Fixing PMDTools

.travis.yml

@@ -42,6 +42,8 @@ script:
   - nf-core lint ${TRAVIS_BUILD_DIR}
   # Run the basic pipeline with the test profile
   - nextflow run ${TRAVIS_BUILD_DIR} -profile test,docker --pairedEnd --saveReference
+  # Test using PMD tools
+  - nextflow run ${TRAVIS_BUILD_DIR} -profile test,docker --run_pmdtools --pairedEnd
   # 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/BWAIndex/Mammoth_MT_Krause.fasta
   # Run the basic pipeline with paired end data without collapsing

CHANGELOG.md

@@ -23,6 +23,8 @@ and this project adheres to [Semantic Versioning](http://semver.org/spec/v2.0.0.
 * [#196](https://github.com/nf-core/eager/pull/196) - Fix reference [issues](https://github.com/nf-core/eager/issues/150)
 * [#196](https://github.com/nf-core/eager/pull/196) - Fix issues with PE data being mapped incompletely
 * [#200](https://github.com/nf-core/eager/pull/200) - Fix minor issue with some [typos](https://github.com/nf-core/eager/pull/196)
+* [#210](https://github.com/nf-core/eager/pull/210) - Fix PMDTools [encoding issue](https://github.com/pontussk/PMDtools/issues/6) from `samtools calmd` generated files by running through `samtools view` first
+
 
 ### `Dependencies`
 

main.nf

@@ -1155,9 +1155,9 @@ process pmdtools {
     }
     """
     #Run Filtering step 
-    samtools fillmd -b $bam $fasta | pmdtools --threshold ${params.pmdtools_threshold} $treatment $snpcap --header | samtools view -@ ${task.cpus} -Sb - > "${bam.baseName}".pmd.bam
+    samtools calmd -b $bam $fasta | samtools view -h - | pmdtools --threshold ${params.pmdtools_threshold} $treatment $snpcap --header | samtools view -@ ${task.cpus} -Sb - > "${bam.baseName}".pmd.bam
     #Run Calc Range step
-    #samtools fillmd -b $bam $fasta | pmdtools --deamination --range ${params.pmdtools_range} $treatment $snpcap -n ${params.pmdtools_max_reads} > "${bam.baseName}".cpg.range."${params.pmdtools_range}".txt 
+    samtools calmd -b $bam $fasta | samtools view -h - | pmdtools --deamination --range ${params.pmdtools_range} $treatment $snpcap -n ${params.pmdtools_max_reads} > "${bam.baseName}".cpg.range."${params.pmdtools_range}".txt 
     """
 }
 

nextflow.config

@@ -6,7 +6,6 @@
  */
 // Global default params, used in configs
 params {
-
   //Pipeline options
   aligner = 'bwa'
 
@@ -21,17 +20,14 @@ params {
   outdir = './results'
 
   bwa_index = false
-
   //More defaults
   complexity_filter = false
   complexity_filter_poly_g_min = 10
   trim_bam = false
-
   //Skipping adapterremoval, trimming or collapsing defaults
   skip_adapterremoval = false
   skip_trim = false
   skip_adapterremoval = false
-
   // Boilerplate options
   name = false
   multiqc_config = "$baseDir/assets/multiqc_config.yaml"
@@ -52,7 +48,6 @@ params {
   config_profile_contact = false
   config_profile_url = false
 }
-
 // Container slug. Stable releases should specify release tag!
 // Developmental code should specify :dev
 process.container = 'nfcore/eager:dev'
@@ -68,25 +63,24 @@ try {
 }
 
 profiles {
-  awsbatch { includeConfig 'conf/awsbatch.config' }
-  conda { process.conda = "$baseDir/environment.yml" }
-  debug { process.beforeScript = 'echo $HOSTNAME' }
+  awsbatch { includeConfig 'conf/awsbatch.config'}
+  conda { process.conda = "$baseDir/environment.yml"}
+  debug { process.beforeScript = 'echo $HOSTNAME'}
   docker {
     docker.enabled = true
   }
   singularity {
     singularity.enabled = true
+    singularity.runOptions = '-B /run/shm:/run/shm'
   }
-  test { includeConfig 'conf/test.config' }
-  testbam { includeConfig 'conf/testbam.config' }
-  test_fna { includeConfig 'conf/test_fna.config' }
+  test { includeConfig 'conf/test.config'}
+  testbam { includeConfig 'conf/testbam.config'}
+  test_fna { includeConfig 'conf/test_fna.config'}
 }
-
 // Load igenomes.config if required
 if(!params.igenomesIgnore){
   includeConfig 'conf/igenomes.config'
 }
-
 // Capture exit codes from upstream processes when piping
 process.shell = ['/bin/bash', '-euo', 'pipefail']
 
@@ -116,7 +110,6 @@ manifest {
   mainScript = 'main.nf'
   nextflowVersion = '>=0.32.0'
 }
-
 // Function to ensure that resource requirements don't go beyond
 // a maximum limit
 def check_max(obj, type) {
@@ -148,4 +141,4 @@ def check_max(obj, type) {
       return obj
     }
   }
-}
+}