Commit 39412fb1 authored by mmassaviol's avatar mmassaviol
Browse files

Update threads options and references files

parent 18bf88fa
......@@ -19,6 +19,16 @@
],
options:
[
{
name: deseq2_threads,
prefix: -t,
type: numeric,
value: 4,
min: 1,
max: NA,
step: 1,
label: "Number of threads to use",
},
{
name: "deseq2_tx2gene",
type: "checkbox",
......
......@@ -15,6 +15,16 @@
outputs: [{ name: de_table }, { name: RData }],
options:
[
{
name: edger_threads,
prefix: -t,
type: numeric,
value: 4,
min: 1,
max: NA,
step: 1,
label: "Number of threads to use",
},
{
name: "edger_tx2gene",
type: "checkbox",
......@@ -34,8 +44,8 @@
documentation: "http://bioconductor.org/packages/release/bioc/manuals/edgeR/man/edgeR.pdf",
install:
{
limma: 'Rscript -e ''BiocManager::install("limma", version = "3.8")''',
edger: 'Rscript -e ''BiocManager::install("edgeR", version = "3.8")''',
limma: 'Rscript -e ''BiocManager::install("limma", version = "3.8",Ncpus=8)''',
edger: 'Rscript -e ''BiocManager::install("edgeR", version = "3.8",Ncpus=8)''',
tximport: 'Rscript -e ''BiocManager::install("tximport", version = "3.8",Ncpus=8)''',
rhdf5: 'Rscript -e ''BiocManager::install("rhdf5", version = "3.8",Ncpus=8)''',
GenomicFeatures: 'Rscript -e ''BiocManager::install("GenomicFeatures", version = "3.8",Ncpus=8)''',
......
......@@ -19,7 +19,7 @@
name: fastqc_threads,
prefix: -t,
type: numeric,
value: 1,
value: 4,
min: 1,
max: NA,
step: 1,
......
......@@ -11,17 +11,17 @@
name: kallisto_index,
command: kallisto index,
output_dir: kallisto/index,
inputs:
inputs: [{ name: kallisto_index_input }],
outputs: [{ name: index }],
options:
[
{
id: kallisto_index_input,
name: kallisto_index_input,
type: text,
value: "",
label: "Address to reference fasta file",
},
],
outputs: [{ name: index }],
options: [],
},
{
name: kallisto_quant,
......@@ -40,7 +40,7 @@
name: kallisto_quant_threads,
prefix: -t,
type: numeric,
value: 1,
value: 4,
min: 1,
max: NA,
step: 1,
......
......@@ -11,7 +11,9 @@
name: salmon_index,
command: salmon index,
output_dir: salmon/index,
inputs:
inputs: [{ name: salmon_index_input }],
outputs: [{ name: index }],
options:
[
{
name: salmon_index_input,
......@@ -20,15 +22,11 @@
value: "",
label: "Address to reference fasta file",
},
],
outputs: [{ name: index }],
options:
[
{
name: salmon_index_threads,
prefix: -p,
type: numeric,
value: 1,
value: 4,
min: 1,
max: NA,
step: 1,
......@@ -53,7 +51,7 @@
name: salmon_quant_threads,
prefix: -t,
type: numeric,
value: 1,
value: 4,
min: 1,
max: NA,
step: 1,
......
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