From 91d05cbba0cd860eee240a24dba99380997f528e Mon Sep 17 00:00:00 2001
From: maxibor <maxime.borry@gmail.com>
Date: Mon, 11 Feb 2019 16:48:58 +0100
Subject: [PATCH 01/29] add noCollase option

---
 .travis.yml |  6 +++++
 main.nf     | 74 +++++++++++++++++++++++++++++++++++++++++++----------
 2 files changed, 67 insertions(+), 13 deletions(-)

diff --git a/.travis.yml b/.travis.yml
index 459e925cb..ecb69d6d6 100644
--- a/.travis.yml
+++ b/.travis.yml
@@ -40,14 +40,20 @@ script:
   - nextflow run ${TRAVIS_BUILD_DIR} -profile test,docker --pairedEnd --saveReference
   # Run the basic pipeline with single end data (pretending its single end actually)
   - nextflow run ${TRAVIS_BUILD_DIR} -profile test,docker --singleEnd --bwa_index results/reference_genome/bwa_index/bwa_index/
+  # Run the basic pipeline with paired end data 
+  - nextflow run ${TRAVIS_BUILD_DIR} -profile test,docker --pairedEnd --noCollapse --saveReference
   # Run the same pipeline testing optional step: fastp, complexity 
   - nextflow run ${TRAVIS_BUILD_DIR} -profile test,docker --pairedEnd --complexity_filter --bwa_index results/reference_genome/bwa_index/bwa_index/
   # Test BAM Trimming
   - nextflow run ${TRAVIS_BUILD_DIR} -profile test,docker --pairedEnd --trim_bam --bwa_index results/reference_genome/bwa_index/bwa_index/
   # Test running with CircularMapper
   - nextflow run ${TRAVIS_BUILD_DIR} -profile test,docker --pairedEnd --circularmapper --circulartarget 'NC_007596.2'
+  # Test running with CircularMapper on paired end without collapsing
+  - nextflow run ${TRAVIS_BUILD_DIR} -profile test,docker --pairedEnd --noCollapse --circularmapper --circulartarget 'NC_007596.2'
   # Test running with BWA Mem
   - nextflow run ${TRAVIS_BUILD_DIR} -profile test,docker --pairedEnd --bwamem --bwa_index results/reference_genome/bwa_index/bwa_index/
+  # Test running with BWA Mem on paired end without collapsing
+  - nextflow run ${TRAVIS_BUILD_DIR} -profile test,docker --pairedEnd --noCollapse --bwamem --bwa_index results/reference_genome/bwa_index/bwa_index/
   # Test with zipped reference input
   - nextflow run ${TRAVIS_BUILD_DIR} -profile test,docker --pairedEnd --fasta 'https://raw.githubusercontent.com/nf-core/test-datasets/eager2/reference/Test.fasta.gz'
   # Run the basic pipeline with the bam input profile
diff --git a/main.nf b/main.nf
index f25ad3e79..12878e70c 100644
--- a/main.nf
+++ b/main.nf
@@ -28,7 +28,8 @@ def helpMessage() {
       --reads                       Path to input data (must be surrounded with quotes)
       -profile                      Hardware config to use (e.g. standard, docker, singularity, conda, aws). Ask your system admin if unsure, or check documentatoin.
       --singleEnd                   Specifies that the input is single end reads (required if not pairedEnd)
-      --pairedEnd                   Specifies that the input is paired end reads (required if not singleend)
+      --pairedEnd                   Specifies that the input is paired end reads (required if not singleEnd)
+      --noCollapse                  Specifies to avoid merging Forward and Reverse reads together. (Only for pairedEnd samples)
       --bam                         Specifies that the input is in BAM format
       --fasta                       Path to Fasta reference (required if not iGenome reference)
       --genome                      Name of iGenomes reference (required if not fasta reference)
@@ -131,6 +132,7 @@ if (params.help){
 params.name = false
 params.singleEnd = false
 params.pairedEnd = false
+params.noCollapse = false
 params.genome = "Custom"
 params.snpcapture = false
 params.bedfile = ''
@@ -265,6 +267,11 @@ if( params.singleEnd || params.pairedEnd || params.bam){
     exit 1, "Please specify either --singleEnd, --pairedEnd to execute the pipeline on FastQ files and --bam for previously processed BAM files!"
 }
 
+//Validate that noCollase is only set to True for pairedEnd reads!
+if (params.noCollapse && params.singleEnd){
+    exit 1, "--noCollapse can only be set for pairedEnd samples!"
+}
+
 
 //AWSBatch sanity checking
 if(workflow.profile == 'awsbatch'){
@@ -349,6 +356,7 @@ summary['Reads']        = params.reads
 summary['Fasta Ref']    = params.fasta
 if(params.bwa_index) summary['BWA Index'] = params.bwa_index
 summary['Data Type']    = params.singleEnd ? 'Single-End' : 'Paired-End'
+summary['Collapse']        = !params.noCollapse ? 'Yes' : 'No'
 summary['Max Memory']   = params.max_memory
 summary['Max CPUs']     = params.max_cpus
 summary['Max Time']     = params.max_time
@@ -508,7 +516,7 @@ process convertBam {
 
     output:
     set val("${base}"), file("*.fastq.gz") into (ch_read_files_converted_fastqc, ch_read_files_converted_fastp)
-    file("*.fastq.gz") into (ch_read_files_converted_mapping_bwa, ch_read_files_converted_mapping_cm, ch_read_files_converted_mapping_bwamem)
+    set val("${base}"), file("*.fastq.gz") into (ch_read_files_converted_mapping_bwa, ch_read_files_converted_mapping_cm, ch_read_files_converted_mapping_bwamem)
 
     script:
     base = "${bam.baseName}"
@@ -594,19 +602,25 @@ process adapter_removal {
     //Readprefixing only required for PE data with merging
     fixprefix = (params.singleEnd) ? "" : "AdapterRemovalFixPrefix ${prefix}.combined.fq.gz ${prefix}.combined.prefixed.fq.gz"
     
-    if( !params.singleEnd ){
+    if( !params.singleEnd && !params.noCollapse){
     """
-    AdapterRemoval --file1 ${reads[0]} --file2 ${reads[1]} --basename ${prefix} --gzip --threads ${task.cpus} --trimns --trimqualities --adapter1 ${params.clip_forward_adaptor} --adapter2 ${params.clip_reverse_adaptor} --minlength ${params.clip_readlength} --minquality ${params.clip_min_read_quality} --minadapteroverlap ${params.min_adap_overlap} --collapse
+    AdapterRemoval --file1 ${reads[0]} --file2 ${reads[1]} --basename ${name} --gzip --threads ${task.cpus} --trimns --trimqualities --adapter1 ${params.clip_forward_adaptor} --adapter2 ${params.clip_reverse_adaptor} --minlength ${params.clip_readlength} --minquality ${params.clip_min_read_quality} --minadapteroverlap ${params.min_adap_overlap} --collapse
     #Combine files
-    zcat *.collapsed.gz *.collapsed.truncated.gz *.singleton.truncated.gz *.pair1.truncated.gz *.pair2.truncated.gz | gzip > ${prefix}.combined.fq.gz
-    ${fixprefix}
-    rm ${prefix}.combined.fq.gz
+    zcat *.collapsed.gz *.collapsed.truncated.gz *.singleton.truncated.gz *.pair1.truncated.gz *.pair2.truncated.gz | gzip > ${name}.combined.fq.gz
     """
-    } else {
+    } else if (!params.singleEnd && params.noCollapse) {
+    """
+    AdapterRemoval --file1 ${reads[0]} --file2 ${reads[1]} --basename ${name} --gzip --threads ${task.cpus} --trimns --trimqualities --adapter1 ${params.clip_forward_adaptor} --adapter2 ${params.clip_reverse_adaptor} --minlength ${params.clip_readlength} --minquality ${params.clip_min_read_quality} --minadapteroverlap ${params.min_adap_overlap}
+    #Rename files
+    mv ${name}.pair1.truncated.gz ${name}.pair1.combined.fq.gz
+    mv ${name}.pair2.truncated.gz ${name}.pair2.combined.fq.gz
     """
-    AdapterRemoval --file1 ${reads[0]} --basename ${prefix} --gzip --threads ${task.cpus} --trimns --trimqualities --adapter1 ${params.clip_forward_adaptor} --minlength ${params.clip_readlength} --minquality ${params.clip_min_read_quality} 
+    } 
+    else {
+    """
+    AdapterRemoval --file1 ${reads[0]} --basename ${name} --gzip --threads ${task.cpus} --trimns --trimqualities --adapter1 ${params.clip_forward_adaptor} --minlength ${params.clip_readlength} --minquality ${params.clip_min_read_quality} 
     # Pseudo-Combine
-    mv *.truncated.gz ${prefix}.combined.fq.gz
+    mv *.truncated.gz ${name}.combined.fq.gz
     """
     }
 }
@@ -615,7 +629,7 @@ process adapter_removal {
  * STEP 2.1 - FastQC after clipping/merging (if applied!)
  */
 process fastqc_after_clipping {
-    tag "${reads[0].baseName}"
+    tag "${prefix}"
     publishDir "${params.outdir}/FastQC/after_clipping", mode: 'copy',
         saveAs: {filename -> filename.indexOf(".zip") > 0 ? "zips/$filename" : "$filename"}
 
@@ -628,6 +642,7 @@ process fastqc_after_clipping {
     file "*_fastqc.{zip,html}" optional true into ch_fastqc_after_clipping
 
     script:
+    prefix = reads[0].toString().tokenize('.')[0]
     """
     fastqc -q $reads
     """
@@ -654,13 +669,24 @@ process bwa {
     
 
     script:
+    fasta = "${index}/*.fasta"
+    if (!params.singleEnd && params.noCollapse){
+    prefix = reads[0].toString().tokenize('.')[0]
+    """ 
+    bwa aln -t ${task.cpus} $fasta ${reads[0]} -n ${params.bwaalnn} -l ${params.bwaalnl} -k ${params.bwaalnk} -f ${prefix}.r1.sai
+    bwa aln -t ${task.cpus} $fasta ${reads[1]} -n ${params.bwaalnn} -l ${params.bwaalnl} -k ${params.bwaalnk} -f ${prefix}.r2.sai
+    bwa sampe -r "@RG\\tID:ILLUMINA-${prefix}\\tSM:${prefix}\\tPL:illumina" $fasta ${prefix}.r1.sai ${prefix}.r2.sai ${reads[0]} ${reads[1]} | samtools sort -@ ${task.cpus} -O bam - > ${prefix}.sorted.bam
+    samtools index ${prefix}.sorted.bam
+    """
+    } else {
     prefix = reads[0].toString() - ~/(_R1)?(\.combined\.)?(prefixed)?(_trimmed)?(_val_1)?(\.fq)?(\.fastq)?(\.gz)?$/
-    fasta = "${index}/*.fasta" 
     """ 
     bwa aln -t ${task.cpus} $fasta $reads -n ${params.bwaalnn} -l ${params.bwaalnl} -k ${params.bwaalnk} -f "${reads.baseName}.sai"
     bwa samse -r "@RG\\tID:ILLUMINA-${prefix}\\tSM:${prefix}\\tPL:illumina" $fasta "${reads.baseName}".sai $reads | samtools sort -@ ${task.cpus} -O bam - > "${prefix}".sorted.bam
     samtools index "${prefix}".sorted.bam
     """
+    }
+    
 }
 
 process circulargenerator{
@@ -708,9 +734,21 @@ process circularmapper{
     
     script:
     filter = "${params.circularfilter}" ? '' : '-f true -x false'
-    prefix = reads[0].toString() - ~/(_R1)?(\.combined\.)?(prefixed)?(_trimmed)?(_val_1)?(\.fq)?(\.fastq)?(\.gz)?$/
+    
     fasta = "${index}/*_*.fasta"
 
