Commit c735ddd1 authored by mmassaviol's avatar mmassaviol
Browse files

Update yaml files

parent 3ca3e366
......@@ -5,6 +5,8 @@
website: "https://bioconductor.org/packages/release/bioc/html/DESeq2.html",
git: "git clone https://git.bioconductor.org/packages/DESeq2",
description: "Differential gene expression analysis based on the negative binomial distribution. Using normalized count data.",
version: "3.8",
documentation: "https://bioconductor.org/packages/release/bioc/manuals/DESeq2/man/DESeq2.pdf",
commands:
[
{
......@@ -44,7 +46,7 @@
{
name: deseq2_fitType,
type: radio,
selected: "parametric",
value: "parametric",
choices: [parametric: parametric, local: local, mean: mean],
label: "Type of fitting of dispersions to the mean intensity",
},
......@@ -57,23 +59,21 @@
{
name: deseq2_testType,
type: radio,
selected: "LRT",
value: "LRT",
choices: [LRT: LRT, Wald: Wald],
label: "Test type: Use either Wald significance tests, or the likelihood ratio test on the difference in deviance between a full and reduced model formula",
},
],
},
],
version: "3.8",
documentation: "https://bioconductor.org/packages/release/bioc/manuals/DESeq2/man/DESeq2.pdf",
install:
{
DESeq2: 'Rscript -e ''BiocManager::install("DESeq2", version = "3.8",Ncpus=8)''',
apeglm: 'Rscript -e ''BiocManager::install("apeglm", version = "3.8",Ncpus=8)''',
BiocParallel: 'Rscript -e ''BiocManager::install("BiocParallel", 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)''',
DESeq2: 'Rscript -e ''BiocManager::install("DESeq2", version = "3.8",Ncpus=8, clean=TRUE)''',
apeglm: 'Rscript -e ''BiocManager::install("apeglm", version = "3.8",Ncpus=8, clean=TRUE)''',
BiocParallel: 'Rscript -e ''BiocManager::install("BiocParallel", version = "3.8",Ncpus=8, clean=TRUE)''',
tximport: 'Rscript -e ''BiocManager::install("tximport", version = "3.8",Ncpus=8, clean=TRUE)''',
rhdf5: 'Rscript -e ''BiocManager::install("rhdf5", version = "3.8",Ncpus=8, clean=TRUE)''',
GenomicFeatures: 'Rscript -e ''BiocManager::install("GenomicFeatures", version = "3.8",Ncpus=8, clean=TRUE)''',
},
script: deseq2.script.R,
}
......@@ -5,6 +5,8 @@
website: "http://bioconductor.org/packages/release/bioc/html/edgeR.html",
git: "git clone https://git.bioconductor.org/packages/edgeR",
description: "Empirical Analysis of Digital Gene Expression Data.",
version: "3.14.0",
documentation: "http://bioconductor.org/packages/release/bioc/manuals/edgeR/man/edgeR.pdf",
commands:
[
{
......@@ -12,7 +14,11 @@
command: ~,
output_dir: edger,
inputs: [{ name: counts }],
outputs: [{ name: de_table }, { name: RData }],
outputs:
[
{ name: de_table, file: de_table.csv },
{ name: RData, file: data.RData },
],
options:
[
{
......@@ -40,8 +46,9 @@
{
name: edger_normfact,
type: radio,
selected: "TMM",
choices: [TMM: TMM, RLE: RLE, upperquartile: upperquartile, none: none],
value: "TMM",
choices:
[TMM: TMM, RLE: RLE, upperquartile: upperquartile, none: none],
label: "Calculate normalization factors to scale the raw library sizes.",
},
{
......@@ -53,22 +60,20 @@
{
name: edger_testType,
type: radio,
selected: "exactTest",
value: "exactTest",
choices: [exactTest: exactTest, glmLRT: glmLRT],
label: "Test type: exactTest: Computes p-values for differential abundance for each gene between two samples, conditioning on the total count for each gene. The counts in each group are assumed to follow a binomial distribution\nglmLRT: Fits a negative binomial generalized log-linear model to the read counts for each gene and conducts genewise statistical tests.",
},
],
},
],
version: "3.14.0",
documentation: "http://bioconductor.org/packages/release/bioc/manuals/edgeR/man/edgeR.pdf",
install:
{
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)''',
limma: 'Rscript -e ''BiocManager::install("limma", version = "3.8",Ncpus=8, clean=TRUE)''',
edger: 'Rscript -e ''BiocManager::install("edgeR", version = "3.8",Ncpus=8, clean=TRUE)''',
