Changing param name from shard_fastq to run_fastq_sharding

nf-core · Aug 25, 2023 · efd07f2 · efd07f2
1 parent 29a3b3a
commit efd07f2
Show file tree

Hide file tree

Showing 5 changed files with 10 additions and 10 deletions.
diff --git a/conf/modules.config b/conf/modules.config
@@ -368,7 +368,7 @@ process {
     withName: SEQKIT_SPLIT2 {
         tag = { "${meta.sample_id}_${meta.library_id}_L${meta.lane}" }
         ext.prefix = "out"
-        ext.args = "-s ${params.shard_size}"
+        ext.args = "-s ${params.fastq_shard_size}"
         publishDir = [
             enabled: false
         ]
@@ -457,7 +457,7 @@ process {
         publishDir = [
             enabled: false
         ]
-        ext.args = { params.shard_fastq ? "-c -p" : "" }
+        ext.args = { params.run_fastq_sharding ? "-c -p" : "" }
     }
 
     withName: SAMTOOLS_SORT_MERGED_LANES {

diff --git a/conf/test.config b/conf/test.config
@@ -28,8 +28,8 @@ params {
     fasta = 'https://raw.githubusercontent.com/nf-core/test-datasets/eager/reference/Mammoth/Mammoth_MT_Krause.fasta'
 
     // Sharding FASTQ
-    shard_fastq                           = true
-    shard_size                             = 5000
+    run_fastq_sharding                           = true
+    fastq_shard_size                             = 5000
 
     // BAM filtering
     run_bamfiltering                      = true

diff --git a/nextflow.config b/nextflow.config
@@ -33,8 +33,8 @@ params {
     multiqc_methods_description = null
 
     // Shard Fastq options
-    shard_fastq                = false
-    shard_size                 = 1000000
+    run_fastq_sharding                = false
+    fastq_shard_size                  = 1000000
 
     // bedtools options
     run_bedtools_coverage         = false

diff --git a/nextflow_schema.json b/nextflow_schema.json
@@ -476,18 +476,18 @@
             "description": "Options for aligning reads against reference genome(s)",
             "default": "",
             "properties": {
-                "shard_fastq": {
+                "run_fastq_sharding": {
                     "type": "boolean",
                     "description": "Turn on sharding to split reads into smaller chunks before mapping",
                     "fa_icon": "fas fa-power-off",
                     "help_text": "Sharding reads before mapping can help parallelise mapping for very large FASTQs.  "
                 },
-                "shard_size": {
+                "fastq_shard_size": {
                     "type": "integer",
                     "default": 1000000,
                     "description": "Specify the number of reads in each shard when splitting.",
                     "fa_icon": "fas fa-arrows-alt-v",
-                    "help_text": "Make sure to choose a value that makes sense for your dataset. Small values can create many files. Needs `--shard_fastq`"
+                    "help_text": "Make sure to choose a value that makes sense for your dataset. Small values can create many files. Needs `--run_fastq_sharding`"
                 },
                 "mapping_tool": {
                     "type": "string",

diff --git a/subworkflows/local/map.nf b/subworkflows/local/map.nf
@@ -20,7 +20,7 @@ workflow MAP {
     ch_versions       = Channel.empty()
     ch_multiqc_files  = Channel.empty()
 
-    if ( params.shard_fastq ) {
+    if ( params.run_fastq_sharding ) {
 
         ch_input_for_sharding = reads