+    if (!params.singleEnd && params.noCollapse){
+    prefix = reads[0].toString().tokenize('.')[0]
+    """ 
+    bwa aln -t ${task.cpus} $fasta ${reads[0]} -n ${params.bwaalnn} -l ${params.bwaalnl} -k ${params.bwaalnk} -f ${prefix}.r1.sai
+    bwa aln -t ${task.cpus} $fasta ${reads[0]} -n ${params.bwaalnn} -l ${params.bwaalnl} -k ${params.bwaalnk} -f ${prefix}.r2.sai
+    bwa sampe -r "@RG\\tID:ILLUMINA-${prefix}\\tSM:${prefix}\\tPL:illumina" $fasta ${prefix}.r1.sai ${prefix}.r1.sai ${reads[0]} ${reads[0]} > tmp.out
+    realignsamfile -e ${params.circularextension} -i tmp.out -r $fasta $filter 
+    samtools sort -@ ${task.cpus} -O bam tmp_realigned.bam > ${prefix}.sorted.bam
+    samtools index ${prefix}.sorted.bam
+    """
+    } else {
+    prefix = reads[0].toString() - ~/(_R1)?(\.combined\.)?(prefixed)?(_trimmed)?(_val_1)?(\.fq)?(\.fastq)?(\.gz)?$/
     """ 
     bwa aln -t ${task.cpus} $fasta $reads -n ${params.bwaalnn} -l ${params.bwaalnl} -k ${params.bwaalnk} -f "${reads.baseName}.sai"
     bwa samse -r "@RG\\tID:ILLUMINA-${prefix}\\tSM:${prefix}\\tPL:illumina" $fasta "${reads.baseName}".sai $reads > tmp.out
@@ -718,6 +756,8 @@ process circularmapper{
     samtools sort -@ ${task.cpus} -O bam tmp_realigned.bam > "${prefix}".sorted.bam
     samtools index "${prefix}".sorted.bam
     """
+    }
+    
 }
 
 process bwamem {
@@ -738,10 +778,18 @@ process bwamem {
     script:
     prefix = reads[0].toString() - ~/(_R1)?(\.combined\.)?(prefixed)?(_trimmed)?(_val_1)?(\.fq)?(\.fastq)?(\.gz)?$/
     fasta = "${index}/*.fasta"
+    if (!params.singleEnd && params.noCollapse){
+    """
+    bwa mem -t ${task.cpus} $fasta ${reads[0]} ${reads[1]} -R "@RG\\tID:ILLUMINA-${prefix}\\tSM:${prefix}\\tPL:illumina" | samtools sort -@ ${task.cpus} -O bam - > "${prefix}".sorted.bam
+    samtools index -@ ${task.cpus} "${prefix}".sorted.bam
+    """
+    } else {
     """
     bwa mem -t ${task.cpus} $fasta $reads -R "@RG\\tID:ILLUMINA-${prefix}\\tSM:${prefix}\\tPL:illumina" | samtools sort -@ ${task.cpus} -O bam - > "${prefix}".sorted.bam
     samtools index -@ ${task.cpus} "${prefix}".sorted.bam
     """
+    }
+    
 }
 
 /*

From 758fb7fa53b7711e4563ed6bb059cea372c21087 Mon Sep 17 00:00:00 2001
From: maxibor <maxime.borry@gmail.com>
Date: Mon, 11 Feb 2019 16:53:37 +0100
Subject: [PATCH 02/29] fix nf-PE read index

---
 main.nf | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/main.nf b/main.nf
index 12878e70c..b6d9a32bf 100644
--- a/main.nf
+++ b/main.nf
@@ -741,8 +741,8 @@ process circularmapper{
     prefix = reads[0].toString().tokenize('.')[0]
     """ 
     bwa aln -t ${task.cpus} $fasta ${reads[0]} -n ${params.bwaalnn} -l ${params.bwaalnl} -k ${params.bwaalnk} -f ${prefix}.r1.sai
-    bwa aln -t ${task.cpus} $fasta ${reads[0]} -n ${params.bwaalnn} -l ${params.bwaalnl} -k ${params.bwaalnk} -f ${prefix}.r2.sai
-    bwa sampe -r "@RG\\tID:ILLUMINA-${prefix}\\tSM:${prefix}\\tPL:illumina" $fasta ${prefix}.r1.sai ${prefix}.r1.sai ${reads[0]} ${reads[0]} > tmp.out
+    bwa aln -t ${task.cpus} $fasta ${reads[1]} -n ${params.bwaalnn} -l ${params.bwaalnl} -k ${params.bwaalnk} -f ${prefix}.r2.sai
+    bwa sampe -r "@RG\\tID:ILLUMINA-${prefix}\\tSM:${prefix}\\tPL:illumina" $fasta ${prefix}.r1.sai ${prefix}.r2.sai ${reads[0]} ${reads[1]} > tmp.out
     realignsamfile -e ${params.circularextension} -i tmp.out -r $fasta $filter 
     samtools sort -@ ${task.cpus} -O bam tmp_realigned.bam > ${prefix}.sorted.bam
     samtools index ${prefix}.sorted.bam

From e2aaba071e8595d2c3df0f403cb8fc443ad13d74 Mon Sep 17 00:00:00 2001
From: maxibor <maxime.borry@gmail.com>
Date: Mon, 11 Feb 2019 16:58:24 +0100
Subject: [PATCH 03/29] update doc with noCollapse

---
 docs/usage.md | 8 ++++++++
 1 file changed, 8 insertions(+)

diff --git a/docs/usage.md b/docs/usage.md
index 6f0838d7d..02000d1b5 100644
--- a/docs/usage.md
+++ b/docs/usage.md
@@ -162,6 +162,14 @@ A normal glob pattern, enclosed in quotation marks, can then be used for `--read
 --pairedEnd --reads '*.fastq'
 ```
 
+### `--noCollapse`
+If you have paired-end data, but you don't want to merge them, add the commind line argument `--noCollapse`. 
+
+For example
+```bash
+--pairedEnd --noCollapse '*.fastq'
+```
+
 ### `--fasta`
 If you prefer, you can specify the full path to your reference genome when you run the pipeline:
 

From 55743dd25b85562549d290cbdca93b11b4153858 Mon Sep 17 00:00:00 2001
From: maxibor <maxime.borry@gmail.com>
Date: Mon, 11 Feb 2019 17:31:39 +0100
Subject: [PATCH 04/29] main.nf to dev

---
 main.nf | 3 ---
 1 file changed, 3 deletions(-)

diff --git a/main.nf b/main.nf
index 090d86e00..b71ca88b4 100644
--- a/main.nf
+++ b/main.nf
@@ -29,10 +29,7 @@ def helpMessage() {
       -profile                      Institution or personal hardware config to use (e.g. standard, docker, singularity, conda, aws). Ask your system admin if unsure, or check documentation.
       --singleEnd                   Specifies that the input is single end reads (required if not pairedEnd)
       --pairedEnd                   Specifies that the input is paired end reads (required if not singleEnd)
-<<<<<<< HEAD
-=======
       --noCollapse                  Specifies to avoid merging Forward and Reverse reads together. (Only for pairedEnd samples)
->>>>>>> master
       --bam                         Specifies that the input is in BAM format
       --fasta                       Path to Fasta reference (required if not iGenome reference)
       --genome                      Name of iGenomes reference (required if not fasta reference)

From 8ec9d674a94016369190ba04ab21a09da9018ce7 Mon Sep 17 00:00:00 2001
From: maxibor <maxime.borry@gmail.com>
Date: Mon, 11 Feb 2019 18:14:19 +0100
Subject: [PATCH 05/29] fix funky prefix

---
 main.nf | 18 +++++++++---------
 1 file changed, 9 insertions(+), 9 deletions(-)

diff --git a/main.nf b/main.nf
index b71ca88b4..6a179c0dd 100644
--- a/main.nf
+++ b/main.nf
@@ -678,11 +678,11 @@ process bwa {
     samtools index ${prefix}.sorted.bam
     """
     } else {
-    prefix = reads[0].toString() - ~/(_R1)?(\.combined\.)?(prefixed)?(_trimmed)?(_val_1)?(\.fq)?(\.fastq)?(\.gz)?$/
+    prefix = reads[0].toString().tokenize('.')[0]
     """ 
-    bwa aln -t ${task.cpus} $fasta $reads -n ${params.bwaalnn} -l ${params.bwaalnl} -k ${params.bwaalnk} -f "${reads.baseName}.sai"
-    bwa samse -r "@RG\\tID:ILLUMINA-${prefix}\\tSM:${prefix}\\tPL:illumina" $fasta "${reads.baseName}".sai $reads | samtools sort -@ ${task.cpus} -O bam - > "${prefix}".sorted.bam
-    samtools index "${prefix}".sorted.bam
+    bwa aln -t ${task.cpus} $fasta $reads -n ${params.bwaalnn} -l ${params.bwaalnl} -k ${params.bwaalnk} -f ${prefix}.sai
+    bwa samse -r "@RG\\tID:ILLUMINA-${prefix}\\tSM:${prefix}\\tPL:illumina" $fasta ${prefix}.sai $reads | samtools sort -@ ${task.cpus} -O bam - > "${prefix}".sorted.bam
+    samtools index ${prefix}.sorted.bam
     """
     }
     
@@ -747,13 +747,13 @@ process circularmapper{
     samtools index ${prefix}.sorted.bam
     """
     } else {
-    prefix = reads[0].toString() - ~/(_R1)?(\.combined\.)?(prefixed)?(_trimmed)?(_val_1)?(\.fq)?(\.fastq)?(\.gz)?$/
+    prefix = reads[0].toString().tokenize('.')[0]
     """ 
-    bwa aln -t ${task.cpus} $fasta $reads -n ${params.bwaalnn} -l ${params.bwaalnl} -k ${params.bwaalnk} -f "${reads.baseName}.sai"
-    bwa samse -r "@RG\\tID:ILLUMINA-${prefix}\\tSM:${prefix}\\tPL:illumina" $fasta "${reads.baseName}".sai $reads > tmp.out
+    bwa aln -t ${task.cpus} $fasta $reads -n ${params.bwaalnn} -l ${params.bwaalnl} -k ${params.bwaalnk} -f ${prefix}.sai
+    bwa samse -r "@RG\\tID:ILLUMINA-${prefix}\\tSM:${prefix}\\tPL:illumina" $fasta ${prefix}.sai $reads > tmp.out
     realignsamfile -e ${params.circularextension} -i tmp.out -r $fasta $filter 
-    samtools sort -@ ${task.cpus} -O bam tmp_realigned.bam > "${prefix}".sorted.bam
-    samtools index "${prefix}".sorted.bam
+    samtools sort -@ ${task.cpus} -O bam tmp_realigned.bam > ${prefix}.sorted.bam
+    samtools index ${prefix}.sorted.bam
     """
     }
     

From 6d864e10dfef753edd9a8678b63e2fc906388611 Mon Sep 17 00:00:00 2001
From: Alexander Peltzer <apeltzer@users.noreply.github.com>
Date: Mon, 11 Feb 2019 23:49:00 +0100
Subject: [PATCH 06/29] Update docs/usage.md

Co-Authored-By: maxibor <maxibor@users.noreply.github.com>
---
 docs/usage.md | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/docs/usage.md b/docs/usage.md
index 8a17ecee5..34dd9f9bb 100644
--- a/docs/usage.md
+++ b/docs/usage.md
@@ -163,7 +163,7 @@ A normal glob pattern, enclosed in quotation marks, can then be used for `--read
 ```
 
 ### `--noCollapse`
-If you have paired-end data, but you don't want to merge them, add the commind line argument `--noCollapse`. 
+If you have paired-end data, but you don't want to merge them, add the command line argument `--noCollapse`. 
 
