Commit 56971a55 authored by khalid's avatar khalid
Browse files

Add a group_file inpput to edger and deseq2

parent 1457d60f
......@@ -16,7 +16,8 @@
command: ~,
category: "differential_expression",
output_dir: deseq2,
inputs: [{ name: counts, type: "tsv" }],
inputs: [{ name: counts, type: "tsv" }
{ name: group_file, type: "popmap", file: "", description: "Path to tsv file with samples conditions"}],
outputs:
[
{ name: de_table, type: "tsv", file: de_table.csv, description: "Tableau d'expression différentielle" },
......
......@@ -15,7 +15,9 @@
command: ~,
category: "differential_expression",
output_dir: edger,
inputs: [{ name: counts, type: "tsv" }],
inputs: [{ name: counts, type: "tsv" },
{ name: group_file, type: "popmap", file: "", description: "Path to tsv file with samples conditions"},
]
outputs:
[
{ name: de_table, type: "csv", file: de_table.csv, description: "Tableau d'expression différentielle" },
......
......@@ -18,7 +18,7 @@ if config["SeOrPe"] == "PE":
maxins = config["<step_name>__hisat2_maxins_PE"],
orientation = config["<step_name>__hisat2_orientation_PE"],
shell:
"{params.command} "
"{params.command} --new-summary "
"--threads {threads} "
"-x {params.indexPrefix} "
"-I {params.minins} "
......
......@@ -7,7 +7,7 @@
description: "A tool to quantify gene expression in RNA-Seq and similar experiments.",
version: "release_0.13.5",
documentation: "https://htseq.readthedocs.io",
multiqc: "htseq-count",
multiqc: "htseq",
commands:
[
{
......
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