Merge pull request #50 from nf-core/dev

PR for next release

.travis.yml

@@ -10,21 +10,26 @@ matrix:
   fast_finish: true
 
 before_install:
-  # PRs made to 'master' branch should always orginate from another repo or the 'dev' branch
+  # PRs to master are only ok if coming from dev branch
   - '[ $TRAVIS_PULL_REQUEST = "false" ] || [ $TRAVIS_BRANCH != "master" ] || ([ $TRAVIS_PULL_REQUEST_SLUG = $TRAVIS_REPO_SLUG ] && [ $TRAVIS_PULL_REQUEST_BRANCH = "dev" ])'
-  - docker pull nfcore/hlatyping
-  - docker tag nfcore/hlatyping nfcore/hlatyping:1.1.3
+  # Pull the docker image first so the test doesn't wait for this
+  - docker pull nfcore/hlatyping:dev
+  - docker tag nfcore/hlatyping:dev nfcore/hlatyping:1.1.3
 
 install:
   # Install Nextflow
-  - mkdir /tmp/nextflow
-  - cd /tmp/nextflow
+  - mkdir /tmp/nextflow && cd /tmp/nextflow
   - wget -qO- get.nextflow.io | bash
   - sudo ln -s /tmp/nextflow/nextflow /usr/local/bin/nextflow
   # Install nf-core/tools
-  - pip install nf-core==1.3
+  - pip install nf-core
+  # Install Conda 
+  - wget https://repo.continuum.io/miniconda/Miniconda3-latest-Linux-x86_64.sh
+  - bash Miniconda3-latest-Linux-x86_64.sh -b -f -p $HOME/miniconda
+  - export PATH="$HOME/miniconda/bin:$PATH"
   # Reset
-  - cd ${TRAVIS_BUILD_DIR}
+  - mkdir -p ${TRAVIS_BUILD_DIR}/tests && cd ${TRAVIS_BUILD_DIR}/tests
+
 
 env:
   - NXF_VER='18.10.1' # Specify a minimum NF version that should be tested and work

CHANGELOG.md

@@ -1,7 +1,7 @@
-## 1.1.3 - Patch release - 2018-12-12
+## 1.1.3 - Patch release - 2019-02-04
 
 - Multiple smaller bugfixes, cleaned up code basis
-
+- [#48](https://github.com/nf-core/hlatyping/issues/48) - Utilizes RNA/DNA reference genome for remapping correctly
 
 ## 1.1.2 - Patch release - 2018-12-12
 

conf/base.config

@@ -26,6 +26,13 @@ process {
     executor = 'local'
     errorStrategy = { task.exitStatus in [143,137] ? 'retry' : 'ignore' }
   }
+  withname:remap_to_hla{
+    cpus = { check_max( 4 * task.attempt, 'cpus' ) }
+  }
+  withname:pre_map_hla{
+    cpus = { check_max( 4 * task.attempt, 'cpus' ) }
+  }
+
 }
 
 params {

conf/test_rna.config

@@ -0,0 +1,23 @@
+/*
+ * -------------------------------------------------
+ *  Nextflow config file for running tests
+ * -------------------------------------------------
+ * Defines bundled input files and everything required
+ * to run a fast and simple test. Use as follows:
+ *   nextflow run nf-core/hlatyping -profile test
+ */
+
+params {
+  max_cpus = 2
+  max_memory = 7.GB
+  max_time = 48.h
+  singleEnd = false
+  readPaths = [
+   ['test_data', ['https://github.com/nf-core/test-datasets/raw/hlatyping/rna/CRC_81_N_1_fished.fastq.gz',
+        'https://github.com/nf-core/test-datasets/raw/hlatyping/rna/CRC_81_N_2_fished.fastq.gz']]
+  ]
+  solver = 'glpk'
+  seqtype = 'rna'
+  bam = false
+  outdir = "results"
+}

main.nf

@@ -27,7 +27,7 @@ def helpMessage() {
 
     Mandatory arguments:
       --reads                       Path to input data (must be surrounded with quotes)
-      --rna/--dna                   Use with RNA/DNA sequencing data.
+      --seqtype rna/dna             Use with RNA/DNA sequencing data.
       --outdir OUTDIR               The output directory where the results will be saved
       -profile                      Hardware config to use. docker / aws
 
@@ -69,7 +69,7 @@ ch_multiqc_config = Channel.fromPath(params.multiqc_config)
 
 // Validate inputs
 params.reads ?: params.readPaths ?: { log.error "No read data privided. Make sure you have used the '--reads' option."; exit 1 }()
-params.seqtype ?: { log.error "No sequence type provided, you need to add '--dna/--rna.'"; exit 1 }()
+(params.seqtype == 'rna' || params.seqtype == 'dna') ?: { log.error "No or incorrect sequence type provided, you need to add '--seqtype 'dna'' or '--seqtype 'rna''."; exit 1 }()
 if( params.bam ) params.index ?: { log.error "For BAM option, you need to provide a path to the HLA reference index (yara; --index) "; exit 1 }()
 params.outdir = params.outdir ?: { log.warn "No output directory provided. Will put the results into './results'"; return "./results" }()
 