 For example
 ```bash

From f3a6ff7adf80ed9820a092f6b15fe21b1549d3f2 Mon Sep 17 00:00:00 2001
From: Alexander Peltzer <apeltzer@users.noreply.github.com>
Date: Tue, 12 Feb 2019 14:52:16 +0100
Subject: [PATCH 07/29] Update docs/usage.md

Co-Authored-By: maxibor <maxibor@users.noreply.github.com>
---
 docs/usage.md | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/docs/usage.md b/docs/usage.md
index 34dd9f9bb..fecaa9c13 100644
--- a/docs/usage.md
+++ b/docs/usage.md
@@ -167,7 +167,7 @@ If you have paired-end data, but you don't want to merge them, add the command l
 
 For example
 ```bash
---pairedEnd --noCollapse '*.fastq'
+--pairedEnd --noCollapse  --reads '*.fastq'
 ```
 
 ### `--fasta`

From 0e03a000d6e3fe11dc91657215074a30645d096e Mon Sep 17 00:00:00 2001
From: maxibor <maxime.borry@gmail.com>
Date: Tue, 12 Feb 2019 17:32:34 +0100
Subject: [PATCH 08/29] skip trimming and collapsing

---
 docs/usage.md | 28 ++++++++++++++-------
 main.nf       | 69 +++++++++++++++++++++++++++++++++------------------
 2 files changed, 64 insertions(+), 33 deletions(-)

diff --git a/docs/usage.md b/docs/usage.md
index fecaa9c13..bee24f9ba 100644
--- a/docs/usage.md
+++ b/docs/usage.md
@@ -162,14 +162,6 @@ A normal glob pattern, enclosed in quotation marks, can then be used for `--read
 --pairedEnd --reads '*.fastq'
 ```
 
-### `--noCollapse`
-If you have paired-end data, but you don't want to merge them, add the command line argument `--noCollapse`. 
-
-For example
-```bash
---pairedEnd --noCollapse  --reads '*.fastq'
-```
-
 ### `--fasta`
 If you prefer, you can specify the full path to your reference genome when you run the pipeline:
 
@@ -287,12 +279,30 @@ This part of the documentation contains a list of user-adjustable parameters in
 
 ## Step skipping parameters
 
-Some of the steps in the pipeline can be executed optionally. If you specify specific steps to be skipped, there won't be any output related to these modules. 
+Some of the steps in the pipeline can be executed optionally. If you specify specific steps to be skipped, there won't be any output related to these modules.
 
 ### `--skip_preseq`
 
 Turns off the computation of library complexity estimation.  
 
+### `--skip_collapse`
+If you have paired-end data, but you don't want to merge them, add the command line argument `--noCollapse`. 
+
+For example
+```bash
+--pairedEnd --skip_collapse  --reads '*.fastq'
+```
+
+### `--skip_trimming`
+
+Turns off the adaptor and quality trimming
+
+For example
+```bash
+--pairedEnd --skip_trimming  --reads '*.fastq'
+```
+
+
 ### `--skip_damage_calculation`
 
 Turns off the DamageProfiler module to compute DNA damage profiles. 
diff --git a/main.nf b/main.nf
index 6a179c0dd..c98aadee6 100644
--- a/main.nf
+++ b/main.nf
@@ -29,7 +29,6 @@ def helpMessage() {
       -profile                      Institution or personal hardware config to use (e.g. standard, docker, singularity, conda, aws). Ask your system admin if unsure, or check documentation.
       --singleEnd                   Specifies that the input is single end reads (required if not pairedEnd)
       --pairedEnd                   Specifies that the input is paired end reads (required if not singleEnd)
-      --noCollapse                  Specifies to avoid merging Forward and Reverse reads together. (Only for pairedEnd samples)
       --bam                         Specifies that the input is in BAM format
       --fasta                       Path to Fasta reference (required if not iGenome reference)
       --genome                      Name of iGenomes reference (required if not fasta reference)
@@ -45,6 +44,8 @@ def helpMessage() {
       --saveReference               Saves reference genome indices for later reusage
 
     Skipping                        Skip any of the mentioned steps
+      --skip_collapse               Skip merging Forward and Reverse reads together. (Only for pairedEnd samples)
+      --skip_trim                   Skip adaptor and quality trimming
       --skip_preseq
       --skip_damage_calculation
       --skip_qualimap
@@ -131,7 +132,6 @@ if (params.help){
 params.name = false
 params.singleEnd = false
 params.pairedEnd = false
-params.noCollapse = false
 params.genome = "Custom"
 params.snpcapture = false
 params.bedfile = ''
@@ -147,6 +147,8 @@ params.email = false
 params.plaintext_email = false
 
 // Skipping parts of the pipeline for impatient users
+params.skip_collapse = false
+params.skip_trim = false
 params.skip_preseq = false
 params.skip_damage_calculation = false
 params.skip_qualimap = false
@@ -266,12 +268,11 @@ if( params.singleEnd || params.pairedEnd || params.bam){
     exit 1, "Please specify either --singleEnd, --pairedEnd to execute the pipeline on FastQ files and --bam for previously processed BAM files!"
 }
 
-//Validate that noCollase is only set to True for pairedEnd reads!
-if (params.noCollapse && params.singleEnd){
+//Validate that skip_collapse is only set to True for pairedEnd reads!
+if (params.skip_collapse  && params.singleEnd){
     exit 1, "--noCollapse can only be set for pairedEnd samples!"
 }
 
-
 //AWSBatch sanity checking
 if(workflow.profile == 'awsbatch'){
     if (!params.awsqueue || !params.awsregion) exit 1, "Specify correct --awsqueue and --awsregion parameters on AWSBatch!"
@@ -355,7 +356,8 @@ summary['Reads']        = params.reads
 summary['Fasta Ref']    = params.fasta
 if(params.bwa_index) summary['BWA Index'] = params.bwa_index
 summary['Data Type']    = params.singleEnd ? 'Single-End' : 'Paired-End'
-summary['Collapse']        = !params.noCollapse ? 'Yes' : 'No'
+summary['Skip Collapsing'] = params.skip_collapse ? 'Yes' : 'No'
+summary['Skip Trimming']  = params.skip_trim  ? 'Yes' : 'No' 
 summary['Max Memory']   = params.max_memory
 summary['Max CPUs']     = params.max_cpus
 summary['Max Time']     = params.max_time
@@ -375,7 +377,7 @@ if(workflow.profile == 'awsbatch'){
    summary['AWS Queue'] = params.awsqueue
 }
 if(params.email) summary['E-mail Address'] = params.email
-log.info summary.collect { k,v -> "${k.padRight(15)}: $v" }.join("\n")
+log.info summary.collect { k,v -> "${k.padRight(35)}: $v" }.join("\n")
 log.info "========================================="
 
 
@@ -587,6 +589,8 @@ process adapter_removal {
     tag "$name"
     publishDir "${params.outdir}/read_merging", mode: 'copy'
 
+    echo true
+
     when: !params.bam
 
     input:
@@ -594,32 +598,49 @@ process adapter_removal {
 
     output:
     file "*.combined*.gz" into (ch_clipped_reads, ch_clipped_reads_for_fastqc,ch_clipped_reads_circularmapper,ch_clipped_reads_bwamem)
-    file "*.settings" into ch_adapterremoval_logs
+    file("*.settings") optional true into ch_adapterremoval_logs
 
     script:
-    prefix = reads[0].toString() - ~/(_R1)?(_trimmed)?(_val_1)?(\.fq)?(\.fastq)?(\.gz)?$/
-    //Readprefixing only required for PE data with merging
-    fixprefix = (params.singleEnd) ? "" : "AdapterRemovalFixPrefix ${prefix}.combined.fq.gz ${prefix}.combined.prefixed.fq.gz"
+    base = reads[0].baseName
     
-    if( !params.singleEnd && !params.noCollapse){
+    if( !params.singleEnd && !params.skip_collapse && !params.skip_trim){
     """
-    AdapterRemoval --file1 ${reads[0]} --file2 ${reads[1]} --basename ${name} --gzip --threads ${task.cpus} --trimns --trimqualities --adapter1 ${params.clip_forward_adaptor} --adapter2 ${params.clip_reverse_adaptor} --minlength ${params.clip_readlength} --minquality ${params.clip_min_read_quality} --minadapteroverlap ${params.min_adap_overlap} --collapse
+    AdapterRemoval --file1 ${reads[0]} --file2 ${reads[1]} --basename ${base} --gzip --threads ${task.cpus} --trimns --trimqualities --adapter1 ${params.clip_forward_adaptor} --adapter2 ${params.clip_reverse_adaptor} --minlength ${params.clip_readlength} --minquality ${params.clip_min_read_quality} --minadapteroverlap ${params.min_adap_overlap} --collapse
     #Combine files
-    zcat *.collapsed.gz *.collapsed.truncated.gz *.singleton.truncated.gz *.pair1.truncated.gz *.pair2.truncated.gz | gzip > ${name}.combined.fq.gz
+    zcat *.collapsed.gz *.collapsed.truncated.gz *.singleton.truncated.gz *.pair1.truncated.gz *.pair2.truncated.gz | gzip > ${base}.combined.fq.gz
+    """
+    } else if (!params.singleEnd && params.skip_collapse && !params.skip_trim) {
+    """
+    AdapterRemoval --file1 ${reads[0]} --file2 ${reads[1]} --basename ${base} --gzip --threads ${task.cpus} --trimns --trimqualities --adapter1 ${params.clip_forward_adaptor} --adapter2 ${params.clip_reverse_adaptor} --minlength ${params.clip_readlength} --minquality ${params.clip_min_read_quality} --minadapteroverlap ${params.min_adap_overlap}
+    #Rename files
+    mv ${base}.pair1.truncated.gz ${base}.pair1.combined.fq.gz
+    mv ${base}.pair2.truncated.gz ${base}.pair2.combined.fq.gz
     """
-    } else if (!params.singleEnd && params.noCollapse) {
+    } else if (!params.singleEnd && !params.skip_collapse && params.skip_trim) {
+    bogus_adaptor = "NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN"
     """
-    AdapterRemoval --file1 ${reads[0]} --file2 ${reads[1]} --basename ${name} --gzip --threads ${task.cpus} --trimns --trimqualities --adapter1 ${params.clip_forward_adaptor} --adapter2 ${params.clip_reverse_adaptor} --minlength ${params.clip_readlength} --minquality ${params.clip_min_read_quality} --minadapteroverlap ${params.min_adap_overlap}
+    AdapterRemoval --file1 ${reads[0]} --file2 ${reads[1]} --basename ${base} --gzip --threads ${task.cpus} --basename ${base} --collapse --adapter1 $bogus_adaptor --adapter2 $bogus_adaptor
     #Rename files
-    mv ${name}.pair1.truncated.gz ${name}.pair1.combined.fq.gz
-    mv ${name}.pair2.truncated.gz ${name}.pair2.combined.fq.gz
+    mv ${base}.pair1.truncated.gz ${base}.pair1.combined.fq.gz
+    mv ${base}.pair2.truncated.gz ${base}.pair2.combined.fq.gz
     """
-    } 
+    } else if (params.singleEnd && params.skip_collapse && params.skip_trim){
+    """
+    mv ${reads[0]} ${base}.combined.fq.gz
+    echo "Skipped trimming and merging by AdapterRemoval"
+    """
+    } else if (params.pairedEnd && params.skip_collapse && params.skip_trim){
+    """
+    mv ${reads[0]} ${base}.pair1.combined.fq.gz
+    mv ${reads[1]} ${base}.pair2.combined.fq.gz
+    echo "Skipped trimming and merging by AdapterRemoval"
+    """
+    }
     else {
     """
-    AdapterRemoval --file1 ${reads[0]} --basename ${name} --gzip --threads ${task.cpus} --trimns --trimqualities --adapter1 ${params.clip_forward_adaptor} --minlength ${params.clip_readlength} --minquality ${params.clip_min_read_quality} 
+    AdapterRemoval --file1 ${reads[0]} --basename ${base} --gzip --threads ${task.cpus} --trimns --trimqualities --adapter1 ${params.clip_forward_adaptor} --minlength ${params.clip_readlength} --minquality ${params.clip_min_read_quality} 
     # Pseudo-Combine
-    mv *.truncated.gz ${name}.combined.fq.gz
+    mv *.truncated.gz ${base}.combined.fq.gz
     """
     }
 }
@@ -669,7 +690,7 @@ process bwa {
 
