From 966011bb839471670d0eb3874931d151ca0333ee Mon Sep 17 00:00:00 2001
From: Mia Croiset <mia.croiset@ens-lyon.fr>
Date: Thu, 22 Feb 2024 15:18:43 +0100
Subject: [PATCH] remove duplicated arguments between the two workflows
---
conf/modules.config | 4 +---
docs/hicstuff_usage.md | 13 +++----------
nextflow.config | 3 ---
nextflow_schema.json | 14 --------------
4 files changed, 4 insertions(+), 30 deletions(-)
diff --git a/conf/modules.config b/conf/modules.config
index f593dad..25fb8d3 100644
--- a/conf/modules.config
+++ b/conf/modules.config
@@ -432,8 +432,7 @@ process {
ext.output_rev = { "${meta2.id}_${meta2.chunk}_${meta2.mates}_digested.fastq" }
ext.args = { [
" -m ${params.cutsite_mode}",
- " -s ${params.cutsite_seed}",
- " -c ${params.cutsite_cpu}"
+ " -s ${params.cutsite_seed}"
].join('').trim()
}
publishDir = [
@@ -447,7 +446,6 @@ process {
ext.prefix = { "${meta.id}_${meta.chunk}_${meta.mates}" }
ext.args = { [
" -t ${params.hicstuff_tmp_dir}",
- " -n ${params.hicstuff_cpu}",
" -m ${params.hicstuff_min_qual}",
" -l ${params.hicstuff_read_len}"
].join('').trim()
diff --git a/docs/hicstuff_usage.md b/docs/hicstuff_usage.md
index a89057e..f7b4b3e 100644
--- a/docs/hicstuff_usage.md
+++ b/docs/hicstuff_usage.md
@@ -280,16 +280,9 @@ Common name of matrix files. Default: 'abs_fragments_contacts_weighted.txt'
--hicstuff_matrix '[Name of matrix file]'
```
-#### `--hicstuff_bin`
-Binsize for plotting matrix. Default: 10000
-
-```bash
---hicstuff_bin [binsize]
-```
-
-> :warning: **Warning**: Depending of the size of your input, the bin size may not correspond and make the pipeline fail
->>10000 is default for human genome.
->>For yeast for example you may want to use a smaller bin
+> :warning: **Warning**: Hicstuff builds matrices based on the fragments file
+>> For matrices build with fixed bin size, it's done in the COOLER subworkflow.
+>> See [bin_size](usage.md#bin_size) to change the size of the bin for fixed bin matrices.
### `--skip_plot_matrix`
diff --git a/nextflow.config b/nextflow.config
index 3c268a4..a9d73c3 100644
--- a/nextflow.config
+++ b/nextflow.config
@@ -149,7 +149,6 @@ params {
hicstuff_valid_idx = 'valid_idx.pairs'
hicstuff_min_qual = 30
hicstuff_matrix = 'abs_fragments_contacts_weighted.txt'
- hicstuff_bin = 10000
hicstuff_valid_idx_filtered = 'valid_idx_filtered.pairs'
hicstuff_plot_events = 'false'
hicstuff_pie_plot = 'distrib'
@@ -162,7 +161,6 @@ params {
hicstuff_distance_out_plot = 'plot_distance_law.pdf'
hicstuff_filter_pcr_out_file = 'valid_idx_pcrfree.pairs'
hicstuff_read_len = 'None'
- hicstuff_cpu = 4
hicstuff_tmp_dir = 'None'
//Hicstuff optional modules
@@ -176,7 +174,6 @@ params {
//Cutsite
cutsite_mode = 'for_vs_rev'
cutsite_seed = 0
- cutsite_cpu = 4
save_digested = false
cutsite = false
diff --git a/nextflow_schema.json b/nextflow_schema.json
index 2067b79..3568326 100644
--- a/nextflow_schema.json
+++ b/nextflow_schema.json
@@ -579,12 +579,6 @@
"default": false,
"fa_icon": "fas fa-cogs"
},
- "hicstuff_bin": {
- "type": "integer",
- "description": "Binsize for plotting matrix",
- "default": 10000,
- "fa_icon": "fas fa-cogs"
- },
"hicstuff_output_contigs": {
"type": "string",
"description": "Name of info contigs file",
@@ -723,10 +717,6 @@
"type": "boolean",
"description": "If true, do cutsite process to pre digest reads"
},
- "cutsite_cpu": {
- "type": "integer",
- "description": "Number of cpu to use for cutsite"
- },
"cutsite_seed": {
"type": "integer",
"description": "Minimum size of a fragment (i.e. seed size used in mapping as reads smaller won't be mapped.)"
@@ -744,10 +734,6 @@
"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"
--
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