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Merge pull request #162 from genomic-medicine-sweden/short_reads_samtools
Add samtools stats for short-reads
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commit
67e264b7a9
3 changed files with 30 additions and 7 deletions
13
README.md
13
README.md
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@ -34,9 +34,10 @@ On release, automated continuous integration tests run the pipeline on a full-si
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2. Performs optional read pre-processing
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- Adapter clipping and merging (short-read: [fastp](https://github.com/OpenGene/fastp), [AdapterRemoval2](https://github.com/MikkelSchubert/adapterremoval); long-read: [porechop](https://github.com/rrwick/Porechop))
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- Low complexity and quality filtering (short-read: [bbduk](https://jgi.doe.gov/data-and-tools/software-tools/bbtools/), [PRINSEQ++](https://github.com/Adrian-Cantu/PRINSEQ-plus-plus); long-read: [Filtlong](https://github.com/rrwick/Filtlong))
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- Host read removal (short-read: [BowTie2](http://bowtie-bio.sourceforge.net/bowtie2/); long-read: [Minimap2](https://github.com/lh3/minimap2))
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- Host-read removal (short-read: [BowTie2](http://bowtie-bio.sourceforge.net/bowtie2/); long-read: [Minimap2](https://github.com/lh3/minimap2))
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- Run merging
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3. Performs taxonomic profiling using one or more of:
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3. Supports statistics for host-read removal ([Samtools](http://www.htslib.org/))
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4. Performs taxonomic profiling using one or more of:
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- [Kraken2](https://ccb.jhu.edu/software/kraken2/)
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- [MetaPhlAn3](https://huttenhower.sph.harvard.edu/metaphlan/)
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- [MALT](https://uni-tuebingen.de/fakultaeten/mathematisch-naturwissenschaftliche-fakultaet/fachbereiche/informatik/lehrstuehle/algorithms-in-bioinformatics/software/malt/)
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@ -45,11 +46,11 @@ On release, automated continuous integration tests run the pipeline on a full-si
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- [Kaiju](https://kaiju.binf.ku.dk/)
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- [mOTUs](https://motu-tool.org/)
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- [KrakenUniq](https://github.com/fbreitwieser/krakenuniq)
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4. Perform optional post-processing with:
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5. Perform optional post-processing with:
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- [bracken](https://ccb.jhu.edu/software/bracken/)
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5. Standardises output tables
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6. Present QC for raw reads ([`MultiQC`](http://multiqc.info/))
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7. Plotting Kraken2, Centrifuge, Kaiju and MALT results ([`Krona`](https://hpc.nih.gov/apps/kronatools.html))
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6. Standardises output tables
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7. Present QC for raw reads ([`MultiQC`](http://multiqc.info/))
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8. Plotting Kraken2, Centrifuge, Kaiju and MALT results ([`Krona`](https://hpc.nih.gov/apps/kronatools.html))
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## Quick Start
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@ -236,7 +236,6 @@ process {
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publishDir = [
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path: { "${params.outdir}/samtools/stats" },
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mode: params.publish_dir_mode,
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enabled: params.save_hostremoval_unmapped,
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pattern: '*stats'
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]
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}
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@ -4,6 +4,9 @@
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include { BOWTIE2_BUILD } from '../../modules/nf-core/bowtie2/build/main'
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include { BOWTIE2_ALIGN } from '../../modules/nf-core/bowtie2/align/main'
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include { SAMTOOLS_INDEX } from '../../modules/nf-core/samtools/index/main'
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include { SAMTOOLS_STATS } from '../../modules/nf-core/samtools/stats/main'
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include { SAMTOOLS_VIEW } from '../../modules/nf-core/samtools/view/main'
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workflow SHORTREAD_HOSTREMOVAL {
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take:
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@ -26,7 +29,27 @@ workflow SHORTREAD_HOSTREMOVAL {
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ch_versions = ch_versions.mix( BOWTIE2_ALIGN.out.versions.first() )
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ch_multiqc_files = ch_multiqc_files.mix( BOWTIE2_ALIGN.out.log )
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ch_bowtie2_mapped = BOWTIE2_ALIGN.out.bam
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.map {
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meta, reads ->
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[ meta, reads, [] ]
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}
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SAMTOOLS_VIEW ( ch_bowtie2_mapped, [], [] )
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ch_versions = ch_versions.mix( SAMTOOLS_VIEW.out.versions.first() )
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SAMTOOLS_INDEX ( SAMTOOLS_VIEW.out.bam )
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ch_versions = ch_versions.mix( SAMTOOLS_INDEX.out.versions.first() )
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bam_bai = SAMTOOLS_VIEW.out.bam
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.join(SAMTOOLS_INDEX.out.bai, remainder: true)
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SAMTOOLS_STATS ( bam_bai, reference )
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ch_versions = ch_versions.mix(SAMTOOLS_STATS.out.versions.first())
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ch_multiqc_files = ch_multiqc_files.mix( SAMTOOLS_STATS.out.stats )
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emit:
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stats = SAMTOOLS_STATS.out.stats
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reads = BOWTIE2_ALIGN.out.fastq // channel: [ val(meta), [ reads ] ]
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versions = ch_versions // channel: [ versions.yml ]
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mqc = ch_multiqc_files
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