, options:options, publish_dir:getSoftwareName(task.process), publish_id:meta.id) }
container "quay.io/biocontainers/rseqc:3.0.1--py37h516909a_1" container "quay.io/biocontainers/rseqc:4.0.0--py38h0213d0e_0"
//container "https://depot.galaxyproject.org/singularity/rseqc:3.0.1--py37h516909a_1" //container "https://depot.galaxyproject.org/singularity/rseqc:4.0.0--py38h0213d0e_0"
conda (params.conda ? "bioconda::rseqc=3.0.1" : null) conda (params.conda ? "bioconda::rseqc=4.0.0" : null)
input: input:
tuple val(meta), path(bam) tuple val(meta), path(bam)

6
software/rseqc/junctionannotation/main.nf
View file

@ -8,10 +8,10 @@ process RSEQC_JUNCTIONANNOTATION {
mode: params.publish_dir_mode, mode: params.publish_dir_mode,
saveAs: { filename -> saveFiles(filename:filename, options:options, publish_dir:getSoftwareName(task.process), publish_id:meta.id) } saveAs: { filename -> saveFiles(filename:filename, options:options, publish_dir:getSoftwareName(task.process), publish_id:meta.id) }
container "quay.io/biocontainers/rseqc:3.0.1--py37h516909a_1" container "quay.io/biocontainers/rseqc:4.0.0--py38h0213d0e_0"
//container "https://depot.galaxyproject.org/singularity/rseqc:3.0.1--py37h516909a_1" //container "https://depot.galaxyproject.org/singularity/rseqc:4.0.0--py38h0213d0e_0"
conda (params.conda ? "bioconda::rseqc=3.0.1" : null) conda (params.conda ? "bioconda::rseqc=4.0.0" : null)
input: input:
tuple val(meta), path(bam) tuple val(meta), path(bam)

6
software/rseqc/junctionsaturation/main.nf
View file

@ -8,10 +8,10 @@ process RSEQC_JUNCTIONSATURATION {
mode: params.publish_dir_mode, mode: params.publish_dir_mode,
saveAs: { filename -> saveFiles(filename:filename, options:options, publish_dir:getSoftwareName(task.process), publish_id:meta.id) } saveAs: { filename -> saveFiles(filename:filename, options:options, publish_dir:getSoftwareName(task.process), publish_id:meta.id) }
container "quay.io/biocontainers/rseqc:3.0.1--py37h516909a_1" container "quay.io/biocontainers/rseqc:4.0.0--py38h0213d0e_0"
//container "https://depot.galaxyproject.org/singularity/rseqc:3.0.1--py37h516909a_1" //container "https://depot.galaxyproject.org/singularity/rseqc:4.0.0--py38h0213d0e_0"
conda (params.conda ? "bioconda::rseqc=3.0.1" : null) conda (params.conda ? "bioconda::rseqc=4.0.0" : null)
input: input:
tuple val(meta), path(bam) tuple val(meta), path(bam)

6
software/rseqc/readdistribution/main.nf
View file

@ -8,10 +8,10 @@ process RSEQC_READDISTRIBUTION {
mode: params.publish_dir_mode, mode: params.publish_dir_mode,
saveAs: { filename -> saveFiles(filename:filename, options:options, publish_dir:getSoftwareName(task.process), publish_id:meta.id) } saveAs: { filename -> saveFiles(filename:filename, options:options, publish_dir:getSoftwareName(task.process), publish_id:meta.id) }
container "quay.io/biocontainers/rseqc:3.0.1--py37h516909a_1" container "quay.io/biocontainers/rseqc:4.0.0--py38h0213d0e_0"
//container "https://depot.galaxyproject.org/singularity/rseqc:3.0.1--py37h516909a_1" //container "https://depot.galaxyproject.org/singularity/rseqc:4.0.0--py38h0213d0e_0"
conda (params.conda ? "bioconda::rseqc=3.0.1" : null) conda (params.conda ? "bioconda::rseqc=4.0.0" : null)
input: input:
tuple val(meta), path(bam) tuple val(meta), path(bam)

6
software/rseqc/readduplication/main.nf
View file

@ -8,10 +8,10 @@ process RSEQC_READDUPLICATION {
mode: params.publish_dir_mode, mode: params.publish_dir_mode,
saveAs: { filename -> saveFiles(filename:filename, options:options, publish_dir:getSoftwareName(task.process), publish_id:meta.id) } saveAs: { filename -> saveFiles(filename:filename, options:options, publish_dir:getSoftwareName(task.process), publish_id:meta.id) }
container "quay.io/biocontainers/rseqc:3.0.1--py37h516909a_1" container "quay.io/biocontainers/rseqc:4.0.0--py38h0213d0e_0"
//container "https://depot.galaxyproject.org/singularity/rseqc:3.0.1--py37h516909a_1" //container "https://depot.galaxyproject.org/singularity/rseqc:4.0.0--py38h0213d0e_0"
conda (params.conda ? "bioconda::rseqc=3.0.1" : null) conda (params.conda ? "bioconda::rseqc=4.0.0" : null)
input: input:
tuple val(meta), path(bam) tuple val(meta), path(bam)

6
software/stringtie/main.nf
View file

@ -8,10 +8,10 @@ process STRINGTIE {
mode: params.publish_dir_mode, mode: params.publish_dir_mode,
saveAs: { filename -> saveFiles(filename:filename, options:options, publish_dir:getSoftwareName(task.process), publish_id:meta.id) } saveAs: { filename -> saveFiles(filename:filename, options:options, publish_dir:getSoftwareName(task.process), publish_id:meta.id) }
container "quay.io/biocontainers/stringtie:2.1.2--h7e0af3c_1" container "quay.io/biocontainers/stringtie:2.1.4--h7e0af3c_0"
//container "https://depot.galaxyproject.org/singularity/stringtie:2.1.2--h7e0af3c_1" //container "https://depot.galaxyproject.org/singularity/stringtie:2.1.4--h7e0af3c_0"
conda (params.conda ? "bioconda::stringtie=2.1.2" : null) conda (params.conda ? "bioconda::stringtie=2.1.4" : null)
input: input:
tuple val(meta), path(bam) tuple val(meta), path(bam)

6
software/trimgalore/main.nf
View file

@ -8,10 +8,10 @@ process TRIMGALORE {
mode: params.publish_dir_mode, mode: params.publish_dir_mode,
saveAs: { filename -> saveFiles(filename:filename, options:options, publish_dir:getSoftwareName(task.process), publish_id:meta.id) } saveAs: { filename -> saveFiles(filename:filename, options:options, publish_dir:getSoftwareName(task.process), publish_id:meta.id) }
container "quay.io/biocontainers/trim-galore:0.6.5--0" container "quay.io/biocontainers/trim-galore:0.6.6--0"
//container "https://depot.galaxyproject.org/singularity/trim-galore:0.6.5--0" //container "https://depot.galaxyproject.org/singularity/trim-galore:0.6.6--0"
conda (params.conda ? "bioconda::trim-galore=0.6.5" : null) conda (params.conda ? "bioconda::trim-galore=0.6.6" : null)
input: input:
tuple val(meta), path(reads) tuple val(meta), path(reads)