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Fix ref genomes & other behaviour #194

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merged 19 commits into from Apr 12, 2019
Merged

Fix ref genomes & other behaviour #194

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7008c07
Get rid of channels in non-required cases
apeltzer Apr 10, 2019
6c00819
Clean up some template merging mess
apeltzer Apr 10, 2019
e8ebf5c
Add mini changelog
apeltzer Apr 10, 2019
75dc4a6
Cleaned up FastA file channels
apeltzer Apr 10, 2019
6f50495
Getting rid of the first() operators
apeltzer Apr 10, 2019
e7e79ce
This should fix handling all kinds of references
apeltzer Apr 11, 2019
5659251
Do more with less code
apeltzer Apr 11, 2019
a537866
Attempting to copy the ATACseq approach here
apeltzer Apr 11, 2019
713fb5f
Fixing parts of the issues now
apeltzer Apr 11, 2019
2d9ebbe
Both paths work now, no more need for FastA file extensions
apeltzer Apr 11, 2019
5554c60
Clean up multiqc report for email feature
apeltzer Apr 11, 2019
a497427
Python3.6.7 is required
apeltzer Apr 11, 2019
0c184cf
Fix tests
apeltzer Apr 11, 2019
1366a43
Get rid of last bit of gz
apeltzer Apr 12, 2019
7a9495d
Add default for bwa_index [skip ci]
apeltzer Apr 12, 2019
b999721
Required fixes for CircularMapper
apeltzer Apr 12, 2019
8084e70
Fix warning
apeltzer Apr 12, 2019
2c7c8d4
Add more bugfixes
apeltzer Apr 12, 2019
1dd1df4
Get rid of damageprofiler warning [skip ci]
apeltzer Apr 12, 2019
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8 changes: 4 additions & 4 deletions .travis.yml
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Expand Up @@ -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
Expand All @@ -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
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3 changes: 2 additions & 1 deletion CHANGELOG.md
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Expand Up @@ -15,7 +15,8 @@ and this project adheres to [Semantic Versioning](http://semver.org/spec/v2.0.0.

### `Fixed`
* [#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`

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2 changes: 1 addition & 1 deletion conf/base.config
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Expand Up @@ -65,7 +65,7 @@ process {
errorStrategy = 'ignore'
}

withName: extract_unmapped_reads {
withName: strip_input_fastq {
cpus = { check_max(8 * task.attempt, 'cpus') }
memory = { check_max( 8.GB * task.attempt, 'memory' ) }
}
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2 changes: 1 addition & 1 deletion environment.yml
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Expand Up @@ -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