Merge pull request #413 from nf-core/remove_harsh_trimming

remove harsh trimming option --trim

CHANGELOG.md

@@ -15,6 +15,8 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 ### Removed
 
+- Remove harsh trimming option `--trim` [#413](https://github.com/nf-core/rnafusion/pull/413)
+
 ## v2.4.0 - [2023/09/22]
 
 ### Added

docs/usage.md

@@ -184,10 +184,7 @@ You can also generate such `YAML`/`JSON` files via [nf-core/launch](https://nf-c
 
 #### Trimming
 
-There are 2 options to trim
-
-1. Fastp
-   In this case all tools use the trimmed reads. Quality and adapter trimming by default. In addition, tail trimming and adapter_fastq specification are possible. Example usage:
+When the flag `--fastp_trim` is used, `fastp` is used to provide all tools with trimmed reads. Quality and adapter trimming by default. In addition, tail trimming and adapter_fastq specification are possible. Example usage:
 
 ```bash
 nextflow run nf-core/rnafusion \
@@ -200,19 +197,7 @@ nextflow run nf-core/rnafusion \
 --adapter_fastq <PATH/TO/ADAPTER/FASTQ> (optional)
 ```
 
-2. Hard trimming
-   In this case, only reads fed to fusioncatcher are trimmed. This is a harsh workaround in case of high read-through. The recommended trimming is thus the fastp_trim one. The trimming is done at 75 bp from the tails. Example usage:
-
-```bash
-nextflow run nf-core/rnafusion \
---<tool1> --<tool2> ... \
---input <SAMPLE_SHEET.CSV> \
---genomes_base <PATH/TO/REFERENCES> \
---outdir <OUTPUT/PATH> \
---trim
-```
-
-#### Filter out fusions detected by less than INT tools
+#### Filter fusions detected by 2 or more tools
 
 ```bash
 nextflow run nf-core/rnafusion \

nextflow.config

@@ -35,7 +35,6 @@ params {
     tools_cutoff               = 1
 
     // Trimming
-    trim                       = false
     fastp_trim                 = false
     trim_tail                  = null
     adapter_fasta              = []

nextflow_schema.json

@@ -267,11 +267,6 @@
             "fa_icon": "fas fa-cut",
             "description": "Options to adjust read trimming criteria.",
             "properties": {
-                "trim": {
-                    "type": "boolean",
-                    "description": "Preform trimming of reads, default: false",
-                    "fa_icon": "fas fa-cut"
-                },
                 "fastp_trim": {
                     "type": "boolean",
                     "description": "Preform fastp trimming of reads, default: false",

subworkflows/local/trim_workflow.nf

@@ -1,4 +1,3 @@
-include { REFORMAT }                    from '../../modules/local/reformat/main'
 include { FASTQC as FASTQC_FOR_TRIM }   from '../../modules/nf-core/fastqc/main'
 include { FASTP }                       from '../../modules/nf-core/fastp/main'
 include { FASTQC as FASTQC_FOR_FASTP }  from '../../modules/nf-core/fastqc/main'
@@ -11,17 +10,7 @@ workflow TRIM_WORKFLOW {
     main:
         ch_versions = Channel.empty()
 
-        if (params.trim) {
-
-            REFORMAT( reads )
-            ch_versions = ch_versions.mix(REFORMAT.out.versions)
-            FASTQC_FOR_TRIM (REFORMAT.out.reads_out)
-            ch_versions = ch_versions.mix(FASTQC_FOR_TRIM.out.versions)
-
-            ch_reads_all = reads
-            ch_reads_fusioncatcher = REFORMAT.out.reads_out
-        }
-        else if (params.fastp_trim) {
+        if (params.fastp_trim) {
             FASTP(reads, params.adapter_fasta, false, false)
             ch_versions = ch_versions.mix(FASTP.out.versions)