     script:
     fasta = "${index}/*.fasta"
-    if (!params.singleEnd && params.noCollapse){
+    if (!params.singleEnd && params.skip_collapse ){
     prefix = reads[0].toString().tokenize('.')[0]
     """ 
     bwa aln -t ${task.cpus} $fasta ${reads[0]} -n ${params.bwaalnn} -l ${params.bwaalnl} -k ${params.bwaalnk} -f ${prefix}.r1.sai
@@ -736,7 +757,7 @@ process circularmapper{
     
     fasta = "${index}/*_*.fasta"
 
-    if (!params.singleEnd && params.noCollapse){
+    if (!params.singleEnd && params.skip_collapse ){
     prefix = reads[0].toString().tokenize('.')[0]
     """ 
     bwa aln -t ${task.cpus} $fasta ${reads[0]} -n ${params.bwaalnn} -l ${params.bwaalnl} -k ${params.bwaalnk} -f ${prefix}.r1.sai
@@ -777,7 +798,7 @@ process bwamem {
     script:
     prefix = reads[0].toString() - ~/(_R1)?(\.combined\.)?(prefixed)?(_trimmed)?(_val_1)?(\.fq)?(\.fastq)?(\.gz)?$/
     fasta = "${index}/*.fasta"
-    if (!params.singleEnd && params.noCollapse){
+    if (!params.singleEnd && params.skip_collapse ){
     """
     bwa mem -t ${task.cpus} $fasta ${reads[0]} ${reads[1]} -R "@RG\\tID:ILLUMINA-${prefix}\\tSM:${prefix}\\tPL:illumina" | samtools sort -@ ${task.cpus} -O bam - > "${prefix}".sorted.bam
     samtools index -@ ${task.cpus} "${prefix}".sorted.bam

From 757e930003034026af27cc851b849edadc59f585 Mon Sep 17 00:00:00 2001
From: maxibor <maxime.borry@gmail.com>
Date: Tue, 12 Feb 2019 17:45:07 +0100
Subject: [PATCH 09/29] update test

---
 .travis.yml | 10 ++++------
 1 file changed, 4 insertions(+), 6 deletions(-)

diff --git a/.travis.yml b/.travis.yml
index ecb69d6d6..7fe187219 100644
--- a/.travis.yml
+++ b/.travis.yml
@@ -40,20 +40,18 @@ script:
   - nextflow run ${TRAVIS_BUILD_DIR} -profile test,docker --pairedEnd --saveReference
   # Run the basic pipeline with single end data (pretending its single end actually)
   - nextflow run ${TRAVIS_BUILD_DIR} -profile test,docker --singleEnd --bwa_index results/reference_genome/bwa_index/bwa_index/
-  # Run the basic pipeline with paired end data 
-  - nextflow run ${TRAVIS_BUILD_DIR} -profile test,docker --pairedEnd --noCollapse --saveReference
+  # Run the basic pipeline with paired end data without collapsing
+  - nextflow run ${TRAVIS_BUILD_DIR} -profile test,docker --pairedEnd --skip_collapse --saveReference
+    # Run the basic pipeline with paired end data without collapsing nor trimming
+  - nextflow run ${TRAVIS_BUILD_DIR} -profile test,docker --pairedEnd --skip_collapse --skip_trim --saveReference
   # Run the same pipeline testing optional step: fastp, complexity 
   - nextflow run ${TRAVIS_BUILD_DIR} -profile test,docker --pairedEnd --complexity_filter --bwa_index results/reference_genome/bwa_index/bwa_index/
   # Test BAM Trimming
   - nextflow run ${TRAVIS_BUILD_DIR} -profile test,docker --pairedEnd --trim_bam --bwa_index results/reference_genome/bwa_index/bwa_index/
   # Test running with CircularMapper
   - nextflow run ${TRAVIS_BUILD_DIR} -profile test,docker --pairedEnd --circularmapper --circulartarget 'NC_007596.2'
-  # Test running with CircularMapper on paired end without collapsing
-  - nextflow run ${TRAVIS_BUILD_DIR} -profile test,docker --pairedEnd --noCollapse --circularmapper --circulartarget 'NC_007596.2'
   # Test running with BWA Mem
   - nextflow run ${TRAVIS_BUILD_DIR} -profile test,docker --pairedEnd --bwamem --bwa_index results/reference_genome/bwa_index/bwa_index/
-  # Test running with BWA Mem on paired end without collapsing
-  - nextflow run ${TRAVIS_BUILD_DIR} -profile test,docker --pairedEnd --noCollapse --bwamem --bwa_index results/reference_genome/bwa_index/bwa_index/
   # Test with zipped reference input
   - nextflow run ${TRAVIS_BUILD_DIR} -profile test,docker --pairedEnd --fasta 'https://raw.githubusercontent.com/nf-core/test-datasets/eager2/reference/Test.fasta.gz'
   # Run the basic pipeline with the bam input profile

From 3320464a5586077ceb714d8bee5b95c74953093e Mon Sep 17 00:00:00 2001
From: Alexander Peltzer <alex.peltzer@gmail.com>
Date: Mon, 4 Mar 2019 11:19:14 +0100
Subject: [PATCH 10/29] move size out of the if clause

---
 main.nf | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/main.nf b/main.nf
index 5b323b662..c8781788b 100644
--- a/main.nf
+++ b/main.nf
@@ -685,9 +685,10 @@ process bwa {
 
     script:
     fasta = "${index}/*.fasta"
+    size = "${params.large_ref}" ? '-c' : ''
+
     if (!params.singleEnd && params.skip_collapse ){
     prefix = reads[0].toString().tokenize('.')[0]
-    size = "${params.large_ref}" ? '-c' : ''
     """ 
     bwa aln -t ${task.cpus} $fasta ${reads[0]} -n ${params.bwaalnn} -l ${params.bwaalnl} -k ${params.bwaalnk} -f ${prefix}.r1.sai
     bwa aln -t ${task.cpus} $fasta ${reads[1]} -n ${params.bwaalnn} -l ${params.bwaalnl} -k ${params.bwaalnk} -f ${prefix}.r2.sai

From def1b350c4836c123aca29dded1a0207cfe0faaf Mon Sep 17 00:00:00 2001
From: Maxime <maxime.borry@gmail.com>
Date: Mon, 4 Mar 2019 17:21:08 +0100
Subject: [PATCH 11/29] match skip_* pattern

---
 docs/usage.md | 37 ++++++++++++++++++--------------
 main.nf       | 59 ++++++++++++++++++++++++++++++++++-----------------
 2 files changed, 61 insertions(+), 35 deletions(-)

diff --git a/docs/usage.md b/docs/usage.md
index 1c8894865..2d78d15d0 100644
--- a/docs/usage.md
+++ b/docs/usage.md
@@ -289,23 +289,10 @@ Some of the steps in the pipeline can be executed optionally. If you specify spe
 
 Turns off the computation of library complexity estimation.  
 
-### `--skip_collapse`
-If you have paired-end data, but you don't want to merge them, add the command line argument `--noCollapse`. 
-
-For example
-```bash
---pairedEnd --skip_collapse  --reads '*.fastq'
-```
-
-### `--skip_trimming`
-
-Turns off the adaptor and quality trimming
-
-For example
-```bash
---pairedEnd --skip_trimming  --reads '*.fastq'
-```
+### `--skip_adapterremoval`
 
+Turns off adaptor trimming and paired-end read merging.
+Equivalent to setting both `--skip_collapse` and `--skip_trim`
 
 ### `--skip_damage_calculation`
 
@@ -351,6 +338,24 @@ Defines the minimum read quality per base that is required for a base to be kept
 ### `--clip_min_adap_overlap` 1
 Sets the minimum overlap between two reads when read merging is performed. Default is set to `1` base overlap.
 
+### `--skip_collapse`
+
+Turns off the paired-end read merging. 
+
+For example
+```bash
+--pairedEnd --skip_collapse  --reads '*.fastq'
+```
+
+### `--skip_trim`
+
+Turns off the adaptor and quality trimming.
+
+For example
+```bash
+--pairedEnd --skip_trim  --reads '*.fastq'
+```
+
 ## Read Mapping Parameters
 
 ## BWA (default)
diff --git a/main.nf b/main.nf
index c8781788b..81540b346 100644
--- a/main.nf
+++ b/main.nf
@@ -44,8 +44,7 @@ def helpMessage() {
       --saveReference               Saves reference genome indices for later reusage
 
     Skipping                        Skip any of the mentioned steps
-      --skip_collapse               Skip merging Forward and Reverse reads together. (Only for pairedEnd samples)
-      --skip_trim                   Skip adaptor and quality trimming
+      --skip_adapterremoval         
       --skip_preseq
       --skip_damage_calculation
       --skip_qualimap
@@ -61,6 +60,8 @@ def helpMessage() {
       --clip_readlength             Specify read minimum length to be kept for downstream analysis
       --clip_min_read_quality       Specify minimum base quality for not trimming off bases
       --min_adap_overlap            Specify minimum adapter overlap
+      --skip_collapse               Skip merging Forward and Reverse reads together. (Only for pairedEnd samples)
+      --skip_trim                   Skip adaptor and quality trimming
     
     BWA Mapping
       --bwaalnn                     Specify the -n parameter for BWA aln.
@@ -147,8 +148,7 @@ params.email = false
 params.plaintext_email = false
 
 // Skipping parts of the pipeline for impatient users
-params.skip_collapse = false
-params.skip_trim = false
+params.skip_adapterremoval = false
 params.skip_preseq = false
 params.skip_damage_calculation = false
 params.skip_qualimap = false
@@ -164,6 +164,8 @@ params.clip_reverse_adaptor = "AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTA"
 params.clip_readlength = 30
 params.clip_min_read_quality = 20
 params.min_adap_overlap = 1
+params.skip_collapse = false
+params.skip_trim = false
 
 //Read mapping parameters (default = BWA aln default)
 params.bwaalnn = 0.04
@@ -267,6 +269,25 @@ if (params.skip_collapse  && params.singleEnd){
     exit 1, "--noCollapse can only be set for pairedEnd samples!"
 }
 
