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Replace samtools -o with redirect for stability in CI test #761

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Jun 1, 2021
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Replace samtools -o with redirect for stability in CI test #761

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1 change: 1 addition & 0 deletions CHANGELOG.md
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Expand Up @@ -20,6 +20,7 @@ and this project adheres to [Semantic Versioning](http://semver.org/spec/v2.0.0.
- [#750](https://github.com/nf-core/eager/issues/750) - Fixed piped commands requesting the same number of CPUs at each command step
- [#757](https://github.com/nf-core/eager/issues/757) - Removed confusing 'Data Type' variable from MultiQC workflow summary (not consistent with TSV input)
- [#759](https://github.com/nf-core/eager/pull/759) - Fixed malformed software scraping regex that resulted in N/A in MultiQC report
- [#761](https://github.com/nf-core/eager/pull/759) - Fixed issues related to instability of samtools filtering related CI tests

### `Dependencies`

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118 changes: 59 additions & 59 deletions main.nf
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Expand Up @@ -1540,87 +1540,87 @@ process samtools_filter {
tuple samplename, libraryid, lane, seqtype, organism, strandedness, udg, file("*.unmapped.bam") optional true

// Using shell block rather than script because we are playing with awk
shell:
script:

size = !{params.large_ref} ? '-c' : ''
def size = params.large_ref ? '-c' : ''

// Unmapped/MAPQ Filtering WITHOUT min-length filtering
if ( "${params.bam_unmapped_type}" == "keep" && params.bam_filter_minreadlength == 0 ) {
'''
samtools view -h -b !{bam} -@ !{task.cpus} -q !{params.bam_mapping_quality_threshold} -o !{libraryid}.filtered.bam
samtools index !{libraryid}.filtered.bam !{size}
'''
"""
samtools view -h ${bam} -@ ${task.cpus} -q ${params.bam_mapping_quality_threshold} -b > ${libraryid}.filtered.bam
samtools index ${libraryid}.filtered.bam ${size}
"""
} else if ( "${params.bam_unmapped_type}" == "discard" && params.bam_filter_minreadlength == 0 ){
'''
samtools view -h -b !{bam} -@ !{task.cpus} -F4 -q !{params.bam_mapping_quality_threshold} -o !{libraryid}.filtered.bam
samtools index !{libraryid}.filtered.bam !{size}
'''
"""
samtools view -h ${bam} -@ ${task.cpus} -F4 -q ${params.bam_mapping_quality_threshold} -b > ${libraryid}.filtered.bam
samtools index ${libraryid}.filtered.bam ${size}
"""
} else if ( "${params.bam_unmapped_type}" == "bam" && params.bam_filter_minreadlength == 0 ){
'''
samtools view -h !{bam} -@ !{task.cpus} -f4 -o !{libraryid}.unmapped.bam
samtools view -h !{bam} -@ !{task.cpus} -F4 -q !{params.bam_mapping_quality_threshold} -o !{libraryid}.filtered.bam
samtools index !{libraryid}.filtered.bam !{size}
'''
"""
samtools view -h ${bam} -@ ${task.cpus} -f4 -b > ${libraryid}.unmapped.bam
samtools view -h ${bam} -@ ${task.cpus} -F4 -q ${params.bam_mapping_quality_threshold} -b > ${libraryid}.filtered.bam
samtools index ${libraryid}.filtered.bam ${size}
"""
} else if ( "${params.bam_unmapped_type}" == "fastq" && params.bam_filter_minreadlength == 0 ){
'''
samtools view -h !{bam} -@ !{task.cpus} -f4 -o !{libraryid}.unmapped.bam
samtools view -h !{bam} -@ !{task.cpus} -F4 -q !{params.bam_mapping_quality_threshold} -o !{libraryid}.filtered.bam
samtools index !{libraryid}.filtered.bam !{size}
"""
samtools view -h ${bam} -@ ${task.cpus} -f4 -b > ${libraryid}.unmapped.bam
samtools view -h ${bam} -@ ${task.cpus} -F4 -q ${params.bam_mapping_quality_threshold} -b > ${libraryid}.filtered.bam
samtools index ${libraryid}.filtered.bam ${size}

## FASTQ
samtools fastq -tn !{libraryid}.unmapped.bam | pigz -p !{task.cpus - 1} > !{libraryid}.unmapped.fastq.gz
rm !{libraryid}.unmapped.bam
'''
samtools fastq -tn ${libraryid}.unmapped.bam | pigz -p ${task.cpus - 1} > ${libraryid}.unmapped.fastq.gz
rm ${libraryid}.unmapped.bam
"""
} else if ( "${params.bam_unmapped_type}" == "both" && params.bam_filter_minreadlength == 0 ){
'''
samtools view -h !{bam} -@ !{task.cpus} -f4 -o !{libraryid}.unmapped.bam
samtools view -h !{bam} -@ !{task.cpus} -F4 -q !{params.bam_mapping_quality_threshold} -o !{libraryid}.filtered.bam
samtools index !{libraryid}.filtered.bam !{size}
"""
samtools view -h ${bam} -@ ${task.cpus} -f4 -b > ${libraryid}.unmapped.bam
samtools view -h ${bam} -@ ${task.cpus} -F4 -q ${params.bam_mapping_quality_threshold} -b > ${libraryid}.filtered.bam
samtools index ${libraryid}.filtered.bam ${size}

