Merge pull request #80 from nf-core/index_file_handling

Index file handling fixing #79

Author: apeltzer

.travis.yml

@@ -37,16 +37,16 @@ script:
   # Lint the pipeline code
   - nf-core lint ${TRAVIS_BUILD_DIR}
   # Run the basic pipeline with the test profile
-  - nextflow run ${TRAVIS_BUILD_DIR} -profile test,docker --pairedEnd
+  - 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 
+  - nextflow run ${TRAVIS_BUILD_DIR} -profile test,docker --singleEnd --bwa_index results/reference_genome/bwa_index/
   # Run the same pipeline testing optional step: fastp, complexity 
-  - nextflow run ${TRAVIS_BUILD_DIR} -profile test,docker --pairedEnd --complexity_filter 
+  - nextflow run ${TRAVIS_BUILD_DIR} -profile test,docker --pairedEnd --complexity_filter --bwa_index results/reference_genome/bwa_index/
   # Test BAM Trimming
-  - nextflow run ${TRAVIS_BUILD_DIR} -profile test,docker --pairedEnd --trim_bam 
+  - nextflow run ${TRAVIS_BUILD_DIR} -profile test,docker --pairedEnd --trim_bam --bwa_index results/reference_genome/bwa_index/
   # Test running with CircularMapper
   - nextflow run ${TRAVIS_BUILD_DIR} -profile test,docker --pairedEnd --circularmapper --circulartarget 'NC_007596.2'
   # Test running with BWA Mem
-  - nextflow run ${TRAVIS_BUILD_DIR} -profile test,docker --pairedEnd --bwamem
+  - nextflow run ${TRAVIS_BUILD_DIR} -profile test,docker --pairedEnd --bwamem --bwa_index results/reference_genome/bwa_index/
   # Test basic pipeline with Conda too 
-  - nextflow run ${TRAVIS_BUILD_DIR} -profile test,conda --pairedEnd
+  - travis_wait 25 nextflow run ${TRAVIS_BUILD_DIR} -profile test,conda --pairedEnd --bwa_index results/reference_genome/bwa_index/

CHANGELOG.md

@@ -6,6 +6,9 @@ and this project adheres to [Semantic Versioning](http://semver.org/spec/v2.0.0.
 
 ## unpublished
 
+### `Added`
+* [#80](https://github.com/nf-core/eager/pull/80) - BWA Index file handling 
+* [#77](https://github.com/nf-core/eager/pull/77) - Lots of documentation updates by [@jfy133](https://github.com/jfy133)
 
 ## [2.0.2] - 2018-11-03
 

environment.yml

@@ -4,26 +4,26 @@ channels:
   - bioconda
   - conda-forge
 dependencies:
-  - openjdk=8.0.152
-  - fastqc=0.11.8
-  - adapterremoval=2.2.2
-  - adapterremovalfixprefix=0.0.4
-  - bwa=0.7.17
-  - picard=2.18.15
-  - samtools=1.9
-  - dedup=0.12.3
-  - angsd=0.923
-  - circularmapper=1.93.4
-  - gatk4=4.0.11.0
-  - qualimap=2.2.2b
-  - vcf2genome=0.91
-  - damageprofiler=0.3.11
-  - multiqc=1.6
-  - pmdtools=0.60
-  - r-rmarkdown=1.10
-  - libiconv=1.15
-  - sequencetools=1.2.2
-  - preseq=2.0.3
-  - fastp=0.19.4
-  - bamutil=1.0.14
+  - anaconda::openjdk=8.0.152
+  - bioconda::fastqc=0.11.8
+  - bioconda::adapterremoval=2.2.2
+  - bioconda::adapterremovalfixprefix=0.0.4
+  - bioconda::bwa=0.7.17
+  - bioconda::picard=2.18.15
+  - bioconda::samtools=1.9
+  - bioconda::dedup=0.12.3
+  - bioconda::angsd=0.923
+  - bioconda::circularmapper=1.93.4
+  - bioconda::gatk4=4.0.11.0
+  - bioconda::qualimap=2.2.2b
+  - bioconda::vcf2genome=0.91
+  - bioconda::damageprofiler=0.3.11
+  - bioconda::multiqc=1.6
+  - bioconda::pmdtools=0.60
+  - conda-forge::r-rmarkdown=1.10
+  - conda-forge::libiconv=1.15
+  - bioconda::sequencetools=1.2.2
+  - bioconda::preseq=2.0.3
+  - bioconda::fastp=0.19.4
+  - bioconda::bamutil=1.0.14
   #Missing Schmutzi,snpAD

main.nf

@@ -211,9 +211,24 @@ wherearemyfiles = file("$baseDir/assets/where_are_my_files.txt")
 