+
+
+//Skip adapterremoval compatibility with skip_trim and skip_collapse
+
+skip_collapse = params.skip_collapse
+skip_trim = params.skip_trim
+skip_adapterremoval = params.skip_adapterremoval
+
+if (params.skip_collapse && params.skip_trim){
+    skip_adapterremoval = true
+}
+
+if (params.skip_adapterremoval){
+    skip_adapterremoval = true
+    skip_collapse = true
+    skip_trim = true
+}
+
+
 //AWSBatch sanity checking
 if(workflow.profile == 'awsbatch'){
     if (!params.awsqueue || !params.awsregion) exit 1, "Specify correct --awsqueue and --awsregion parameters on AWSBatch!"
@@ -351,8 +372,8 @@ summary['Fasta Ref']    = params.fasta
 summary['BAM Index Type'] = (params.large_ref == "") ? 'BAI' : 'CSI'
 if(params.bwa_index) summary['BWA Index'] = params.bwa_index
 summary['Data Type']    = params.singleEnd ? 'Single-End' : 'Paired-End'
-summary['Skip Collapsing'] = params.skip_collapse ? 'Yes' : 'No'
-summary['Skip Trimming']  = params.skip_trim  ? 'Yes' : 'No' 
+summary['Skip Collapsing'] = skip_collapse ? 'Yes' : 'No'
+summary['Skip Trimming']  = skip_trim  ? 'Yes' : 'No' 
 summary['Max Memory']   = params.max_memory
 summary['Max CPUs']     = params.max_cpus
 summary['Max Time']     = params.max_time
@@ -579,7 +600,6 @@ process fastp {
  * STEP 2 - Adapter Clipping / Read Merging
  */
 
-
 process adapter_removal {
     tag "$name"
     publishDir "${params.outdir}/read_merging", mode: 'copy'
@@ -598,20 +618,20 @@ process adapter_removal {
     script:
     base = reads[0].baseName
     
-    if( !params.singleEnd && !params.skip_collapse && !params.skip_trim){
+    if( !params.singleEnd && !skip_collapse && !params.skip_trim && !skip_adapterremoval){
     """
     AdapterRemoval --file1 ${reads[0]} --file2 ${reads[1]} --basename ${base} --gzip --threads ${task.cpus} --trimns --trimqualities --adapter1 ${params.clip_forward_adaptor} --adapter2 ${params.clip_reverse_adaptor} --minlength ${params.clip_readlength} --minquality ${params.clip_min_read_quality} --minadapteroverlap ${params.min_adap_overlap} --collapse
     #Combine files
     zcat *.collapsed.gz *.collapsed.truncated.gz *.singleton.truncated.gz *.pair1.truncated.gz *.pair2.truncated.gz | gzip > ${base}.combined.fq.gz
     """
-    } else if (!params.singleEnd && params.skip_collapse && !params.skip_trim) {
+    } else if (!params.singleEnd && skip_collapse && !params.skip_trim && !skip_adapterremoval) {
     """
     AdapterRemoval --file1 ${reads[0]} --file2 ${reads[1]} --basename ${base} --gzip --threads ${task.cpus} --trimns --trimqualities --adapter1 ${params.clip_forward_adaptor} --adapter2 ${params.clip_reverse_adaptor} --minlength ${params.clip_readlength} --minquality ${params.clip_min_read_quality} --minadapteroverlap ${params.min_adap_overlap}
     #Rename files
     mv ${base}.pair1.truncated.gz ${base}.pair1.combined.fq.gz
     mv ${base}.pair2.truncated.gz ${base}.pair2.combined.fq.gz
     """
-    } else if (!params.singleEnd && !params.skip_collapse && params.skip_trim) {
+    } else if (!params.singleEnd && !skip_collapse && params.skip_trim && !skip_adapterremoval) {
     bogus_adaptor = "NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN"
     """
     AdapterRemoval --file1 ${reads[0]} --file2 ${reads[1]} --basename ${base} --gzip --threads ${task.cpus} --basename ${base} --collapse --adapter1 $bogus_adaptor --adapter2 $bogus_adaptor
@@ -619,19 +639,18 @@ process adapter_removal {
     mv ${base}.pair1.truncated.gz ${base}.pair1.combined.fq.gz
     mv ${base}.pair2.truncated.gz ${base}.pair2.combined.fq.gz
     """
-    } else if (params.singleEnd && params.skip_collapse && params.skip_trim){
+    } else if (params.singleEnd && skip_adapterremoval){
     """
     mv ${reads[0]} ${base}.combined.fq.gz
     echo "Skipped trimming and merging by AdapterRemoval"
     """
-    } else if (params.pairedEnd && params.skip_collapse && params.skip_trim){
+    } else if (params.pairedEnd && skip_adapterremoval){
     """
     mv ${reads[0]} ${base}.pair1.combined.fq.gz
     mv ${reads[1]} ${base}.pair2.combined.fq.gz
     echo "Skipped trimming and merging by AdapterRemoval"
     """
-    }
-    else {
+    } else {
     """
     AdapterRemoval --file1 ${reads[0]} --basename ${base} --gzip --threads ${task.cpus} --trimns --trimqualities --adapter1 ${params.clip_forward_adaptor} --minlength ${params.clip_readlength} --minquality ${params.clip_min_read_quality} 
     # Pseudo-Combine
@@ -640,9 +659,11 @@ process adapter_removal {
     }
 }
 
+
+
 /*
- * STEP 2.1 - FastQC after clipping/merging (if applied!)
- */
+* STEP 2.1 - FastQC after clipping/merging (if applied!)
+*/
 process fastqc_after_clipping {
     tag "${prefix}"
     publishDir "${params.outdir}/FastQC/after_clipping", mode: 'copy',
@@ -687,7 +708,7 @@ process bwa {
     fasta = "${index}/*.fasta"
     size = "${params.large_ref}" ? '-c' : ''
 
-    if (!params.singleEnd && params.skip_collapse ){
+    if (!params.singleEnd && skip_collapse ){
     prefix = reads[0].toString().tokenize('.')[0]
     """ 
     bwa aln -t ${task.cpus} $fasta ${reads[0]} -n ${params.bwaalnn} -l ${params.bwaalnl} -k ${params.bwaalnk} -f ${prefix}.r1.sai
@@ -755,7 +776,7 @@ process circularmapper{
     fasta = "${index}/*_*.fasta"
     size = "${params.large_ref}" ? '-c' : ''
 
-    if (!params.singleEnd && params.skip_collapse ){
+    if (!params.singleEnd && skip_collapse ){
     prefix = reads[0].toString().tokenize('.')[0]
     """ 
     bwa aln -t ${task.cpus} $fasta ${reads[0]} -n ${params.bwaalnn} -l ${params.bwaalnl} -k ${params.bwaalnk} -f ${prefix}.r1.sai
@@ -798,7 +819,7 @@ process bwamem {
     fasta = "${index}/*.fasta"
     size = "${params.large_ref}" ? '-c' : ''
 
-    if (!params.singleEnd && params.skip_collapse ){
+    if (!params.singleEnd && skip_collapse ){
     """
     bwa mem -t ${task.cpus} $fasta ${reads[0]} ${reads[1]} -R "@RG\\tID:ILLUMINA-${prefix}\\tSM:${prefix}\\tPL:illumina" | samtools sort -@ ${task.cpus} -O bam - > "${prefix}".sorted.bam
     samtools index "${size}" -@ ${task.cpus} "${prefix}".sorted.bam

From 2bef839be75de13538d21d7d70a7196770a741fc Mon Sep 17 00:00:00 2001
From: Maxime <maxime.borry@gmail.com>
Date: Mon, 4 Mar 2019 17:21:24 +0100
Subject: [PATCH 12/29] update travis test

---
 .travis.yml | 6 ++++--
 1 file changed, 4 insertions(+), 2 deletions(-)

diff --git a/.travis.yml b/.travis.yml
index 7fe187219..dab87ae31 100644
--- a/.travis.yml
+++ b/.travis.yml
@@ -42,8 +42,10 @@ script:
   - nextflow run ${TRAVIS_BUILD_DIR} -profile test,docker --singleEnd --bwa_index results/reference_genome/bwa_index/bwa_index/
   # Run the basic pipeline with paired end data without collapsing
   - nextflow run ${TRAVIS_BUILD_DIR} -profile test,docker --pairedEnd --skip_collapse --saveReference
-    # Run the basic pipeline with paired end data without collapsing nor trimming
-  - nextflow run ${TRAVIS_BUILD_DIR} -profile test,docker --pairedEnd --skip_collapse --skip_trim --saveReference
+  # Run the basic pipeline with paired end data without trimming
+  - nextflow run ${TRAVIS_BUILD_DIR} -profile test,docker --pairedEnd --skip_trim --saveReference
+   # Run the basic pipeline with paired end data without adapterRemoval
+  - nextflow run ${TRAVIS_BUILD_DIR} -profile test,docker --pairedEnd --skip_adapterremoval --saveReference
   # Run the same pipeline testing optional step: fastp, complexity 
   - nextflow run ${TRAVIS_BUILD_DIR} -profile test,docker --pairedEnd --complexity_filter --bwa_index results/reference_genome/bwa_index/bwa_index/
   # Test BAM Trimming

From e62b5032be1d65ad3b8354dfebadf00ba0ab669b Mon Sep 17 00:00:00 2001
From: Maxime <maxime.borry@gmail.com>
Date: Mon, 4 Mar 2019 17:21:52 +0100
Subject: [PATCH 13/29] local executor for skipping AR process

---
 nextflow.config | 8 ++++++++
 1 file changed, 8 insertions(+)

diff --git a/nextflow.config b/nextflow.config
index 150d9bc25..5a701555c 100644
--- a/nextflow.config
+++ b/nextflow.config
@@ -38,6 +38,14 @@ params {
   custom_config_version = 'master'
 }
 
+if(params.skip_adapterremoval){
+  process {
+    withName: adapter_removal{
+      executor = 'local'
+    }
+  }
+}
+
 // Load base.config by default for all pipelines
 includeConfig 'conf/base.config'
 

From e807c5859de9edbe6e9c6d3e62f2be4ad1145b98 Mon Sep 17 00:00:00 2001
From: Maxime <maxime.borry@gmail.com>
Date: Mon, 4 Mar 2019 17:33:29 +0100
Subject: [PATCH 14/29] initialize skip_adapterremoval

---
 nextflow.config | 1 +
 1 file changed, 1 insertion(+)

diff --git a/nextflow.config b/nextflow.config
index 5a701555c..584710829 100644
--- a/nextflow.config
+++ b/nextflow.config
@@ -14,6 +14,7 @@ params {
 
   //Pipeline options
   aligner = 'bwa'
+  skip_adapterremoval = false
   saveReference = false
   saveTrimmed = true
   saveAlignedIntermediates = false

From 01d056c613b616bbf0d474990696fad727b1309d Mon Sep 17 00:00:00 2001
From: Maxime <maxime.borry@gmail.com>
Date: Mon, 4 Mar 2019 18:26:02 +0100
Subject: [PATCH 15/29] fix bam test

---
 main.nf | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/main.nf b/main.nf
index 81540b346..fd6d1f663 100644
--- a/main.nf
+++ b/main.nf
@@ -533,7 +533,7 @@ process convertBam {
 
     output:
     set val("${base}"), file("*.fastq.gz") into (ch_read_files_converted_fastqc, ch_read_files_converted_fastp)
-    set val("${base}"), file("*.fastq.gz") into (ch_read_files_converted_mapping_bwa, ch_read_files_converted_mapping_cm, ch_read_files_converted_mapping_bwamem)
+    file("*.fastq.gz") into (ch_read_files_converted_mapping_bwa, ch_read_files_converted_mapping_cm, ch_read_files_converted_mapping_bwamem)
 
     script:
     base = "${bam.baseName}"

