Merge pull request #194 from apeltzer/fix-ref-genomes

Fix ref genomes & other behaviour

Author: apeltzer

.travis.yml

@@ -43,7 +43,7 @@ script:
   # Run the basic pipeline with the test profile
   - 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/
+  - 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
   - nextflow run ${TRAVIS_BUILD_DIR} -profile test,docker --pairedEnd --skip_collapse --saveReference
   # Run the basic pipeline with paired end data without trimming
@@ -53,13 +53,13 @@ script:
    # Run the basic pipeline with output unmapped reads as fastq
   - nextflow run ${TRAVIS_BUILD_DIR} -profile test,docker --pairedEnd --strip_input_fastq
   # 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/
+  - nextflow run ${TRAVIS_BUILD_DIR} -profile test,docker --pairedEnd --complexity_filter --bwa_index results/reference_genome/bwa_index/BWAIndex/Mammoth_MT_Krause.fasta
   # Test BAM Trimming
-  - nextflow run ${TRAVIS_BUILD_DIR} -profile test,docker --pairedEnd --trim_bam --bwa_index results/reference_genome/bwa_index/bwa_index/
+  - nextflow run ${TRAVIS_BUILD_DIR} -profile test,docker --pairedEnd --trim_bam --bwa_index results/reference_genome/bwa_index/BWAIndex/Mammoth_MT_Krause.fasta
   # 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 --bwa_index results/reference_genome/bwa_index/bwa_index/
+  - nextflow run ${TRAVIS_BUILD_DIR} -profile test,docker --pairedEnd --bwamem --bwa_index results/reference_genome/bwa_index/BWAIndex/Mammoth_MT_Krause.fasta
   # 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

CHANGELOG.md

@@ -17,7 +17,8 @@ and this project adheres to [Semantic Versioning](http://semver.org/spec/v2.0.0.
 * [#152](https://github.com/nf-core/eager/pull/152) - DamageProfiler errors [won't crash entire pipeline anymore](https://github.com/nf-core/eager/issues/171)
 * [#176](https://github.com/nf-core/eager/pull/176) - Increase runtime for DamageProfiler on [large reference genomes](https://github.com/nf-core/eager/issues/173)
 * [#172](https://github.com/nf-core/eager/pull/152) - DamageProfiler errors [won't crash entire pipeline anymore](https://github.com/nf-core/eager/issues/171)
-* [#174](https://github.com/nf-core/eager/pull/190) - Publish DeDup files [properly](https://github.com/nf-core/eager/issues/183) 
+* [#174](https://github.com/nf-core/eager/pull/190) - Publish DeDup files [properly](https://github.com/nf-core/eager/issues/183)
+* TBF - Fix reference [issues](https://github.com/nf-core/eager/issues/150)
 
 ### `Dependencies`
 

conf/base.config

@@ -67,7 +67,7 @@ process {
     params.large_ref ? "time = { check_max(8.h * task.attempt, 'time') }" : "time = { check_max(2.h * task.attempt, 'time') }"
   }
 
-  withName: extract_unmapped_reads {
+  withName: strip_input_fastq {
     cpus = { check_max(8 * task.attempt, 'cpus') }
     memory = { check_max( 8.GB * task.attempt, 'memory' ) }
   }

environment.yml

@@ -29,5 +29,5 @@ dependencies:
   - bioconda::bamutil=1.0.14
   - bioconda::mtnucratio=0.5
   - pysam=0.15.2
-  - python=3.6
+  - python=3.6.7
   #Missing Schmutzi,snpAD