From 2d1bd8f770be689433552ebb5fd2ac93d1bc3786 Mon Sep 17 00:00:00 2001
From: Mia Croiset <mia.croiset@ens-lyon.fr>
Date: Wed, 7 Feb 2024 14:06:46 +0100
Subject: [PATCH] update json and usage files
---
docs/hicstuff_usage.md | 9 +++++++++
nextflow_schema.json | 16 ++++++++++++++++
2 files changed, 25 insertions(+)
diff --git a/docs/hicstuff_usage.md b/docs/hicstuff_usage.md
index c084b0c..a89057e 100644
--- a/docs/hicstuff_usage.md
+++ b/docs/hicstuff_usage.md
@@ -168,6 +168,15 @@ Default: false
Use [`--hicstuff_min_qual`](#hicstuff_min_qual) to set the minimum quality for the iterative alignment.
+#### `--hicstuff_read_len`
+
+Read length in the fasta file. If set to None, the length of the first read is used. Set this value to the longest read length in the file if you have different read lengths.
+Default: None
+
+```bash
+--hicstuff_read_len '[Wanted read length]'
+```
+
#### `--save_bam`
If specified, save BAM files after mapping (works for normal and iterative mode). Default: false
diff --git a/nextflow_schema.json b/nextflow_schema.json
index f5f0617..2067b79 100644
--- a/nextflow_schema.json
+++ b/nextflow_schema.json
@@ -735,6 +735,22 @@
"type": "string",
"description": "Mode to use to make the digestion.",
"enum": ["all", "for_vs_rev", "pile"]
+ },
+ "iteralign": {
+ "type": "boolean",
+ "description": "If true, do iterative alignment"
+ },
+ "hicstuff_tmp_dir": {
+ "type": "string",
+ "description": "Path where temporary files should be written"
+ },
+ "hicstuff_cpu": {
+ "type": "integer",
+ "description": "The number of CPUs to use for the iterative alignment"
+ },
+ "hicstuff_read_len": {
+ "type": "integer",
+ "description": "Read length in the fasta file. If set to None, the first read is used. Set this value to the longest read length in the file if you have different read lengths"
}
}
}
--
GitLab