Merge pull request #81 from nf-core/rename_bam_flags

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

Author: apeltzer

CHANGELOG.md

@@ -9,10 +9,12 @@ and this project adheres to [Semantic Versioning](http://semver.org/spec/v2.0.0.
 ### `Added`
 * [#80](https://github.com/nf-core/eager/pull/80) - BWA Index file handling 
 * [#77](https://github.com/nf-core/eager/pull/77) - Lots of documentation updates by [@jfy133](https://github.com/jfy133)
+* [#81](https://github.com/nf-core/eager/pull/81) - Renaming of certain BAM options
 
 ### `Fixed`
 * [#84](https://github.com/nf-core/eager/pull/85) - Fix for [Samtools index issues](https://github.com/nf-core/eager/issues/84)
 
+
 ## [2.0.2] - 2018-11-03
 
 ### `Changed`

conf/binac.config

@@ -10,7 +10,7 @@ singularity {
 }
 
 process {
-    beforeScript = 'module load devel/singularity/2.4.1'
+    beforeScript = 'module load devel/singularity/2.6.0'
     executor = 'pbs'
     queue = 'short'
 }

docs/usage.md

@@ -383,17 +383,25 @@ 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_retain_unmapped`
 
-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.
+Specify this to keep also unmapped reads in the BAM file. This is the default setting, only mapping quality filters are applied to all reads. 
 
-### `--bam_keep_all`
+### `--bam_separate_unmapped`
 
-Turned on by default, keeps all reads that were mapped in the dataset. 
+Separates the mapped and unmapepd reads, keeps only mapped reads in the BAM file for downstream analysis.
 
-### `--bam_filter_reads`
+### `--bam_unmapped_to_fastq`
 
-Specify this, if you want to filter reads for downstream analysis. 
+Converted unmapped reads in BAM format to compressed FastQ format. 
+
+### `--bam_discard_unmapped`
+
+Discards unmapped reads in either FastQ or BAM format, depending on the choice of the `--bam_unmapped_rm_type`. 
+
+### `--bam_unmapped_rm_type`
+
+Defines which unmapped read format to discard, options available are `bam` or `fastq.gz`. By default, `fastq.gz` format will be kept and `bam` will be removed.
 
 ### `--bam_mapping_quality_threshold`
 

main.nf

@@ -76,9 +76,12 @@ 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_mapping_quality_threshold   Minimum mapping quality for reads filter
+      --bam_retain_unmapped         Retains all unmapped reads in the BAM file (default)
+      --bam_separate_unmapped       Separates mapped and unmapped reads, keep mapped BAM for downstream analysis.
+      --bam_unmapped_to_fastq       Converts unmapped reads in BAM format to fastq.gz format.
+      --bam_discard_unmapped        Discards unmapped reads in either FASTQ or BAM format, depending on choice in --bam_unmapped_rm_type
+      --bam_unmapped_rm_type        Defines which unmapped read format to discard, options are "bam" or "fastq.gz".
+      --bam_mapping_quality_threshold   Minimum mapping quality for reads filter, default 0.
     
     DeDuplication
       --dedupper                    Deduplication method to use
@@ -173,11 +176,15 @@ 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_keep_all = true
-params.bam_filter_reads = false
+params.bam_retain_unmapped = true
+params.bam_separate_unmapped = false
+params.bam_discard_unmapped = false
+params.bam_unmapped_to_fastq = false 
+params.bam_unmapped_rm_type = 'bam'
+
 params.bam_mapping_quality_threshold = 0
 
+
 //DamageProfiler settings
 params.damageprofiler_length = 100
 params.damageprofiler_threshold = 15
@@ -715,22 +722,25 @@ process samtools_filter {
     file "*.unmapped.bam" optional true
     file "*.bai"
 
-    when: "${params.bam_filter_reads}"
-
     script:
     prefix="$bam" - ~/(\.bam)?/
+    rm_type = "${params.bam_unmapped_rm_type}" == 'bam' ? 'bam' : 'fastq.gz'
+    rm_unmapped = "${params.bam_discard_unmapped}" ? "rm *.unmapped.${rm_type}" : ''
+    fq_convert = "${params.bam_unmapped_to_fastq}" ? "samtools fastq -tn ${prefix}.unmapped.bam | pigz -p ${task.cpus} > ${prefix}.unmapped.fq.gz" : ''
+    
 
-    if("${params.bam_keep_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"
-    samtools index ${prefix}.filtered.bam
-    """
+    if("${params.bam_separate_unmapped}"){
+        """
+        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 index ${prefix}.filtered.bam
+        $fq_convert
+        $rm_unmapped
+        """
     } else {
-    """
-    samtools view -h $bam | tee >(samtools view - -@ ${task.cpus} -f4 -q ${params.bam_mapping_quality_threshold} -o ${prefix}.unmapped.bam) >(samtools view - -@ ${task.cpus} -q ${params.bam_mapping_quality_threshold} -o ${prefix}.filtered.bam)
-    samtools index ${prefix}.filtered.bam
-    """
+        """
+        samtools view -h $bam -@ ${task.cpus} -q ${params.bam_mapping_quality_threshold} -o ${prefix}.filtered.bam)
+        samtools index ${prefix}.filtered.bam
+        """
     }  
 }