## FASTQ
samtools fastq -tn !{libraryid}.unmapped.bam | pigz -p !{task.cpus -1} > !{libraryid}.unmapped.fastq.gz
'''
samtools fastq -tn ${libraryid}.unmapped.bam | pigz -p ${task.cpus -1} > ${libraryid}.unmapped.fastq.gz
"""
// Unmapped/MAPQ Filtering WITH min-length filtering
} else if ( "${params.bam_unmapped_type}" == "keep" && params.bam_filter_minreadlength != 0 ) {
'''
samtools view -h -b !{bam} -@ !{task.cpus} -q !{params.bam_mapping_quality_threshold} -o tmp_mapped.bam
filter_bam_fragment_length.py -a -l !{params.bam_filter_minreadlength} -o !{libraryid} tmp_mapped.bam
samtools index !{libraryid}.filtered.bam !{size}
'''
"""
samtools view -h ${bam} -@ ${task.cpus} -q ${params.bam_mapping_quality_threshold} -b > tmp_mapped.bam
filter_bam_fragment_length.py -a -l ${params.bam_filter_minreadlength} -o ${libraryid} tmp_mapped.bam
samtools index ${libraryid}.filtered.bam ${size}
"""
} else if ( "${params.bam_unmapped_type}" == "discard" && params.bam_filter_minreadlength != 0 ){
'''
samtools view -h -b !{bam} -@ !{task.cpus} -F4 -q !{params.bam_mapping_quality_threshold} -o tmp_mapped.bam
filter_bam_fragment_length.py -a -l !{params.bam_filter_minreadlength} -o !{libraryid} tmp_mapped.bam
samtools index !{libraryid}.filtered.bam !{size}
'''
"""
samtools view -h ${bam} -@ ${task.cpus} -F4 -q ${params.bam_mapping_quality_threshold} -b > tmp_mapped.bam
filter_bam_fragment_length.py -a -l ${params.bam_filter_minreadlength} -o ${libraryid} tmp_mapped.bam
samtools index ${libraryid}.filtered.bam ${size}
"""
} else if ( "${params.bam_unmapped_type}" == "bam" && params.bam_filter_minreadlength != 0 ){
'''
samtools view -h !{bam} -@ !{task.cpus} -f4 -o !{libraryid}.unmapped.bam
samtools view -h !{bam} -@ !{task.cpus} -F4 -q !{params.bam_mapping_quality_threshold} -o tmp_mapped.bam
filter_bam_fragment_length.py -a -l !{params.bam_filter_minreadlength} -o !{libraryid} tmp_mapped.bam
samtools index !{libraryid}.filtered.bam !{size}
'''
"""
samtools view -h ${bam} -@ ${task.cpus} -f4 -b > ${libraryid}.unmapped.bam
samtools view -h ${bam} -@ ${task.cpus} -F4 -q ${params.bam_mapping_quality_threshold} -b > tmp_mapped.bam
filter_bam_fragment_length.py -a -l ${params.bam_filter_minreadlength} -o ${libraryid} tmp_mapped.bam
samtools index ${libraryid}.filtered.bam ${size}
"""
} else if ( "${params.bam_unmapped_type}" == "fastq" && params.bam_filter_minreadlength != 0 ){
'''
samtools view -h !{bam} -@ !{task.cpus} -f4 -o !{libraryid}.unmapped.bam
samtools view -h !{bam} -@ !{task.cpus} -F4 -q !{params.bam_mapping_quality_threshold} -o tmp_mapped.bam
filter_bam_fragment_length.py -a -l !{params.bam_filter_minreadlength} -o !{libraryid} tmp_mapped.bam
samtools index !{libraryid}.filtered.bam !{size}
"""
samtools view -h ${bam} -@ ${task.cpus} -f4 -b > ${libraryid}.unmapped.bam
samtools view -h ${bam} -@ ${task.cpus} -F4 -q ${params.bam_mapping_quality_threshold} -b > tmp_mapped.bam
filter_bam_fragment_length.py -a -l ${params.bam_filter_minreadlength} -o ${libraryid} tmp_mapped.bam
samtools index ${libraryid}.filtered.bam ${size}

## FASTQ
samtools fastq -tn !{libraryid}.unmapped.bam | pigz -p !{task.cpus - 1} > !{libraryid}.unmapped.fastq.gz
rm !{libraryid}.unmapped.bam
'''
samtools fastq -tn ${libraryid}.unmapped.bam | pigz -p ${task.cpus - 1} > ${libraryid}.unmapped.fastq.gz
rm ${libraryid}.unmapped.bam
"""
} else if ( "${params.bam_unmapped_type}" == "both" && params.bam_filter_minreadlength != 0 ){
'''
samtools view -h !{bam} -@ !{task.cpus} -f4 -o !{libraryid}.unmapped.bam
samtools view -h !{bam} -@ !{task.cpus} -F4 -q !{params.bam_mapping_quality_threshold} -o tmp_mapped.bam
filter_bam_fragment_length.py -a -l !{params.bam_filter_minreadlength} -o !{libraryid} tmp_mapped.bam
samtools index !{libraryid}.filtered.bam !{size}
"""
samtools view -h ${bam} -@ ${task.cpus} -f4 -b > ${libraryid}.unmapped.bam
samtools view -h ${bam} -@ ${task.cpus} -F4 -q ${params.bam_mapping_quality_threshold} -b > tmp_mapped.bam
filter_bam_fragment_length.py -a -l ${params.bam_filter_minreadlength} -o ${libraryid} tmp_mapped.bam
samtools index ${libraryid}.filtered.bam ${size}

## FASTQ
samtools fastq -tn !{libraryid}.unmapped.bam | pigz -p !{task.cpus} > !{libraryid}.unmapped.fastq.gz
'''
samtools fastq -tn ${libraryid}.unmapped.bam | pigz -p ${task.cpus} > ${libraryid}.unmapped.fastq.gz
"""
}
}

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