From a38c5ff8c3895db8a7131a82ae88ee8de7ccbb86 Mon Sep 17 00:00:00 2001
From: Alexander Peltzer <alex.peltzer@gmail.com>
Date: Mon, 4 Mar 2019 21:22:08 +0100
Subject: [PATCH 16/29] Define defaults in nextflow.config

---
 nextflow.config | 7 ++++++-
 1 file changed, 6 insertions(+), 1 deletion(-)

diff --git a/nextflow.config b/nextflow.config
index 584710829..86736297f 100644
--- a/nextflow.config
+++ b/nextflow.config
@@ -14,7 +14,7 @@ params {
 
   //Pipeline options
   aligner = 'bwa'
-  skip_adapterremoval = false
+  
   saveReference = false
   saveTrimmed = true
   saveAlignedIntermediates = false
@@ -31,6 +31,11 @@ params {
   complexity_filter_poly_g_min = 10
   trim_bam = false
 
+  //Skipping adapterremoval, trimming or collapsing defaults
+  skip_adapterremoval = false
+  skip_trim = false
+  skip_adapterremoval = false
+
   // AWS Batch
   awsqueue = false
   awsregion = 'eu-west-1'

From 20177fa6d421b1ef966b2eaec8a54129591ab04c Mon Sep 17 00:00:00 2001
From: Alexander Peltzer <alex.peltzer@gmail.com>
Date: Mon, 4 Mar 2019 21:22:31 +0100
Subject: [PATCH 17/29] Starting to polish PR

---
 main.nf | 64 ++++++++++++++++++++++-----------------------------------
 1 file changed, 24 insertions(+), 40 deletions(-)

diff --git a/main.nf b/main.nf
index fd6d1f663..b38a4ba51 100644
--- a/main.nf
+++ b/main.nf
@@ -60,7 +60,7 @@ def helpMessage() {
       --clip_readlength             Specify read minimum length to be kept for downstream analysis
       --clip_min_read_quality       Specify minimum base quality for not trimming off bases
       --min_adap_overlap            Specify minimum adapter overlap
-      --skip_collapse               Skip merging Forward and Reverse reads together. (Only for pairedEnd samples)
+      --skip_collapse               Skip merging Forward and Reverse reads together. (Only for PE samples)
       --skip_trim                   Skip adaptor and quality trimming
     
     BWA Mapping
@@ -266,17 +266,9 @@ if( params.singleEnd || params.pairedEnd || params.bam){
 
 //Validate that skip_collapse is only set to True for pairedEnd reads!
 if (params.skip_collapse  && params.singleEnd){
-    exit 1, "--noCollapse can only be set for pairedEnd samples!"
+    exit 1, "--skip_collapse can only be set for pairedEnd samples!"
 }
 
-
-
-//Skip adapterremoval compatibility with skip_trim and skip_collapse
-
-skip_collapse = params.skip_collapse
-skip_trim = params.skip_trim
-skip_adapterremoval = params.skip_adapterremoval
-
 if (params.skip_collapse && params.skip_trim){
     skip_adapterremoval = true
 }
@@ -372,8 +364,8 @@ summary['Fasta Ref']    = params.fasta
 summary['BAM Index Type'] = (params.large_ref == "") ? 'BAI' : 'CSI'
 if(params.bwa_index) summary['BWA Index'] = params.bwa_index
 summary['Data Type']    = params.singleEnd ? 'Single-End' : 'Paired-End'
-summary['Skip Collapsing'] = skip_collapse ? 'Yes' : 'No'
-summary['Skip Trimming']  = skip_trim  ? 'Yes' : 'No' 
+summary['Skip Collapsing'] = params.skip_collapse ? 'Yes' : 'No'
+summary['Skip Trimming']  = params.skip_trim  ? 'Yes' : 'No' 
 summary['Max Memory']   = params.max_memory
 summary['Max CPUs']     = params.max_cpus
 summary['Max Time']     = params.max_time
@@ -604,57 +596,49 @@ process adapter_removal {
     tag "$name"
     publishDir "${params.outdir}/read_merging", mode: 'copy'
 
-    echo true
-
-    when: !params.bam
+    when: !params.bam && !params.skip_adapterremoval
 
     input:
     set val(name), file(reads) from ( params.complexity_filter_poly_g ? ch_clipped_reads_complexity_filtered_poly_g : ch_read_files_clip )
 
     output:
-    file "*.combined*.gz" into (ch_clipped_reads, ch_clipped_reads_for_fastqc,ch_clipped_reads_circularmapper,ch_clipped_reads_bwamem)
-    file("*.settings") optional true into ch_adapterremoval_logs
+    file "output/*.fq.gz" into (ch_clipped_reads, ch_clipped_reads_for_fastqc,ch_clipped_reads_circularmapper,ch_clipped_reads_bwamem)
+    file("*.settings") into ch_adapterremoval_logs
 
     script:
     base = reads[0].baseName
     
-    if( !params.singleEnd && !skip_collapse && !params.skip_trim && !skip_adapterremoval){
+    //PE, collapse & trim reads
+    if( !params.singleEnd && !params.skip_collapse && !params.skip_trim && !params.skip_adapterremoval){
     """
+    mkdir -p output
     AdapterRemoval --file1 ${reads[0]} --file2 ${reads[1]} --basename ${base} --gzip --threads ${task.cpus} --trimns --trimqualities --adapter1 ${params.clip_forward_adaptor} --adapter2 ${params.clip_reverse_adaptor} --minlength ${params.clip_readlength} --minquality ${params.clip_min_read_quality} --minadapteroverlap ${params.min_adap_overlap} --collapse
     #Combine files
-    zcat *.collapsed.gz *.collapsed.truncated.gz *.singleton.truncated.gz *.pair1.truncated.gz *.pair2.truncated.gz | gzip > ${base}.combined.fq.gz
+    zcat *.collapsed.gz *.collapsed.truncated.gz *.singleton.truncated.gz *.pair1.truncated.gz *.pair2.truncated.gz | gzip > output/${base}.combined.fq.gz
     """
-    } else if (!params.singleEnd && skip_collapse && !params.skip_trim && !skip_adapterremoval) {
+    //PE, don't collapse, but trim reads
+    } else if (!params.singleEnd && params.skip_collapse && !params.skip_trim && !params.skip_adapterremoval) {
     """
+    mkdir -p output
     AdapterRemoval --file1 ${reads[0]} --file2 ${reads[1]} --basename ${base} --gzip --threads ${task.cpus} --trimns --trimqualities --adapter1 ${params.clip_forward_adaptor} --adapter2 ${params.clip_reverse_adaptor} --minlength ${params.clip_readlength} --minquality ${params.clip_min_read_quality} --minadapteroverlap ${params.min_adap_overlap}
-    #Rename files
-    mv ${base}.pair1.truncated.gz ${base}.pair1.combined.fq.gz
-    mv ${base}.pair2.truncated.gz ${base}.pair2.combined.fq.gz
+    mv ${base}.pair*.truncated.gz output/
     """
-    } else if (!params.singleEnd && !skip_collapse && params.skip_trim && !skip_adapterremoval) {
+    //PE, collapse, but don't trim reads
+    } else if (!params.singleEnd && !params.skip_collapse && params.skip_trim && !params.skip_adapterremoval) {
     bogus_adaptor = "NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN"
     """
+    mkdir -p output
     AdapterRemoval --file1 ${reads[0]} --file2 ${reads[1]} --basename ${base} --gzip --threads ${task.cpus} --basename ${base} --collapse --adapter1 $bogus_adaptor --adapter2 $bogus_adaptor
-    #Rename files
-    mv ${base}.pair1.truncated.gz ${base}.pair1.combined.fq.gz
-    mv ${base}.pair2.truncated.gz ${base}.pair2.combined.fq.gz
-    """
-    } else if (params.singleEnd && skip_adapterremoval){
-    """
-    mv ${reads[0]} ${base}.combined.fq.gz
-    echo "Skipped trimming and merging by AdapterRemoval"
-    """
-    } else if (params.pairedEnd && skip_adapterremoval){
-    """
-    mv ${reads[0]} ${base}.pair1.combined.fq.gz
-    mv ${reads[1]} ${base}.pair2.combined.fq.gz
-    echo "Skipped trimming and merging by AdapterRemoval"
+    
+    mv ${base}.pair*.truncated.gz output/
     """
     } else {
+    //SE, collapse not possible, trim reads
     """
+    mkdir -p output
     AdapterRemoval --file1 ${reads[0]} --basename ${base} --gzip --threads ${task.cpus} --trimns --trimqualities --adapter1 ${params.clip_forward_adaptor} --minlength ${params.clip_readlength} --minquality ${params.clip_min_read_quality} 
-    # Pseudo-Combine
-    mv *.truncated.gz ${base}.combined.fq.gz
+    
+    mv *.truncated.gz output/
     """
     }
 }

From f9b79c2e47a70ab4cf459231effcf3944771bdc9 Mon Sep 17 00:00:00 2001
From: Alexander Peltzer <alex.peltzer@gmail.com>
Date: Mon, 4 Mar 2019 21:49:43 +0100
Subject: [PATCH 18/29] Some more fixes for channel handling

---
 main.nf | 28 +++++++++++++++++-----------
 1 file changed, 17 insertions(+), 11 deletions(-)

diff --git a/main.nf b/main.nf
index b38a4ba51..8bfa5049a 100644
--- a/main.nf
+++ b/main.nf
@@ -270,13 +270,13 @@ if (params.skip_collapse  && params.singleEnd){
 }
 
 if (params.skip_collapse && params.skip_trim){
-    skip_adapterremoval = true
+    params.skip_adapterremoval = true
 }
 
 if (params.skip_adapterremoval){
-    skip_adapterremoval = true
-    skip_collapse = true
-    skip_trim = true
+    params.skip_adapterremoval = true
+    params.skip_collapse = true
+    params.skip_trim = true
 }
 
 
@@ -591,7 +591,10 @@ process fastp {
 /*
  * STEP 2 - Adapter Clipping / Read Merging
  */
-
+//Initialize empty channel if we skip adapterremoval entirely
+if(params.skip_adapterremoval) {
+    ch_clipped_reads = Channel.empty()
+}
 process adapter_removal {
     tag "$name"
     publishDir "${params.outdir}/read_merging", mode: 'copy'
@@ -602,7 +605,7 @@ process adapter_removal {
     set val(name), file(reads) from ( params.complexity_filter_poly_g ? ch_clipped_reads_complexity_filtered_poly_g : ch_read_files_clip )
 
     output:
-    file "output/*.fq.gz" into (ch_clipped_reads, ch_clipped_reads_for_fastqc,ch_clipped_reads_circularmapper,ch_clipped_reads_bwamem)
+    set val(base), file "output/*.gz" into (ch_clipped_reads,ch_clipped_reads_for_fastqc,ch_clipped_reads_circularmapper,ch_clipped_reads_bwamem)
     file("*.settings") into ch_adapterremoval_logs
 
     script:
@@ -653,7 +656,7 @@ process fastqc_after_clipping {
     publishDir "${params.outdir}/FastQC/after_clipping", mode: 'copy',
         saveAs: {filename -> filename.indexOf(".zip") > 0 ? "zips/$filename" : "$filename"}
 
-    when: !params.bam
+    when: !params.bam && !params.skip_adapterremoval
 
     input:
     file(reads) from ch_clipped_reads_for_fastqc
@@ -679,7 +682,8 @@ process bwa {
     when: !params.circularmapper && !params.bwamem
 
     input:
-    file(reads) from ch_clipped_reads.mix(ch_read_files_converted_mapping_bwa)
+    set val(name), file(reads) from ( params.skip_adapterremoval ? ch_read_files_clip : ch_clipped_reads.mix(ch_read_files_converted_mapping_bwa) )
+    
     file index from ch_bwa_index.first()
 