tximport: 'Rscript -e ''BiocManager::install("tximport", version = "3.8",Ncpus=8, clean=TRUE)''',
rhdf5: 'Rscript -e ''BiocManager::install("rhdf5", version = "3.8",Ncpus=8, clean=TRUE)''',
GenomicFeatures: 'Rscript -e ''BiocManager::install("GenomicFeatures", version = "3.8",Ncpus=8, clean=TRUE)''',
},
script: edger.script.R,
}
......@@ -5,14 +5,46 @@
website: "https://www.bioinformatics.babraham.ac.uk/projects/fastqc/",
git: "https://github.com/s-andrews/FastQC",
description: "A quality control tool for high throughput raw sequence data.",
version: "0.11.5",
documentation: "http://www.bioinformatics.babraham.ac.uk/projects/fastqc/Help/",
commands:
[
{
name: fastqc,
name: fastqc_SE,
command: fastqc,
output_dir: fastqc,
inputs: [{ name: reads }],
outputs:
[
{ name: html, file: "{sample}_fastqc.html" },
{ name: zip, file: "{sample}_fastqc.zip" },
],
options:
[
{
name: fastqc_threads,
prefix: -t,
type: numeric,
value: 4,
min: 1,
max: NA,
step: 1,
label: "Number of threads to use",
},
],
},
{
name: fastqc_PE,
command: fastqc,
output_dir: fastqc,
inputs: [{ name: reads }],
outputs: [{ name: html }, { name: zip }],
outputs:
[
{ name: html1, file: "{sample}_1_fastqc.html" },
{ name: zip1, file: "{sample}_1_fastqc.zip" },
{ name: html2, file: "{sample}_2_fastqc.html" },
{ name: zip1, file: "{sample}_2_fastqc.zip" },
],
options:
[
{
......@@ -28,7 +60,5 @@
],
},
],
version: "0.11.5",
documentation: "http://www.bioinformatics.babraham.ac.uk/projects/fastqc/Help/",
install: { fastqc: "conda install -c bioconda fastqc=0.11.5" },
}
......@@ -5,14 +5,16 @@
website: "https://pachterlab.github.io/kallisto/",
git: "https://github.com/pachterlab/kallisto",
description: "kallisto is a program for quantifying abundances of transcripts from RNA-Seq data, or more generally of target sequences using high-throughput sequencing reads.",
version: "0.44.0",
documentation: "https://pachterlab.github.io/kallisto/manual",
commands:
[
{
name: kallisto_index,
command: kallisto index,
output_dir: kallisto/index,
inputs: [{ name: kallisto_index_input }],
outputs: [{ name: index }],
inputs: [{ name: kallisto_index_input, file: ""}],
outputs: [{ name: index, file: index.kidx }],
options:
[
{
......@@ -24,10 +26,10 @@
],
},
{
name: kallisto_quant,
name: kallisto_quant_SE,
command: kallisto quant,
output_dir: kallisto/quant,
inputs: [{ name: index }, { name: reads }],
inputs: [{ name: kallisto_quant_index, file: kallisto/index/index.kidx }, { name: reads }],
outputs:
[
{ name: h5, file: "{sample}/abundance.h5" },
......@@ -47,7 +49,52 @@
label: "Number of threads to use",
},
{
name: kallisto_quant_pe_stranded,
name: kallisto_quant_SE_fragment_length,
prefix: -l,
type: numeric,
value: 300,
min: 1,
max: NA,
step: 1,
label: "Estimated average fragment length",
},
{
name: kallisto_quant_SE_standard_deviation,
prefix: -s,
type: numeric,
value: 2,
min: 1,
max: NA,
step: 1,
label: "Estimated standard deviation of fragment length",
}
],
},
{
name: kallisto_quant_PE,
command: kallisto quant,
output_dir: kallisto/quant,
inputs: [{ name: kallisto_quant_index, file: kallisto/index/index.kidx }, { name: reads }],
outputs:
[
{ name: h5, file: "{sample}/abundance.h5" },
{ name: counts, file: "{sample}/abundance.tsv" },
{ name: run_info, file: "{sample}/run_info.json" },
],
options:
[
{
name: kallisto_quant_threads,
prefix: -t,
type: numeric,
value: 4,
min: 1,
max: NA,
step: 1,
label: "Number of threads to use",
},
{
name: kallisto_quant_PE_stranded,
type: radio,
choices:
[
......@@ -59,10 +106,8 @@
label: For strand specific mode choose --fr-stranded if the first read is forward and choose --rf-stranded if the first read is reverse,
},
],
},
}
],
version: "0.44.0",
documentation: "https://pachterlab.github.io/kallisto/manual",
install:
{ kallisto: "conda install -c bioconda -c conda-forge kallisto=0.44.0" },
}
......@@ -8,10 +8,11 @@
commands:
[
{
name: "",
name: "null",
output_dir: "",
inputs: [],
options: [
]
outputs: [],
options: []
}
],
version: "",
......
