[MERGE] dev nf-core

CHANGELOG.md

@@ -5,7 +5,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 ## v1.3.0 - 2021-22-05
 
-* Change the /tmp/ folder by ./tmp/ folder so that all tmp files are now in the work (#24)
+* Change the `/tmp/` folder to `./tmp/` folder so that all tmp files are now in the work directory (#24)
 * Add `--hicpro_maps` options to generate the raw and normalized HiC-Pro maps. The default is now to use cooler
 * Add chromosome compartments calling with cooltools (#53)
 * Add HiCExplorer distance decay quality control (#54)

docs/usage.md

@@ -145,7 +145,7 @@ process {
 }
 ```
 
-To find the exact name of a process you wish to modify the compute resources, check the live-status of a nextflow run displayed on your terminal or check the nextflow error for a line like so: `Error executing process > 'bwa'`. In this case the name to specify in the custom config file is `bwa`.
+To find the exact name of a process you wish to modify the compute resources, check the live-status of a nextflow run displayed on your terminal or check the nextflow error for a line like so: `Error executing process > 'bowtie2_end_to_end'`. In this case the name to specify in the custom config file is `bowtie2_end_to_end`.
 
 See the main [Nextflow documentation](https://www.nextflow.io/docs/latest/config.html) for more information.
 
@@ -485,7 +485,7 @@ framework to build the raw and balanced contact maps in txt and (m)cool formats.
 ### `--bin_size`
 
 Resolution of contact maps to generate (comma separated).
-Default:'1000000'
+Default:'1000000,500000'
 
 ```bash
 --bins_size '[string]'
@@ -592,7 +592,7 @@ Default: 'insulation'
 #### `--res_tads`
 
 Resolution to run the TADs calling analysis (comma separated).
-Default: '40000'
+Default: '40000,20000'
 
 ```bash
 --res_tads '[string]'

main.nf

@@ -121,9 +121,6 @@ if (params.split_fastq ){
 
 // Reference genome
 if ( params.bwt2_index ){
-   //lastPath = params.bwt2_index.lastIndexOf(File.separator)
-   //bwt2_dir =  params.bwt2_index.substring(0,lastPath+1)
-   //bwt2_base = params.bwt2_index.substring(lastPath+1)
 
    Channel.fromPath( params.bwt2_index , checkIfExists: true)
       .ifEmpty { exit 1, "Genome index: Provided index not found: ${params.bwt2_index}" }
@@ -131,10 +128,6 @@ if ( params.bwt2_index ){
 
 }
 else if ( params.fasta ) {
-   //lastPath = params.fasta.lastIndexOf(File.separator)
-   //fasta_base = params.fasta.substring(lastPath+1)
-   //fasta_base = fasta_base.toString() - ~/(\.fa)?(\.fasta)?(\.fas)?(\.fsa)?$/
-
    Channel.fromPath( params.fasta )
 	.ifEmpty { exit 1, "Genome index: Fasta file not found: ${params.fasta}" }
         .into { fasta_for_index }
@@ -551,9 +544,7 @@ if (!params.dnase){
       set val(oname), file("${prefix}.mapstat") into all_mapstat
 
       script:
-      //sample = prefix.toString() - ~/(_R1|_R2|_val_1|_val_2|_1|_2)/
       sample = prefix.toString() - ~/(_R1|_R2)/
-      //tag = prefix.toString() =~/_R1|_val_1|_1/ ? "R1" : "R2"
       tag = prefix.toString() =~/_R1/ ? "R1" : "R2"
       oname = prefix.toString() - ~/(\.[0-9]+)$/
       """
@@ -699,7 +690,7 @@ process remove_duplicates {
    mkdir -p stats/${sample}
 
    ## Sort valid pairs and remove read pairs with same starts (i.e duplicated read pairs)
-   sort -S 50% -k2,2V -k3,3n -k5,5V -k6,6n -m ${vpairs} | \
+   sort -S 50% -k2,2V -k3,3n -k5,5V -k6,6n -m ${vpairs} | \\
    awk -F"\\t" 'BEGIN{c1=0;c2=0;s1=0;s2=0}(c1!=\$2 || c2!=\$5 || s1!=\$3 || s2!=\$6){print;c1=\$2;c2=\$5;s1=\$3;s2=\$6}' > ${sample}.allValidPairs
 
    echo -n "valid_interaction\t" > ${sample}_allValidPairs.mergestat

nextflow_schema.json

@@ -227,7 +227,8 @@
             "properties": {
                 "bin_size": {
                     "type": "string",
-                    "default": "'1000000,500000'",
+                    "pattern": "^(\\d+)(,\\d+)*$",
+                    "default": "1000000,500000",
                     "description": "Resolution to build the maps (comma separated)"
                 },
                 "hicpro_maps": {
@@ -268,6 +269,7 @@
             "properties": {
                 "res_dist_decay": {
                     "type": "string",
+                    "pattern": "^(\\d+)(,\\d+)*$",
                     "default": "1000000",
                     "description": "Resolution to build count/distance plot"
                 },
@@ -278,11 +280,13 @@
                 },
                 "res_tads": {
                     "type": "string",
+                    "pattern": "^(\\d+)(,\\d+)*$",
                     "default": "40000,20000",
                     "description": "Resolution to run TADs callers (comma separated)"
                 },
                 "res_compartments": {
                     "type": "string",
+                    "pattern": "^(\\d+)(,\\d+)*$",
                     "default": "250000",
                     "description": "Resolution for compartments calling"
                 }