Adjustments for #76 , rename certain options to be more explicit

docs/usage.md

@@ -383,17 +383,17 @@ Turn this on to utilize BWA Mem instead of `bwa aln` for alignment. Can be quite
 
 Users can configure to keep/discard/extract certain groups of reads efficiently in the nf-core/eager pipeline. 
 
-### `--bam_keep_mapped_only`
+### `--bam_analyse_mapped_only`
 
-This can be used to only keep mapped reads for downstream analysis. By default turned off, all reads are kept in the BAM file. Unmapped reads are stored both in BAM and FastQ format e.g. for different downstream processing.
+This can be used to only keep mapped reads in the BAM file for downstream analysis. By default turned off, all reads are kept in the BAM file. Unmapped reads are stored both in BAM and FastQ format e.g. for different downstream processing.
 
 ### `--bam_keep_all`
 
 Turned on by default, keeps all reads that were mapped in the dataset. 
 
-### `--bam_filter_reads`
+### `--bam_retain_all_reads`
 
-Specify this, if you want to filter reads for downstream analysis. 
+Specify this, if you want to filter reads for downstream analysis. This keeps all mapped and unmapped reads in the output, but allows for quality threshold filtering using `--bam_mapping_quality_threshold`.
 
 ### `--bam_mapping_quality_threshold`
 

main.nf

@@ -76,8 +76,8 @@ def helpMessage() {
       --bwamem                      Turn on BWA Mem instead of CM/BWA aln for mapping
 
     BAM Filtering
-      --bam_keep_mapped_only            Only consider mapped reads for downstream analysis. Unmapped reads are extracted to separate output.
-      --bam_filter_reads                Keep all reads in BAM file for downstream analysis
+      --bam_analyse_mapped_only         Only consider mapped reads for downstream analysis. Unmapped reads are extracted to separate output.
+      --bam_retain_all_reads                Keep all reads in BAM file for downstream analysis
       --bam_mapping_quality_threshold   Minimum mapping quality for reads filter
 
     DeDuplication
@@ -173,9 +173,9 @@ params.circularfilter = false
 params.bwamem = false
 
 //BAM Filtering steps (default = keep mapped and unmapped in BAM file)
-params.bam_keep_mapped_only = false
+params.bam_analyse_mapped_only = false
 params.bam_keep_all = true
-params.bam_filter_reads = false
+params.bam_retain_all_reads = false
 params.bam_mapping_quality_threshold = 0
 
 //DamageProfiler settings
@@ -715,12 +715,12 @@ process samtools_filter {
     file "*.unmapped.bam" optional true
     file "*.bai"
 
-    when: "${params.bam_filter_reads}"
+    when: "${params.bam_retain_all_reads}"
 
     script:
     prefix="$bam" - ~/(\.bam)?/
 
-    if("${params.bam_keep_mapped_only}"){
+    if("${params.bam_analyse_mapped_only}"){
     """
     samtools view -h $bam | tee >(samtools view - -@ ${task.cpus} -f4 -q ${params.bam_mapping_quality_threshold} -o ${prefix}.unmapped.bam) >(samtools view - -@ ${task.cpus} -F4 -q ${params.bam_mapping_quality_threshold} -o ${prefix}.filtered.bam)
     samtools fastq -tn "${prefix}.unmapped.bam" | gzip > "${prefix}.unmapped.fq.gz"