......@@ -5,6 +5,8 @@
website: "https://combine-lab.github.io/salmon/",
git: "https://github.com/COMBINE-lab/salmon",
description: "Salmon is a tool for quantifying the expression of transcripts using RNA-seq data. ",
version: "0.11.3",
documentation: "https://salmon.readthedocs.io/en/latest/",
commands:
[
{
......@@ -12,7 +14,7 @@
command: salmon index,
output_dir: salmon/index,
inputs: [{ name: salmon_index_input }],
outputs: [{ name: index }],
outputs: [{ name: index, directory: salmon/index }],
options:
[
{
......@@ -35,10 +37,35 @@
],
},
{
name: salmon_quant,
name: salmon_quant_SE,
command: salmon quant,
output_dir: salmon/quant,
inputs: [{ name: index, directory: salmon/index }, { name: reads }],
outputs:
[
{ name: lib_counts, file: "salmon/quant/{sample}/lib_format_counts.json" },
{ name: counts, file: "salmon/quant/{sample}/quant.sf" },
{ name: run_info, file: "salmon/quant/{sample}/cmd_info.json" },
],
options:
[
{
name: salmon_quant_threads,
prefix: -t,
type: numeric,
value: 4,
min: 1,
max: NA,
step: 1,
label: "Number of threads to use",
},
],
},
{
name: salmon_quant_PE,
command: salmon quant,
output_dir: salmon/quant,
inputs: [{ name: index }, { name: reads }],
inputs: [{ name: index, directory: salmon/index }, { name: reads }],
outputs:
[
{ name: lib_counts, file: "{sample}/lib_format_counts.json" },
......@@ -60,7 +87,5 @@
],
},
],
version: "0.11.3",
documentation: "https://salmon.readthedocs.io/en/latest/",
install: { salmon: "conda install -c bioconda -c conda-forge salmon=0.11.3" },
}
......@@ -5,15 +5,31 @@
website: "http://www.usadellab.org/cms/?page=trimmomatic",
git: ~,
description: A flexible read trimming tool for Illumina NGS data,
version: "0.38",
documentation: "http://www.usadellab.org/cms/uploads/supplementary/Trimmomatic/TrimmomaticManual_V0.32.pdf",
commands:
[
{
name: trimmomaticPE,
inputs: [
{name: raw_reads}
],
options: [
{
name: trimmomatic_PE,
command: java -jar trimmomatic-0.38.jar PE,
output_dir: trimmomatic,
inputs: [{ name: raw_reads }],
outputs:
[
{ name: readFP, file: "{sample}_forward_paired.fq.gz" },
{
name: readFU,
file: "{sample}_forward_unpaired.fq.gz",
},
{ name: readRP, file: "{sample}_reverse_paired.fq.gz" },
{
name: readRU,
file: "{sample}_reverse_unpaired.fq.gz",
},
],
options:
[
{
name: trimmomatic_threads,
prefix: -threads,
type: numeric,
......@@ -22,24 +38,25 @@
max: NA,
step: 1,
label: "Number of threads to use",
},
{
},
{
name: trimmomatic_qc_score,
type: radio,
selected: "-phred64",
value: "-phred64",
choices: [phred33: -phred33, phred64: -phred64],
label: "Quality score encoding",
},
]
],
},
{
name: trimmomaticSE,
inputs: [
{name: raw_reads}
],
options: [
{
name: trimmomatic_SE,
command: java -jar trimmomatic-0.38.jar SE,
output_dir: trimmomatic,
inputs: [{ name: raw_reads }],
outputs: [{ name: read, file: "{sample}_trimmed.fq.gz" }],
options:
[
{
name: trimmomatic_threads,
prefix: -threads,
type: numeric,
......@@ -48,19 +65,16 @@
max: NA,
step: 1,
label: "Number of threads to use",
},
{
},
{
name: trimmomatic_qc_score,
type: radio,
selected: "-phred64",
value: "-phred64",
choices: [phred33: -phred33, phred64: -phred64],
label: "Quality score encoding",
},
]
],
},
],
version: "0.38",
documentation: "http://www.usadellab.org/cms/uploads/supplementary/Trimmomatic/TrimmomaticManual_V0.32.pdf",
install: { trimmomatic: "conda install -c bioconda trimmomatic=0.38" },
}
......@@ -4,13 +4,12 @@
version: "0.0.1",
author: "MBB",
steps:
{
Quality check: { name: quality_check, tools: fastqc },
Quantification: { name: quantification, tools: kallisto
salmon },
Differential expression: { name: DE, tools: edger
deseq2 },
},
[
{ title: Trimming, name: trimming, tools: [trimmomatic, "null"], default: "null" },
{ title: Quality check, name: quality_check, tools: [fastqc], default: fastqc },
{ title: Quantification, name: quantification, tools: [kallisto, salmon], default: kallisto },
{ title: Differential expression, name: DE, tools: [edger, deseq2], default: edger },
],
options:
[
{
......@@ -34,7 +33,7 @@
{
name: "SeOrPe",
type: "radio",
selected: "PE",
value: "PE",
choices: [Single end: SE, Paired end: PE],
label: "Single end reads (SE) or Paired end reads (PE): ",
},
......
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