 
@@ -692,7 +696,8 @@ process bwa {
     fasta = "${index}/*.fasta"
     size = "${params.large_ref}" ? '-c' : ''
 
-    if (!params.singleEnd && skip_collapse ){
+    //PE data without merging, PE data without any AR applied
+    if (!params.singleEnd && (params.skip_collapse || params.skip_adapterremoval)){
     prefix = reads[0].toString().tokenize('.')[0]
     """ 
     bwa aln -t ${task.cpus} $fasta ${reads[0]} -n ${params.bwaalnn} -l ${params.bwaalnl} -k ${params.bwaalnk} -f ${prefix}.r1.sai
@@ -701,6 +706,7 @@ process bwa {
     samtools index "${size}" "${prefix}".sorted.bam
     """
     } else {
+    //PE collapsed, or SE data 
     prefix = reads[0].toString().tokenize('.')[0]
     """ 
     bwa aln -t ${task.cpus} $fasta $reads -n ${params.bwaalnn} -l ${params.bwaalnl} -k ${params.bwaalnk} -f ${prefix}.sai
@@ -747,7 +753,7 @@ process circularmapper{
     when: params.circularmapper
 
     input:
-    file reads from ch_clipped_reads_circularmapper.mix(ch_read_files_converted_mapping_cm)
+    set val(name), file reads from (params.skip_adapterremoval ? ch_clipped_reads : ch_clipped_reads_circularmapper.mix(ch_read_files_converted_mapping_cm) )
     file index from ch_circularmapper_indices.first()
 
     output:
@@ -790,7 +796,7 @@ process bwamem {
     when: params.bwamem && !params.circularmapper
 
     input:
-    file(reads) from ch_clipped_reads_bwamem.mix(ch_read_files_converted_mapping_bwamem)
+    set val(name), file(reads) from (params.skip_adapterremoval ? ch_clipped_reads : ch_clipped_reads_bwamem.mix(ch_read_files_converted_mapping_bwamem) )
     file index from ch_bwa_index_bwamem.first()
 
     output:

From 5caefbfe758ad483bc8fd4bc36b6ffe7e2803ecd Mon Sep 17 00:00:00 2001
From: Alexander Peltzer <alex.peltzer@gmail.com>
Date: Mon, 4 Mar 2019 22:23:16 +0100
Subject: [PATCH 19/29] Fix being able to handle modern data too

---
 main.nf | 29 +++++++++++------------------
 1 file changed, 11 insertions(+), 18 deletions(-)

diff --git a/main.nf b/main.nf
index 8bfa5049a..7c755d9f1 100644
--- a/main.nf
+++ b/main.nf
@@ -269,17 +269,6 @@ if (params.skip_collapse  && params.singleEnd){
     exit 1, "--skip_collapse can only be set for pairedEnd samples!"
 }
 
-if (params.skip_collapse && params.skip_trim){
-    params.skip_adapterremoval = true
-}
-
-if (params.skip_adapterremoval){
-    params.skip_adapterremoval = true
-    params.skip_collapse = true
-    params.skip_trim = true
-}
-
-
 //AWSBatch sanity checking
 if(workflow.profile == 'awsbatch'){
     if (!params.awsqueue || !params.awsregion) exit 1, "Specify correct --awsqueue and --awsregion parameters on AWSBatch!"
@@ -593,8 +582,11 @@ process fastp {
  */
 //Initialize empty channel if we skip adapterremoval entirely
 if(params.skip_adapterremoval) {
-    ch_clipped_reads = Channel.empty()
-}
+    //No logs if no AR is run
+    ch_adapterremoval_logs = Channel.empty()
+    //Either coming from complexity filtering, or directly use reads normally directed to clipping first and push them through to the other channels downstream! 
+    ch_clipped_reads_complexity_filtered_poly_g.mix(ch_read_files_clip).into { ch_clipped_reads;ch_clipped_reads_for_fastqc;ch_clipped_reads_circularmapper;ch_clipped_reads_bwamem }
+} else {
 process adapter_removal {
     tag "$name"
     publishDir "${params.outdir}/read_merging", mode: 'copy'
@@ -605,7 +597,7 @@ process adapter_removal {
     set val(name), file(reads) from ( params.complexity_filter_poly_g ? ch_clipped_reads_complexity_filtered_poly_g : ch_read_files_clip )
 
     output:
-    set val(base), file "output/*.gz" into (ch_clipped_reads,ch_clipped_reads_for_fastqc,ch_clipped_reads_circularmapper,ch_clipped_reads_bwamem)
+    set val(base), file("output/*.gz") into (ch_clipped_reads,ch_clipped_reads_for_fastqc,ch_clipped_reads_circularmapper,ch_clipped_reads_bwamem)
     file("*.settings") into ch_adapterremoval_logs
 
     script:
@@ -645,6 +637,7 @@ process adapter_removal {
     """
     }
 }
+}
 
 
 
@@ -659,7 +652,7 @@ process fastqc_after_clipping {
     when: !params.bam && !params.skip_adapterremoval
 
     input:
-    file(reads) from ch_clipped_reads_for_fastqc
+    set val(name), file(reads) from ch_clipped_reads_for_fastqc
 
     output:
     file "*_fastqc.{zip,html}" optional true into ch_fastqc_after_clipping
@@ -682,7 +675,7 @@ process bwa {
     when: !params.circularmapper && !params.bwamem
 
     input:
-    set val(name), file(reads) from ( params.skip_adapterremoval ? ch_read_files_clip : ch_clipped_reads.mix(ch_read_files_converted_mapping_bwa) )
+    set val(name), file(reads) from ch_clipped_reads.mix(ch_read_files_converted_mapping_bwa)
     
     file index from ch_bwa_index.first()
 
@@ -753,7 +746,7 @@ process circularmapper{
     when: params.circularmapper
 
     input:
-    set val(name), file reads from (params.skip_adapterremoval ? ch_clipped_reads : ch_clipped_reads_circularmapper.mix(ch_read_files_converted_mapping_cm) )
+    set val(name), file(reads) from ch_clipped_reads_circularmapper.mix(ch_read_files_converted_mapping_cm)
     file index from ch_circularmapper_indices.first()
 
     output:
@@ -796,7 +789,7 @@ process bwamem {
     when: params.bwamem && !params.circularmapper
 
     input:
-    set val(name), file(reads) from (params.skip_adapterremoval ? ch_clipped_reads : ch_clipped_reads_bwamem.mix(ch_read_files_converted_mapping_bwamem) )
+    set val(name), file(reads) from ch_clipped_reads_bwamem.mix(ch_read_files_converted_mapping_bwamem)
     file index from ch_bwa_index_bwamem.first()
 
     output:

From 48075bfd94c346c06897938032e03a533a2f65cd Mon Sep 17 00:00:00 2001
From: Alexander Peltzer <alex.peltzer@gmail.com>
Date: Mon, 4 Mar 2019 22:36:11 +0100
Subject: [PATCH 20/29] Remove if clause here

---
 nextflow.config | 7 -------
 1 file changed, 7 deletions(-)

diff --git a/nextflow.config b/nextflow.config
index 86736297f..9fcbb2404 100644
--- a/nextflow.config
+++ b/nextflow.config
@@ -44,13 +44,6 @@ params {
   custom_config_version = 'master'
 }
 
-if(params.skip_adapterremoval){
-  process {
-    withName: adapter_removal{
-      executor = 'local'
-    }
-  }
-}
 
 // Load base.config by default for all pipelines
 includeConfig 'conf/base.config'

From 990140c14316fd8e47dfc961040211e01bebb32d Mon Sep 17 00:00:00 2001
From: phue <patrick.huether@gmail.com>
Date: Tue, 5 Mar 2019 08:45:41 +0100
Subject: [PATCH 21/29] Update main.nf

Co-Authored-By: apeltzer <apeltzer@users.noreply.github.com>
---
 main.nf | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/main.nf b/main.nf
index 7c755d9f1..05d69596f 100644
--- a/main.nf
+++ b/main.nf
@@ -60,7 +60,7 @@ def helpMessage() {
       --clip_readlength             Specify read minimum length to be kept for downstream analysis
       --clip_min_read_quality       Specify minimum base quality for not trimming off bases
       --min_adap_overlap            Specify minimum adapter overlap
-      --skip_collapse               Skip merging Forward and Reverse reads together. (Only for PE samples)
+      --skip_collapse               Skip merging forward and reverse reads together. (Only for PE samples)
       --skip_trim                   Skip adaptor and quality trimming
     
     BWA Mapping

From 9f45104f29d28e66a4f9ee4fb4de614c6d4b03dc Mon Sep 17 00:00:00 2001
From: phue <patrick.huether@gmail.com>
Date: Tue, 5 Mar 2019 08:45:48 +0100
Subject: [PATCH 22/29] Update main.nf

Co-Authored-By: apeltzer <apeltzer@users.noreply.github.com>
---
 main.nf | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/main.nf b/main.nf
index 05d69596f..b833a1cd7 100644
--- a/main.nf
+++ b/main.nf
@@ -604,7 +604,7 @@ process adapter_removal {
     base = reads[0].baseName
     
     //PE, collapse & trim reads
-    if( !params.singleEnd && !params.skip_collapse && !params.skip_trim && !params.skip_adapterremoval){
+    if (!params.singleEnd && !params.skip_collapse && !params.skip_trim && !params.skip_adapterremoval){
     """
     mkdir -p output
     AdapterRemoval --file1 ${reads[0]} --file2 ${reads[1]} --basename ${base} --gzip --threads ${task.cpus} --trimns --trimqualities --adapter1 ${params.clip_forward_adaptor} --adapter2 ${params.clip_reverse_adaptor} --minlength ${params.clip_readlength} --minquality ${params.clip_min_read_quality} --minadapteroverlap ${params.min_adap_overlap} --collapse

From 68fa27df622c67b1483de2e058a967fb9c47ac8d Mon Sep 17 00:00:00 2001
From: phue <patrick.huether@gmail.com>
Date: Tue, 5 Mar 2019 08:45:58 +0100
Subject: [PATCH 23/29] Update main.nf

Co-Authored-By: apeltzer <apeltzer@users.noreply.github.com>
---
 main.nf | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/main.nf b/main.nf
index b833a1cd7..2193d3f10 100644
--- a/main.nf
+++ b/main.nf
@@ -802,7 +802,7 @@ process bwamem {
     fasta = "${index}/*.fasta"
     size = "${params.large_ref}" ? '-c' : ''
 
-    if (!params.singleEnd && skip_collapse ){
+    if (!params.singleEnd && params.skip_collapse){
     """
     bwa mem -t ${task.cpus} $fasta ${reads[0]} ${reads[1]} -R "@RG\\tID:ILLUMINA-${prefix}\\tSM:${prefix}\\tPL:illumina" | samtools sort -@ ${task.cpus} -O bam - > "${prefix}".sorted.bam
     samtools index "${size}" -@ ${task.cpus} "${prefix}".sorted.bam

From b2b9189de3dc30d15ce67c691363c47a8b1e4783 Mon Sep 17 00:00:00 2001
From: Alexander Peltzer <alex.peltzer@gmail.com>
Date: Tue, 5 Mar 2019 08:47:16 +0100
Subject: [PATCH 24/29] Fix remaining issue with circularmapper

---
 main.nf | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/main.nf b/main.nf
index 2193d3f10..ac5ca98ad 100644
--- a/main.nf
+++ b/main.nf
@@ -759,7 +759,7 @@ process circularmapper{
     fasta = "${index}/*_*.fasta"
     size = "${params.large_ref}" ? '-c' : ''
 