 // Validate inputs
 Channel.fromPath("${params.fasta}")
-    .ifEmpty { exit 1, "No genome specified! Please specify one with --fasta or --bwa_index"}
+    .ifEmpty { exit 1, "No genome specified! Please specify one with --fasta"}
     .into {ch_fasta_for_bwa_indexing;ch_fasta_for_faidx_indexing;ch_fasta_for_dict_indexing; ch_fasta_for_bwa_mapping; ch_fasta_for_damageprofiler; ch_fasta_for_qualimap; ch_fasta_for_pmdtools; ch_fasta_for_circularmapper; ch_fasta_for_circularmapper_index;ch_fasta_for_bwamem_mapping}
 
+//Index files provided? Then check whether they are correct and complete
+if (params.aligner != 'bwa' && !params.circularmapper && !params.bwamem){
+    exit 1, "Invalid aligner option. Default is bwa, but specify --circularmapper or --bwamem to use these."
+}
+if( params.bwa_index && (params.aligner == 'bwa' | params.bwamem)){
+    bwa_index = Channel
+        .fromPath("${params.bwa_index}/**.*")
+        .ifEmpty { exit 1, "BWA index not found: ${params.bwa_index}" }
+        .into{ch_bwa_index_existing;ch_bwa_index_bwamem_existing}
+} else {
+    //Create empty channels to make sure later mix() does not fail
+    ch_bwa_index_existing = Channel.empty()
+    ch_bwa_index_bwamem_existing = Channel.empty()
+}
+
 //Validate that either pairedEnd or singleEnd has been specified by the user!
 if( params.singleEnd || params.pairedEnd ){
 } else {
@@ -280,6 +295,7 @@ summary['Pipeline Version'] = workflow.manifest.version
 summary['Run Name']     = custom_runName ?: workflow.runName
 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['Max Memory']   = params.max_memory
 summary['Max CPUs']     = params.max_cpus
@@ -364,7 +380,7 @@ process makeBWAIndex {
             else null
     }
 
-    when: !params.bwa_index && params.fasta && params.aligner == 'bwa'
+    when: !params.bwa_index && params.fasta && (params.aligner == 'bwa' || params.bwamem)
 
     input:
     file fasta from ch_fasta_for_bwa_indexing
@@ -561,7 +577,7 @@ process bwa {
 
     input:
     file(reads) from ch_clipped_reads
-    file "*" from ch_bwa_index
+    file "*" from ch_bwa_index.mix(ch_bwa_index_existing).collect()
     file fasta from ch_fasta_for_bwa_mapping
 
     output:
@@ -638,7 +654,7 @@ process bwamem {
 
     input:
     file(reads) from ch_clipped_reads_bwamem
-    file "*" from ch_bwa_index_bwamem
+    file "*" from ch_bwa_index_bwamem.mix(ch_bwa_index_bwamem_existing).collect()
     file fasta from ch_fasta_for_bwamem_mapping
 
     output:
@@ -868,10 +884,10 @@ process markDup{
 }
 
 //If no deduplication runs, the input is mixed directly from samtools filter, if it runs either markdup or dedup is used thus mixed from these two channels
-ch_dedup_for_pmdtools = Channel.create()
+ch_dedup_for_pmdtools = Channel.empty()
 
 //Bamutils TrimBam Channel
-ch_for_bamutils = Channel.create()
+ch_for_bamutils = Channel.empty()
 
 if(!params.skip_deduplication){
     ch_dedup_for_pmdtools.mix(ch_markdup_bam,ch_dedup_bam).into {ch_for_pmdtools;ch_for_bamutils}