@@ -109,13 +109,14 @@ summary['Run Name']     = custom_runName ?: workflow.runName
 summary['Reads']        = params.readPaths? params.readPaths : params.reads
 summary['Data Type']    = params.singleEnd ? 'Single-End' : 'Paired-End'
 summary['File Type']    = params.bam ? 'BAM' : 'Other (fastq, fastq.gz, ...)'
-summary['Index Location'] = params.index ?: { log.error "You did not provide any path to the mapper indices."; exit 1 }
+summary['Seq Type']   = params.seqtype
+summary['Index Location'] = params.base_index + params.seqtype
 summary['IP solver']    = params.solver
 summary['Enumerations'] = params.enumerations
 summary['Beta'] = params.beta
 summary['Prefix'] = params.prefix
 summary['Max Memory']   = params.max_memory
-summary['Max CP Us']     = params.max_cpus
+summary['Max CPUs']     = params.max_cpus
 summary['Max Time']     = params.max_time
 summary['Output dir']   = params.outdir
 summary['Working dir']  = workflow.workDir
@@ -207,21 +208,22 @@ if ( !params.bam  ) { // FASTQ files processing
         set val(pattern), "mapped_{1,2}.bam" into fished_reads
 
         script:
+        full_index = params.base_index + params.seqtype
         if (params.singleEnd)
         """
         samtools bam2fq $bams > output_1.fastq
-        yara_mapper -e 3 -t ${params.max_cpus} -f bam ${params.index} output_1.fastq > output_1.bam
-        samtools view -h -F 4 -b1 output_1.bam > mapped_1.bam
+        yara_mapper -e 3 -t ${task.cpus} -f bam $full_index output_1.fastq > output_1.bam
+        samtools view -@ ${task.cpus} -h -F 4 -b1 output_1.bam > mapped_1.bam
         """
         else
         """
-        samtools view -h -f 0x40 $bams > output_1.bam
-        samtools view -h -f 0x80 $bams > output_2.bam
+        samtools view -@ ${task.cpus} -h -f 0x40 $bams > output_1.bam
+        samtools view -@ ${task.cpus} -h -f 0x80 $bams > output_2.bam
         samtools bam2fq output_1.bam > output_1.fastq
         samtools bam2fq output_2.bam > output_2.fastq
-        yara_mapper -e 3 -t ${params.max_cpus} -f bam ${params.index} output_1.fastq output_2.fastq > output.bam
-        samtools view -h -F 4 -f 0x40 -b1 output.bam > mapped_1.bam
-        samtools view -h -F 4 -f 0x80 -b1 output.bam > mapped_2.bam
+        yara_mapper -e 3 -t ${task.cpus} -f bam $full_index output_1.fastq output_2.fastq > output.bam
+        samtools view -@ ${task.cpus} -h -F 4 -f 0x40 -b1 output.bam > mapped_1.bam
+        samtools view -@ ${task.cpus} -h -F 4 -f 0x80 -b1 output.bam > mapped_2.bam
         """
 
     }
@@ -271,16 +273,17 @@ process pre_map_hla {
     set val(pattern), "mapped_{1,2}.bam" into fished_reads
 
     script:
+    full_index = params.base_index + params.seqtype
     if (params.singleEnd)
     """
-    yara_mapper -e 3 -t ${params.max_cpus} -f bam ${params.index} $reads > output_1.bam
-    samtools view -h -F 4 -b1 output_1.bam > mapped_1.bam
+    yara_mapper -e 3 -t ${task.cpus} -f bam $full_index $reads > output_1.bam
+    samtools view -@ ${task.cpus} -h -F 4 -b1 output_1.bam > mapped_1.bam
     """
     else
     """
-    yara_mapper -e 3 -t ${params.max_cpus} -f bam ${params.index} $reads > output.bam
-    samtools view -h -F 4 -f 0x40 -b1 output.bam > mapped_1.bam
-    samtools view -h -F 4 -f 0x80 -b1 output.bam > mapped_2.bam
+    yara_mapper -e 3 -t ${task.cpus} -f bam $full_index $reads > output.bam
+    samtools view -@ ${task.cpus} -h -F 4 -f 0x40 -b1 output.bam > mapped_1.bam
+    samtools view -@ ${task.cpus} -h -F 4 -f 0x80 -b1 output.bam > mapped_2.bam
     """
 
 }

nextflow.config

@@ -27,6 +27,9 @@ params {
   enumerations = 1
   beta = 0.009
   prefix = 'hla_run'
+  //use this to combine accordingly for dna/rna samples
+  base_index = "$baseDir/data/indices/yara/hla_reference_"
+  //Simple default case
   index = "$baseDir/data/indices/yara/hla_reference_dna"
 
   igenomesIgnore = false
@@ -50,10 +53,10 @@ profiles {
   }
   singularity {
     singularity.enabled = true
-    process.container = {"shub://${params.container.replace('nfcore', 'nf-core')}"}
   }
   test { includeConfig 'conf/test.config' }
   test_fastq { includeConfig 'conf/test_fastq.config'}
+  test_rna { includeConfig 'conf/test_rna.config'}
 }
 
 // Load igenomes.config if required