Merge branch 'upgrade-samtools' into 'develop'

upgrade samtools to a more recent version See merge request tron/tronflow-bwa-pe!8
TRON-Bioinformatics · Jun 14, 2021 · 30931fc · 30931fc
2 parents b9b2a89 + 5590835
commit 30931fc
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diff --git a/README.md b/README.md
@@ -6,15 +6,15 @@ Nextflow pipeline for the alignment of paired and single end FASTQ files with BW
 
 There are two packages that are required for this pipeline. Both of this are preconfigured when using the conda or docker profiles.
 
-- BWA 0.1.17
-- samtools 0.1.19
+- BWA 0.7.17
+- samtools 1.12
 
 
 ## How to run it
 
 Run it from GitHub as follows:
 ```
-nextflow run tron-bioinformatics/tronflow-bwa -r v1.2.0 --input_files $input --output $output --algorithm aln --library paired -profile conda,standard
+nextflow run tron-bioinformatics/tronflow-bwa --input_files $input --output $output --algorithm aln --library paired -profile conda,standard
 ```
 
 Otherwise download the project and run as follows:

diff --git a/environment.yml b/environment.yml
@@ -7,5 +7,4 @@ channels:
   - defaults
 dependencies:
   - bioconda::bwa=0.7.17
-  - conda-forge::ncurses=5
-  - bioconda::samtools=0.1.16
+  - bioconda::samtools=1.12
diff --git a/main.nf b/main.nf
@@ -119,7 +119,7 @@ if (params.algorithm == "aln" && params.library == "paired" && !params.inception
           set val("${name}"), file("${name}.bam") into sampe_output
 
         """
-        bwa sampe ${params.reference} ${sai1} ${sai2} ${fastq1} ${fastq2} | samtools view -uS - | samtools sort - ${name}
+        bwa sampe ${params.reference} ${sai1} ${sai2} ${fastq1} ${fastq2} | samtools view -uS - | samtools sort - > ${name}.bam
         """
     }
 }
@@ -155,7 +155,7 @@ else if (params.algorithm == "aln" && params.library == "single"  && !params.inc
           set val("${name}"), file("${name}.bam") into samse_output
 
         """
-        bwa samse ${params.reference} ${sai} ${fastq} | samtools view -uS - | samtools sort - ${name}
+        bwa samse ${params.reference} ${sai} ${fastq} | samtools view -uS - | samtools sort - > ${name}.bam
         """
     }
 }
@@ -177,7 +177,7 @@ else if (params.algorithm == "aln" && params.library == "paired" && params.incep
         """
         bwa sampe ${params.reference} <( bwa aln -t ${params.cpus} ${params.reference} ${fastq1} ) \
         <( bwa aln -t ${params.cpus} ${params.reference} ${fastq2} ) ${fastq1} ${fastq2} \
-        | samtools view -uS - | samtools sort - ${name}
+        | samtools view -uS - | samtools sort - > ${name}.bam
         """
     }
 }
@@ -197,7 +197,7 @@ else if (params.algorithm == "mem" && params.library == "paired") {
           set val("${name}"), file("${name}.bam") into sampe_output
 
         """
-        bwa mem -t ${task.cpus} ${params.reference} ${fastq1} ${fastq2} | samtools view -uS - | samtools sort - ${name}
+        bwa mem -t ${task.cpus} ${params.reference} ${fastq1} ${fastq2} | samtools view -uS - | samtools sort - > ${name}.bam
         """
     }
 }
@@ -217,7 +217,7 @@ else if (params.algorithm == "mem" && params.library == "single") {
           set val("${name}"), file("${name}.bam") into sampe_output
 
         """
-        bwa mem -t ${task.cpus} ${params.reference} ${fastq} | samtools view -uS - | samtools sort - ${name}
+        bwa mem -t ${task.cpus} ${params.reference} ${fastq} | samtools view -uS - | samtools sort - > ${name}.bam
         """
     }
 }

diff --git a/nextflow.config b/nextflow.config
@@ -29,7 +29,7 @@ env {
 process.shell = ['/bin/bash', '-euo', 'pipefail']
 
 
-VERSION = "1.3.0"
+VERSION = "1.4.0"
 
 manifest {
   name = 'TRON-Bioinformatics/tronflow-bwa'