-    if (!params.singleEnd && skip_collapse ){
+    if (!params.singleEnd && params.skip_collapse ){
     prefix = reads[0].toString().tokenize('.')[0]
     """ 
     bwa aln -t ${task.cpus} $fasta ${reads[0]} -n ${params.bwaalnn} -l ${params.bwaalnl} -k ${params.bwaalnk} -f ${prefix}.r1.sai

From 5b924db9fd7fe4d98a5826dc2fa87ddd74b5e9b9 Mon Sep 17 00:00:00 2001
From: Alexander Peltzer <alex.peltzer@gmail.com>
Date: Tue, 5 Mar 2019 10:42:09 +0100
Subject: [PATCH 25/29] Fix cardinality issues

---
 main.nf | 3 +--
 1 file changed, 1 insertion(+), 2 deletions(-)

diff --git a/main.nf b/main.nf
index ac5ca98ad..59dfabd46 100644
--- a/main.nf
+++ b/main.nf
@@ -513,8 +513,7 @@ process convertBam {
     file bam from ch_bam_to_fastq_convert
 
     output:
-    set val("${base}"), file("*.fastq.gz") into (ch_read_files_converted_fastqc, ch_read_files_converted_fastp)
-    file("*.fastq.gz") into (ch_read_files_converted_mapping_bwa, ch_read_files_converted_mapping_cm, ch_read_files_converted_mapping_bwamem)
+    set val("${base}"), file("*.fastq.gz") into (ch_read_files_converted_fastqc, ch_read_files_converted_fastp, ch_read_files_converted_mapping_bwa, ch_read_files_converted_mapping_cm, ch_read_files_converted_mapping_bwamem)
 
     script:
     base = "${bam.baseName}"

From 712535fa18b8c4d391a6baeb34be315f19f0f6c5 Mon Sep 17 00:00:00 2001
From: Alexander Peltzer <alex.peltzer@gmail.com>
Date: Tue, 5 Mar 2019 12:38:34 +0100
Subject: [PATCH 26/29] No need to check for AR skipping here

---
 main.nf | 8 +++++---
 1 file changed, 5 insertions(+), 3 deletions(-)

diff --git a/main.nf b/main.nf
index 59dfabd46..203889f92 100644
--- a/main.nf
+++ b/main.nf
@@ -601,9 +601,11 @@ process adapter_removal {
 
     script:
     base = reads[0].baseName
+    //This checks whether we skip trimming and defines a variable respectively
+    trim_me = params.skip_trim ? '' : ''
     
     //PE, collapse & trim reads
-    if (!params.singleEnd && !params.skip_collapse && !params.skip_trim && !params.skip_adapterremoval){
+    if (!params.singleEnd && !params.skip_collapse && !params.skip_trim){
     """
     mkdir -p output
     AdapterRemoval --file1 ${reads[0]} --file2 ${reads[1]} --basename ${base} --gzip --threads ${task.cpus} --trimns --trimqualities --adapter1 ${params.clip_forward_adaptor} --adapter2 ${params.clip_reverse_adaptor} --minlength ${params.clip_readlength} --minquality ${params.clip_min_read_quality} --minadapteroverlap ${params.min_adap_overlap} --collapse
@@ -611,14 +613,14 @@ process adapter_removal {
     zcat *.collapsed.gz *.collapsed.truncated.gz *.singleton.truncated.gz *.pair1.truncated.gz *.pair2.truncated.gz | gzip > output/${base}.combined.fq.gz
     """
     //PE, don't collapse, but trim reads
-    } else if (!params.singleEnd && params.skip_collapse && !params.skip_trim && !params.skip_adapterremoval) {
+    } else if (!params.singleEnd && params.skip_collapse && !params.skip_trim) {
     """
     mkdir -p output
     AdapterRemoval --file1 ${reads[0]} --file2 ${reads[1]} --basename ${base} --gzip --threads ${task.cpus} --trimns --trimqualities --adapter1 ${params.clip_forward_adaptor} --adapter2 ${params.clip_reverse_adaptor} --minlength ${params.clip_readlength} --minquality ${params.clip_min_read_quality} --minadapteroverlap ${params.min_adap_overlap}
     mv ${base}.pair*.truncated.gz output/
     """
     //PE, collapse, but don't trim reads
-    } else if (!params.singleEnd && !params.skip_collapse && params.skip_trim && !params.skip_adapterremoval) {
+    } else if (!params.singleEnd && !params.skip_collapse && params.skip_trim) {
     bogus_adaptor = "NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN"
     """
     mkdir -p output

From f6b7313c14bd90fd8d327e35eb3a6f2764085e93 Mon Sep 17 00:00:00 2001
From: Alexander Peltzer <alex.peltzer@gmail.com>
Date: Tue, 5 Mar 2019 12:51:40 +0100
Subject: [PATCH 27/29] Polish PR even further

---
 main.nf | 14 +++++++-------
 1 file changed, 7 insertions(+), 7 deletions(-)

diff --git a/main.nf b/main.nf
index 203889f92..5b807c8ef 100644
--- a/main.nf
+++ b/main.nf
@@ -602,13 +602,14 @@ process adapter_removal {
     script:
     base = reads[0].baseName
     //This checks whether we skip trimming and defines a variable respectively
-    trim_me = params.skip_trim ? '' : ''
+    trim_me = params.skip_trim ? '' : "--trimns --trimqualities --adapter1 ${params.clip_forward_adaptor} --adapter2 ${params.clip_reverse_adaptor} --minlength ${params.clip_readlength} --minquality ${params.clip_min_read_quality} --minadapteroverlap ${params.min_adap_overlap}"
+    collapse_me = params.skip_collapse ? '' : '--collapse'
     
-    //PE, collapse & trim reads
+    //PE mode, dependent on trim_me and collapse_me the respective procedure is run or not :-) 
     if (!params.singleEnd && !params.skip_collapse && !params.skip_trim){
     """
     mkdir -p output
-    AdapterRemoval --file1 ${reads[0]} --file2 ${reads[1]} --basename ${base} --gzip --threads ${task.cpus} --trimns --trimqualities --adapter1 ${params.clip_forward_adaptor} --adapter2 ${params.clip_reverse_adaptor} --minlength ${params.clip_readlength} --minquality ${params.clip_min_read_quality} --minadapteroverlap ${params.min_adap_overlap} --collapse
+    AdapterRemoval --file1 ${reads[0]} --file2 ${reads[1]} --basename ${base} ${trim_me} --gzip --threads ${task.cpus} ${collapse_me}
     #Combine files
     zcat *.collapsed.gz *.collapsed.truncated.gz *.singleton.truncated.gz *.pair1.truncated.gz *.pair2.truncated.gz | gzip > output/${base}.combined.fq.gz
     """
@@ -616,15 +617,14 @@ process adapter_removal {
     } else if (!params.singleEnd && params.skip_collapse && !params.skip_trim) {
     """
     mkdir -p output
-    AdapterRemoval --file1 ${reads[0]} --file2 ${reads[1]} --basename ${base} --gzip --threads ${task.cpus} --trimns --trimqualities --adapter1 ${params.clip_forward_adaptor} --adapter2 ${params.clip_reverse_adaptor} --minlength ${params.clip_readlength} --minquality ${params.clip_min_read_quality} --minadapteroverlap ${params.min_adap_overlap}
+    AdapterRemoval --file1 ${reads[0]} --file2 ${reads[1]} --basename ${base} --gzip --threads ${task.cpus} ${trim_me} ${collapse_me}
     mv ${base}.pair*.truncated.gz output/
     """
     //PE, collapse, but don't trim reads
     } else if (!params.singleEnd && !params.skip_collapse && params.skip_trim) {
-    bogus_adaptor = "NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN"
     """
     mkdir -p output
-    AdapterRemoval --file1 ${reads[0]} --file2 ${reads[1]} --basename ${base} --gzip --threads ${task.cpus} --basename ${base} --collapse --adapter1 $bogus_adaptor --adapter2 $bogus_adaptor
+    AdapterRemoval --file1 ${reads[0]} --file2 ${reads[1]} --basename ${base} --gzip --threads ${task.cpus} --basename ${base} ${collapse_me} ${trim_me}
     
     mv ${base}.pair*.truncated.gz output/
     """
@@ -632,7 +632,7 @@ process adapter_removal {
     //SE, collapse not possible, trim reads
     """
     mkdir -p output
-    AdapterRemoval --file1 ${reads[0]} --basename ${base} --gzip --threads ${task.cpus} --trimns --trimqualities --adapter1 ${params.clip_forward_adaptor} --minlength ${params.clip_readlength} --minquality ${params.clip_min_read_quality} 
+    AdapterRemoval --file1 ${reads[0]} --basename ${base} --gzip --threads ${task.cpus} ${trim_me}
     
     mv *.truncated.gz output/
     """

From cb72002746969c0ca348dd14a9470108b55b044d Mon Sep 17 00:00:00 2001
From: Alexander Peltzer <alex.peltzer@gmail.com>
Date: Tue, 5 Mar 2019 12:55:47 +0100
Subject: [PATCH 28/29] Typos fixed in usage

---
 docs/usage.md | 9 ++++-----
 1 file changed, 4 insertions(+), 5 deletions(-)

diff --git a/docs/usage.md b/docs/usage.md
index 2d78d15d0..5a848760b 100644
--- a/docs/usage.md
+++ b/docs/usage.md
@@ -291,8 +291,7 @@ Turns off the computation of library complexity estimation.
 
 ### `--skip_adapterremoval`
 
-Turns off adaptor trimming and paired-end read merging.
-Equivalent to setting both `--skip_collapse` and `--skip_trim`
+Turns off adaptor trimming and paired-end read merging. Equivalent to setting both `--skip_collapse` and `--skip_trim`.
 
 ### `--skip_damage_calculation`
 
@@ -340,7 +339,7 @@ Sets the minimum overlap between two reads when read merging is performed. Defau
 
 ### `--skip_collapse`
 
-Turns off the paired-end read merging. 
+Turns off the paired-end read merging.
 
 For example
 ```bash
@@ -349,9 +348,9 @@ For example
 
 ### `--skip_trim`
 
-Turns off the adaptor and quality trimming.
+Turns off adaptor and quality trimming.
 
-For example
+For example:
 ```bash
 --pairedEnd --skip_trim  --reads '*.fastq'
 ```

From 2099a36573407a6acc115ca90b3488371990130a Mon Sep 17 00:00:00 2001
From: Alexander Peltzer <alex.peltzer@gmail.com>
Date: Tue, 5 Mar 2019 12:57:20 +0100
Subject: [PATCH 29/29] Add proper changelog

---
 CHANGELOG.md | 1 +
 1 file changed, 1 insertion(+)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index 661f73ea6..e281225a3 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -10,6 +10,7 @@ and this project adheres to [Semantic Versioning](http://semver.org/spec/v2.0.0.
 
 * [#152](https://github.com/nf-core/eager/pull/152) - Clarified `--complexity_filter` flag to be specifically for poly G trimming.
 * [#155](https://github.com/nf-core/eager/pull/155) - Added [Dedup log to output folders](https://github.com/nf-core/eager/issues/154)
+* [#159](https://github.com/nf-core/eager/pull/159) - Added Possibility to skip AdapterRemoval, skip merging, skip trimming fixing [#64](https://github.com/nf-core/eager/issues/64),[#137](https://github.com/nf-core/eager/issues/137) - thanks to @maxibor, @jfy133
 
 ### `Fixed`